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/srv/reproducible-results/rbuild-debian/r-b-build.7sk61HIx/b1/mia_2.4.7-11_arm64.changes vs.
/srv/reproducible-results/rbuild-debian/r-b-build.7sk61HIx/b2/mia_2.4.7-11_arm64.changes
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1 ·912461c2da4435de163732714ea26bae·88901176·debug·optional·libmia-2.4-4-dbgsym_2.4.7-11_arm64.deb1 ·912461c2da4435de163732714ea26bae·88901176·debug·optional·libmia-2.4-4-dbgsym_2.4.7-11_arm64.deb
2 ·65bd21000ae5145afac22ccee8ffe478·4057832·libs·optional·libmia-2.4-4_2.4.7-11_arm64.deb2 ·65bd21000ae5145afac22ccee8ffe478·4057832·libs·optional·libmia-2.4-4_2.4.7-11_arm64.deb
3 ·eac29da36508b2b1a7913ea2bc701d8f·204524·libdevel·optional·libmia-2.4-dev_2.4.7-11_arm64.deb3 ·eac29da36508b2b1a7913ea2bc701d8f·204524·libdevel·optional·libmia-2.4-dev_2.4.7-11_arm64.deb
4 ·b699ced10913b8a173b1696090a66aa4·4768408·doc·optional·libmia-2.4-doc_2.4.7-11_all.deb4 ·b699ced10913b8a173b1696090a66aa4·4768408·doc·optional·libmia-2.4-doc_2.4.7-11_all.deb
5 ·9c7486d4c060693bc4439c1adbaf0331·26168·science·optional·mia-doctools_2.4.7-11_all.deb5 ·9c7486d4c060693bc4439c1adbaf0331·26168·science·optional·mia-doctools_2.4.7-11_all.deb
6 ·5f251d6d5d35eb916602a7084aaf8473·36085800·debug·optional·mia-tools-dbgsym_2.4.7-11_arm64.deb6 ·5f251d6d5d35eb916602a7084aaf8473·36085800·debug·optional·mia-tools-dbgsym_2.4.7-11_arm64.deb
7 ·2774eafe075cd52489fa4ff20f70a3f1·96304·doc·optional·mia-tools-doc_2.4.7-11_all.deb 
8 ·c384b6289796d4d4ec507efdc0d0ff92·1760192·science·optional·mia-tools_2.4.7-11_arm64.deb7 ·28058e98577df47ce73d3ebc9fe3458f·96288·doc·optional·mia-tools-doc_2.4.7-11_all.deb
 8 ·329881bbe9e82787015b548e76f26522·1760320·science·optional·mia-tools_2.4.7-11_arm64.deb
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mia-tools-doc_2.4.7-11_all.deb
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1 -rw-r--r--···0········0········0········4·2022-08-17·13:27:13.000000·debian-binary1 -rw-r--r--···0········0········0········4·2022-08-17·13:27:13.000000·debian-binary
2 -rw-r--r--···0········0········0·····5944·2022-08-17·13:27:13.000000·control.tar.xz2 -rw-r--r--···0········0········0·····5944·2022-08-17·13:27:13.000000·control.tar.xz
3 -rw-r--r--···0········0········0····90168·2022-08-17·13:27:13.000000·data.tar.xz3 -rw-r--r--···0········0········0····90152·2022-08-17·13:27:13.000000·data.tar.xz
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control.tar.xz
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control.tar
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./md5sums
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./usr/share/doc/mia-2.4/userref/SecPlugintype2dimagefilter.html
    
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57 ····</p><p·class="plugin">57 ····</p><p·class="plugin">
58 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbandpass2dimagefilter"></a>bandpass</h5></div></div></div><p·class="plugindescr">intensity·bandpass·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·the·band</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·the·band</td></tr></tbody></table></div></div><p·class="plugin">58 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbandpass2dimagefilter"></a>bandpass</h5></div></div></div><p·class="plugindescr">intensity·bandpass·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·the·band</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·the·band</td></tr></tbody></table></div></div><p·class="plugin">
59 ····</p><p·class="plugin">59 ····</p><p·class="plugin">
60 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbinarize2dimagefilter"></a>binarize</h5></div></div></div><p·class="plugindescr">image·binarize·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·accepted·range</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·accepted·range</td></tr></tbody></table></div></div><p·class="plugin">60 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbinarize2dimagefilter"></a>binarize</h5></div></div></div><p·class="plugindescr">image·binarize·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·accepted·range</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·accepted·range</td></tr></tbody></table></div></div><p·class="plugin">
61 ····</p><p·class="plugin">61 ····</p><p·class="plugin">
62 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginclose2dimagefilter"></a>close</h5></div></div></div><p·class="plugindescr">morphological·close.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">set</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·Supported·values·are:(black,·white,·)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">62 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginclose2dimagefilter"></a>close</h5></div></div></div><p·class="plugindescr">morphological·close.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">set</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·Supported·values·are:(black,·white,·)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
63 ····</p><p·class="plugin">63 ····</p><p·class="plugin">
64 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincombiner2dimagefilter"></a>combiner</h5></div></div></div><p·class="plugindescr">Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">image</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">second·image·that·is·needed·in·the·combiner.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr><tr><td·align="center"·valign="top">op</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">Image·combiner·to·be·applied·to·the·images.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagecombiner.html"·title="Plugin·type:·2dimage/combiner">Plugin·type:·2dimage/combiner</a></td></tr><tr><td·align="center"·valign="top">reverse</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">reverse·the·order·in·which·the·images·passed·to·the·combiner</td></tr></tbody></table></div></div><p·class="plugin">64 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincombiner2dimagefilter"></a>combiner</h5></div></div></div><p·class="plugindescr">Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">image</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">second·image·that·is·needed·in·the·combiner.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr><tr><td·align="center"·valign="top">op</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">Image·combiner·to·be·applied·to·the·images.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagecombiner.html"·title="Plugin·type:·2dimage/combiner">Plugin·type:·2dimage/combiner</a></td></tr><tr><td·align="center"·valign="top">reverse</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">reverse·the·order·in·which·the·images·passed·to·the·combiner</td></tr></tbody></table></div></div><p·class="plugin">
65 ····</p><p·class="plugin">65 ····</p><p·class="plugin">
66 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginconvert2dimagefilter"></a>convert</h5></div></div></div><p·class="plugindescr">image·pixel·format·conversion·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">a</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">linear·conversion·parameter·a</td></tr><tr><td·align="center"·valign="top">b</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">linear·conversion·parameter·b</td></tr><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">opt</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">conversion·mapping</td></tr><tr><td·align="left"·valign="top">copy:</td><td·align="left"·valign="top">copy·data·when·converting</td></tr><tr><td·align="left"·valign="top">linear:</td><td·align="left"·valign="top">apply·linear·transformation·x·-&gt;·a*x+b</td></tr><tr><td·align="left"·valign="top">range:</td><td·align="left"·valign="top">apply·linear·transformation·that·maps·the·input·data·type·range·to·the·output·data·type·range</td></tr><tr><td·align="left"·valign="top">opt:</td><td·align="left"·valign="top">apply·a·linear·transformation·that·maps·the·real·input·range·to·the·full·output·range</td></tr><tr><td·align="left"·valign="top">optstat:</td><td·align="left"·valign="top">apply·a·linear·transform·that·maps·based·on·input·mean·and·variation·to·the·full·output·range</td></tr></tbody></table></div></td></tr><tr><td·align="center"·valign="top">repn</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">ubyte</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">output·pixel·type</td></tr><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">66 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginconvert2dimagefilter"></a>convert</h5></div></div></div><p·class="plugindescr">image·pixel·format·conversion·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">a</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">linear·conversion·parameter·a</td></tr><tr><td·align="center"·valign="top">b</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">linear·conversion·parameter·b</td></tr><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">opt</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">conversion·mapping</td></tr><tr><td·align="left"·valign="top">copy:</td><td·align="left"·valign="top">copy·data·when·converting</td></tr><tr><td·align="left"·valign="top">linear:</td><td·align="left"·valign="top">apply·linear·transformation·x·-&gt;·a*x+b</td></tr><tr><td·align="left"·valign="top">range:</td><td·align="left"·valign="top">apply·linear·transformation·that·maps·the·input·data·type·range·to·the·output·data·type·range</td></tr><tr><td·align="left"·valign="top">opt:</td><td·align="left"·valign="top">apply·a·linear·transformation·that·maps·the·real·input·range·to·the·full·output·range</td></tr><tr><td·align="left"·valign="top">optstat:</td><td·align="left"·valign="top">apply·a·linear·transform·that·maps·based·on·input·mean·and·variation·to·the·full·output·range</td></tr></tbody></table></div></td></tr><tr><td·align="center"·valign="top">repn</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">ubyte</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">output·pixel·type</td></tr><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">
67 ····</p><p·class="plugin">67 ····</p><p·class="plugin">
68 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincrop2dimagefilter"></a>crop</h5></div></div></div><p·class="plugindescr">Crop·a·region·of·an·image,·the·region·is·always·clamped·to·the·original·image·size..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">end</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[-1,-1]]</td><td·align="left"·valign="top">end·of·crop·region</td></tr><tr><td·align="center"·valign="top">start</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[0,0]]</td><td·align="left"·valign="top">start·of·crop·region</td></tr></tbody></table></div></div><p·class="plugin">68 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincrop2dimagefilter"></a>crop</h5></div></div></div><p·class="plugindescr">Crop·a·region·of·an·image,·the·region·is·always·clamped·to·the·original·image·size..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">end</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[-1,-1]]</td><td·align="left"·valign="top">end·of·crop·region</td></tr><tr><td·align="center"·valign="top">start</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[0,0]]</td><td·align="left"·valign="top">start·of·crop·region</td></tr></tbody></table></div></div><p·class="plugin">
69 ····</p><p·class="plugin">69 ····</p><p·class="plugin">
70 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugindilate2dimagefilter"></a>dilate</h5></div></div></div><p·class="plugindescr">2d·image·stack·dilate·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">set</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·Supported·values·are:(black,·white,·)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">70 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugindilate2dimagefilter"></a>dilate</h5></div></div></div><p·class="plugindescr">2d·image·stack·dilate·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">set</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·Supported·values·are:(black,·white,·)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
71 ····</p><p·class="plugin">71 ····</p><p·class="plugin">
Offset 81, 23 lines modifiedOffset 81, 23 lines modified
81 ····</p><p·class="plugin">81 ····</p><p·class="plugin">
82 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugininvert2dimagefilter"></a>invert</h5></div></div></div><p·class="plugindescr">intensity·invert·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">82 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugininvert2dimagefilter"></a>invert</h5></div></div></div><p·class="plugindescr">intensity·invert·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
83 ····</p><p·class="plugin">83 ····</p><p·class="plugin">
84 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginkmeans2dimagefilter"></a>kmeans</h5></div></div></div><p·class="plugindescr">2D·image·k-means·filter.·In·the·output·image·the·pixel·value·represents·the·class·membership·and·the·class·centers·are·stored·as·attribute·in·the·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">c</td><td·align="center"·valign="top">int·in·[2,·inf)</td><td·align="center"·valign="top">3</td><td·align="left"·valign="top">number·of·classes</td></tr></tbody></table></div></div><p·class="plugin">84 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginkmeans2dimagefilter"></a>kmeans</h5></div></div></div><p·class="plugindescr">2D·image·k-means·filter.·In·the·output·image·the·pixel·value·represents·the·class·membership·and·the·class·centers·are·stored·as·attribute·in·the·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">c</td><td·align="center"·valign="top">int·in·[2,·inf)</td><td·align="center"·valign="top">3</td><td·align="left"·valign="top">number·of·classes</td></tr></tbody></table></div></div><p·class="plugin">
85 ····</p><p·class="plugin">85 ····</p><p·class="plugin">
86 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabel2dimagefilter"></a>label</h5></div></div></div><p·class="plugindescr">Label·connected·components·in·a·binary·2D·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">4n</td><td·align="left"·valign="top">Neighborhood·mask·to·describe·connectivity..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">86 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabel2dimagefilter"></a>label</h5></div></div></div><p·class="plugindescr">Label·connected·components·in·a·binary·2D·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">4n</td><td·align="left"·valign="top">Neighborhood·mask·to·describe·connectivity..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
87 ····</p><p·class="plugin">87 ····</p><p·class="plugin">
88 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelmap2dimagefilter"></a>labelmap</h5></div></div></div><p·class="plugindescr">Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">Label·mapping·file</td></tr></tbody></table></div></div><p·class="plugin">88 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelmap2dimagefilter"></a>labelmap</h5></div></div></div><p·class="plugindescr">Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">Label·mapping·file</td></tr></tbody></table></div></div><p·class="plugin">
89 ····</p><p·class="plugin">89 ····</p><p·class="plugin">
90 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelscale2dimagefilter"></a>labelscale</h5></div></div></div><p·class="plugindescr">A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input·image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target·pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the·corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same·count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">out-size</td><td·align="center"·valign="top">2dbounds</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">target·size·given·as·two·coma·separated·values</td></tr></tbody></table></div></div><p·class="plugin">90 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelscale2dimagefilter"></a>labelscale</h5></div></div></div><p·class="plugindescr">A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input·image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target·pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the·corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same·count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">out-size</td><td·align="center"·valign="top">2dbounds</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">target·size·given·as·two·coma·separated·values</td></tr></tbody></table></div></div><p·class="plugin">
91 ····</p><p·class="plugin">91 ····</p><p·class="plugin">
92 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginload2dimagefilter"></a>load</h5></div></div></div><p·class="plugindescr">Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">name·of·the·input·file·to·load·from..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">92 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginload2dimagefilter"></a>load</h5></div></div></div><p·class="plugindescr">Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">name·of·the·input·file·to·load·from..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
93 ····</p><p·class="plugin">93 ····</p><p·class="plugin">
94 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmask2dimagefilter"></a>mask</h5></div></div></div><p·class="plugindescr">2D·masking,·one·of·the·two·input·images·must·by·of·type·bit..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">fill</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">min</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">fill·style·for·pixels·outside·of·the·mask</td></tr><tr><td·align="left"·valign="top">min:</td><td·align="left"·valign="top">set·values·outside·the·mask·to·the·minimum·value·found·in·the·image.</td></tr><tr><td·align="left"·valign="top">zero:</td><td·align="left"·valign="top">set·the·values·outside·the·mask·to·zero.</td></tr><tr><td·align="left"·valign="top">max:</td><td·align="left"·valign="top">set·values·outside·the·mask·to·the·maximum·value·found·in·the·image..</td></tr></tbody></table></div></td></tr><tr><td·align="center"·valign="top">input</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">second·input·image·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr><tr><td·align="center"·valign="top">inverse</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">set·to·true·to·use·the·inverse·of·the·mask·for·masking</td></tr></tbody></table></div></div><p·class="plugin">94 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmask2dimagefilter"></a>mask</h5></div></div></div><p·class="plugindescr">2D·masking,·one·of·the·two·input·images·must·by·of·type·bit..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">fill</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">min</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">fill·style·for·pixels·outside·of·the·mask</td></tr><tr><td·align="left"·valign="top">min:</td><td·align="left"·valign="top">set·values·outside·the·mask·to·the·minimum·value·found·in·the·image.</td></tr><tr><td·align="left"·valign="top">zero:</td><td·align="left"·valign="top">set·the·values·outside·the·mask·to·zero.</td></tr><tr><td·align="left"·valign="top">max:</td><td·align="left"·valign="top">set·values·outside·the·mask·to·the·maximum·value·found·in·the·image..</td></tr></tbody></table></div></td></tr><tr><td·align="center"·valign="top">input</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">second·input·image·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr><tr><td·align="center"·valign="top">inverse</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">set·to·true·to·use·the·inverse·of·the·mask·for·masking</td></tr></tbody></table></div></div><p·class="plugin">
95 ····</p><p·class="plugin">95 ····</p><p·class="plugin">
96 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmaxflow2dimagefilter"></a>maxflow</h5></div></div></div><p·class="plugindescr">This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">sink-flow</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">Image·of·float·type·to·define·the·per-pixel·flow·to·the·sink.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td>[·...·truncated·by·diffoscope;·len:·143,·SHA:·aa623eb41e2c8f034f99f3e7dca31b285770dbd226cc208abe2aca19f2d5171d·...·])</td><td·align="left"·valign="top">Image·of·float·type·to·define·the·per-pixel·flow·to·the·source.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">96 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmaxflow2dimagefilter"></a>maxflow</h5></div></div></div><p·class="plugindescr">This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">sink-flow</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">Image·of·float·type·to·define·the·per-pixel·flow·to·the·sink.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td>[·...·truncated·by·diffoscope;·len:·143,·SHA:·2a21192e6b88b9c35bdf06a48785c8cabdacff1c4e51c000a4794246b546ddba·...·])</td><td·align="left"·valign="top">Image·of·float·type·to·define·the·per-pixel·flow·to·the·source.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
97 ····</p><p·class="plugin">97 ····</p><p·class="plugin">
98 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmean2dimagefilter"></a>mean</h5></div></div></div><p·class="plugindescr">2D·image·mean·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">98 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmean2dimagefilter"></a>mean</h5></div></div></div><p·class="plugindescr">2D·image·mean·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">
99 ····</p><p·class="plugin">99 ····</p><p·class="plugin">
100 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmeanvar2dimagefilter"></a>meanvar</h5></div></div></div><p·class="plugindescr">Filter·that·evaluates·simultaniously·the·pixel·wise·mean·and·the·variance·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·mean·and·variation·are·set·to·zero.·The·mean·intensity·image·is·directly·passed·as·float·image·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">double·in·[0,·inf)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation</td></tr><tr><td·align="center"·valign="top">varfile</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,output)</td><td·align="left"·valign="top">name·of·the·output·file·to·save·the·variation·image·too..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">uint·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">100 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmeanvar2dimagefilter"></a>meanvar</h5></div></div></div><p·class="plugindescr">Filter·that·evaluates·simultaniously·the·pixel·wise·mean·and·the·variance·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·mean·and·variation·are·set·to·zero.·The·mean·intensity·image·is·directly·passed·as·float·image·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">double·in·[0,·inf)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation</td></tr><tr><td·align="center"·valign="top">varfile</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,output)</td><td·align="left"·valign="top">name·of·the·output·file·to·save·the·variation·image·too..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">uint·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
101 ····</p><p·class="plugin">101 ····</p><p·class="plugin">
102 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmedian2dimagefilter"></a>median</h5></div></div></div><p·class="plugindescr">2D·image·median·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">102 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmedian2dimagefilter"></a>median</h5></div></div></div><p·class="plugindescr">2D·image·median·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">
103 ····</p><p·class="plugin">103 ····</p><p·class="plugin">
Offset 109, 15 lines modifiedOffset 109, 15 lines modified
109 ····</p><p·class="plugin">109 ····</p><p·class="plugin">
110 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginnoise2dimagefilter"></a>noise</h5></div></div></div><p·class="plugindescr">2D·image·noise·filter:·add·additive·or·modulated·noise·to·an·image.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">g</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:mu=0,sigma=10]</td><td·align="left"·valign="top">noise·generator.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypegeneratornoise.html"·title="Plugin·type:·generator/noise">Plugin·type:·generator/noise</a></td></tr><tr><td·align="center"·valign="top">mod</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">additive·or·modulated·noise</td></tr></tbody></table></div></div><p·class="plugin">110 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginnoise2dimagefilter"></a>noise</h5></div></div></div><p·class="plugindescr">2D·image·noise·filter:·add·additive·or·modulated·noise·to·an·image.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">g</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:mu=0,sigma=10]</td><td·align="left"·valign="top">noise·generator.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypegeneratornoise.html"·title="Plugin·type:·generator/noise">Plugin·type:·generator/noise</a></td></tr><tr><td·align="center"·valign="top">mod</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">additive·or·modulated·noise</td></tr></tbody></table></div></div><p·class="plugin">
111 ····</p><p·class="plugin">111 ····</p><p·class="plugin">
112 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginopen2dimagefilter"></a>open</h5></div></div></div><p·class="plugindescr">morphological·open.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">set</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·Supported·values·are:(black,·white,·)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">112 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginopen2dimagefilter"></a>open</h5></div></div></div><p·class="plugindescr">morphological·open.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">set</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·Supported·values·are:(black,·white,·)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
113 ····</p><p·class="plugin">113 ····</p><p·class="plugin">
114 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginpruning2dimagefilter"></a>pruning</h5></div></div></div><p·class="plugindescr">Morphological·pruning.·Pruning·until·convergence·will·erase·all·pixels·but·closed·loops..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">iter</td><td·align="center"·valign="top">int·in·[1,·1000000]</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Number·of·iterations·to·run,·0=until·convergence</td></tr></tbody></table></div></div><p·class="plugin">114 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginpruning2dimagefilter"></a>pruning</h5></div></div></div><p·class="plugindescr">Morphological·pruning.·Pruning·until·convergence·will·erase·all·pixels·but·closed·loops..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">iter</td><td·align="center"·valign="top">int·in·[1,·1000000]</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Number·of·iterations·to·run,·0=until·convergence</td></tr></tbody></table></div></div><p·class="plugin">
115 ····</p><p·class="plugin">115 ····</p><p·class="plugin">
116 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginregiongrow2dimagefilter"></a>regiongrow</h5></div></div></div><p·class="plugindescr">Region·growing·startin·from·a·seed·until·only·along·increasing·gradients.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">8n</td><td·align="left"·valign="top">Neighborhood·shape.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">seed·image·(bit·valued).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">116 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginregiongrow2dimagefilter"></a>regiongrow</h5></div></div></div><p·class="plugindescr">Region·growing·startin·from·a·seed·until·only·along·increasing·gradients.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">8n</td><td·align="left"·valign="top">Neighborhood·shape.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">seed·image·(bit·valued).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
117 ····</p><p·class="plugin">117 ····</p><p·class="plugin">
118 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsandp2dimagefilter"></a>sandp</h5></div></div></div><p·class="plugindescr">salt·and·pepper··3d·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">float·in·(0,·inf)</td><td·align="center"·valign="top">100</td><td·align="left"·valign="top">thresh·value</td></tr><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">118 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsandp2dimagefilter"></a>sandp</h5></div></div></div><p·class="plugindescr">salt·and·pepper··3d·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">float·in·(0,·inf)</td><td·align="center"·valign="top">100</td><td·align="left"·valign="top">thresh·value</td></tr><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
119 ····</p><p·class="plugin">119 ····</p><p·class="plugin">
120 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginscale2dimagefilter"></a>scale</h5></div></div></div><p·class="plugindescr">2D·image·downscale·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">interp</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[bspline:d=3]</td><td·align="left"·valign="top">interpolation·method·to·be·used·.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></td></tr><tr><td·align="center"·valign="top">s</td><td·align="center"·valign="top">2dbounds</td><td·align="center"·valign="top">[[0,0]]</td><td·align="left"·valign="top">target·size·as·2D·vector</td></tr><tr><td·align="center"·valign="top">sx</td><td·align="center"·valign="top">uint·in·[0,·inf)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">target·size·in·x·direction,·0:·use·input·size</td></tr><tr><td·align="center"·valign="top">sy</td><td·align="center"·valign="top">uint·in·[0,·inf)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">target·size·in·y·direction,·0:·use·input·size</td></tr></tbody></table></div></div><p·class="plugin">120 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginscale2dimagefilter"></a>scale</h5></div></div></div><p·class="plugindescr">2D·image·downscale·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">interp</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[bspline:d=3]</td><td·align="left"·valign="top">interpolation·method·to·be·used·.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></td></tr><tr><td·align="center"·valign="top">s</td><td·align="center"·valign="top">2dbounds</td><td·align="center"·valign="top">[[0,0]]</td><td·align="left"·valign="top">target·size·as·2D·vector</td></tr><tr><td·align="center"·valign="top">sx</td><td·align="center"·valign="top">uint·in·[0,·inf)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">target·size·in·x·direction,·0:·use·input·size</td></tr><tr><td·align="center"·valign="top">sy</td><td·align="center"·valign="top">uint·in·[0,·inf)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">target·size·in·y·direction,·0:·use·input·size</td></tr></tbody></table></div></div><p·class="plugin">
121 ····</p><p·class="plugin">121 ····</p><p·class="plugin">
122 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginselectbig2dimagefilter"></a>selectbig</h5></div></div></div><p·class="plugindescr">2D·label·select·biggest·component·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">122 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginselectbig2dimagefilter"></a>selectbig</h5></div></div></div><p·class="plugindescr">2D·label·select·biggest·component·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
123 ····</p><p·class="plugin">123 ····</p><p·class="plugin">
Offset 125, 25 lines modifiedOffset 125, 25 lines modified
125 ····</p><p·class="plugin">125 ····</p><p·class="plugin">
126 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginshmean2dimagefilter"></a>shmean</h5></div></div></div><p·class="plugindescr">2D·image·filter·that·evaluates·the·mean·over·a·given·neighborhood·shape.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">8n</td><td·align="left"·valign="top">neighborhood·shape·to·evaluate·the·mean.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">126 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginshmean2dimagefilter"></a>shmean</h5></div></div></div><p·class="plugindescr">2D·image·filter·that·evaluates·the·mean·over·a·given·neighborhood·shape.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">8n</td><td·align="left"·valign="top">neighborhood·shape·to·evaluate·the·mean.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
127 ····</p><p·class="plugin">127 ····</p><p·class="plugin">
128 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsobel2dimagefilter"></a>sobel</h5></div></div></div><p·class="plugindescr">The·2D·Sobel·filter·for·gradient·evaluation.·Note·that·the·output·pixel·type·of·the·filtered·image·is·the·same·as·the·input·pixel·type,·so·converting·the·input·beforehand·to·a·floating·point·valued·image·is·recommendable..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">dir</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">x</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">Gradient·direction</td></tr><tr><td·align="left"·valign="top">x:</td><td·align="left"·valign="top">gradient·in·x-direction·</td></tr><tr><td·align="left"·valign="top">y:</td><td·align="left"·valign="top">gradient·in·y-direction·</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">128 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsobel2dimagefilter"></a>sobel</h5></div></div></div><p·class="plugindescr">The·2D·Sobel·filter·for·gradient·evaluation.·Note·that·the·output·pixel·type·of·the·filtered·image·is·the·same·as·the·input·pixel·type,·so·converting·the·input·beforehand·to·a·floating·point·valued·image·is·recommendable..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">dir</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">x</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">Gradient·direction</td></tr><tr><td·align="left"·valign="top">x:</td><td·align="left"·valign="top">gradient·in·x-direction·</td></tr><tr><td·align="left"·valign="top">y:</td><td·align="left"·valign="top">gradient·in·y-direction·</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">
129 ····</p><p·class="plugin">129 ····</p><p·class="plugin">
130 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsort-label2dimagefilter"></a>sort-label</h5></div></div></div><p·class="plugindescr">This·plug-in·sorts·the·labels·of·a·gray-scale·image·so·that·the·lowest·label·value·corresponts·to·the·lable·with·themost·pixels.·The·background·(0)·is·not·touched.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">130 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsort-label2dimagefilter"></a>sort-label</h5></div></div></div><p·class="plugindescr">This·plug-in·sorts·the·labels·of·a·gray-scale·image·so·that·the·lowest·label·value·corresponts·to·the·lable·with·themost·pixels.·The·background·(0)·is·not·touched.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
131 ····</p><p·class="plugin">131 ····</p><p·class="plugin">
132 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsws2dimagefilter"></a>sws</h5></div></div></div><p·class="plugindescr">seeded·watershead.·The·algorithm·extracts·exactly·so·many·reagions·as·initial·labels·are·given·in·the·seed·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">grad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Interpret·the·input·image·as·gradient.·</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">seed·input·image·containing·the·lables·for·the·initial·regions</td></tr></tbody></table></div></div><p·class="plugin">132 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsws2dimagefilter"></a>sws</h5></div></div></div><p·class="plugindescr">seeded·watershead.·The·algorithm·extracts·exactly·so·many·reagions·as·initial·labels·are·given·in·the·seed·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">grad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Interpret·the·input·image·as·gradient.·</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">seed·input·image·containing·the·lables·for·the·initial·regions</td></tr></tbody></table></div></div><p·class="plugin">
133 ····</p><p·class="plugin">133 ····</p><p·class="plugin">
134 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintee2dimagefilter"></a>tee</h5></div></div></div><p·class="plugindescr">Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,output)</td><td·align="left"·valign="top">name·of·the·output·file·to·save·the·image·too..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">134 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintee2dimagefilter"></a>tee</h5></div></div></div><p·class="plugindescr">Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,output)</td><td·align="left"·valign="top">name·of·the·output·file·to·save·the·image·too..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
135 ····</p><p·class="plugin">135 ····</p><p·class="plugin">
136 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginthinning2dimagefilter"></a>thinning</h5></div></div></div><p·class="plugindescr">Morphological·thinning.·Thinning·until·convergence·will·result·in·a·8-connected·skeleton.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">iter</td><td·align="center"·valign="top">int·in·[1,·1000000]</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Number·of·iterations·to·run,·0=until·convergence</td></tr></tbody></table></div></div><p·class="plugin">136 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginthinning2dimagefilter"></a>thinning</h5></div></div></div><p·class="plugindescr">Morphological·thinning.·Thinning·until·convergence·will·result·in·a·8-connected·skeleton.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">iter</td><td·align="center"·valign="top">int·in·[1,·1000000]</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Number·of·iterations·to·run,·0=until·convergence</td></tr></tbody></table></div></div><p·class="plugin">
137 ····</p><p·class="plugin">137 ····</p><p·class="plugin">
138 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginthresh2dimagefilter"></a>thresh</h5></div></div></div><p·class="plugindescr">This·filter·sets·all·pixels·of·an·image·to·zero·that·fall·below·a·certain·threshold·and·whose·neighbours·in·a·given·neighborhood·shape·also·fall·below·a·this·threshold.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">4n</td><td·align="left"·valign="top">neighborhood·shape·to·take·into·account.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">double</td><td·align="center"·valign="top">5</td><td·align="left"·valign="top">The·threshold·value</td></tr></tbody></table></div></div><p·class="plugin">138 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginthresh2dimagefilter"></a>thresh</h5></div></div></div><p·class="plugindescr">This·filter·sets·all·pixels·of·an·image·to·zero·that·fall·below·a·certain·threshold·and·whose·neighbours·in·a·given·neighborhood·shape·also·fall·below·a·this·threshold.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">4n</td><td·align="left"·valign="top">neighborhood·shape·to·take·into·account.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">double</td><td·align="center"·valign="top">5</td><td·align="left"·valign="top">The·threshold·value</td></tr></tbody></table></div></div><p·class="plugin">
139 ····</p><p·class="plugin">139 ····</p><p·class="plugin">
140 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintmean2dimagefilter"></a>tmean</h5></div></div></div><p·class="plugindescr">2D·image·thresholded·tmean·filter:·The·output·pixel·value·is·zero·if·the·input·pixel·value·is·below·the·given·threshold,·otherwise·the·pixels·in·the·evaluation·windows·are·only·considered·if·the·input·pixel·intensity·is·above·the·threshold..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">t</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Threshold·for·pixels·not·to·take·into·account</td></tr><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">140 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintmean2dimagefilter"></a>tmean</h5></div></div></div><p·class="plugindescr">2D·image·thresholded·tmean·filter:·The·output·pixel·value·is·zero·if·the·input·pixel·value·is·below·the·given·threshold,·otherwise·the·pixels·in·the·evaluation·windows·are·only·considered·if·the·input·pixel·intensity·is·above·the·threshold..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">t</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Threshold·for·pixels·not·to·take·into·account</td></tr><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">
141 ····</p><p·class="plugin">141 ····</p><p·class="plugin">
142 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintransform2dimagefilter"></a>transform</h5></div></div></div><p·class="plugindescr">Transform·the·input·image·with·the·given·transformation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">Name·of·the·file·containing·the·transformation..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></td></tr></tbody></table></div></div><p·class="plugin">142 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintransform2dimagefilter"></a>transform</h5></div></div></div><p·class="plugindescr">Transform·the·input·image·with·the·given·transformation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">Name·of·the·file·containing·the·transformation..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></td></tr></tbody></table></div></div><p·class="plugin">
143 ····</p><p·class="plugin">143 ····</p><p·class="plugin">
144 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginws2dimagefilter"></a>ws</h5></div></div></div><p·class="plugindescr">basic·watershead·segmentation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">evalgrad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Set·to·1·if·the·input·image·does·not·represent·a·gradient·norm·image</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">float·in·[0,·1)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Relative·gradient·norm·threshold.·The·actual·value·threshold·value·is·thresh·*·(max_grad·-·min_grad)·+·min_grad.·Bassins·separated·by·gradients·with·a·lower·norm·will·be·joined</td></tr></tbody></table></div></div><p·class="plugin">144 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginws2dimagefilter"></a>ws</h5></div></div></div><p·class="plugindescr">basic·watershead·segmentation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">evalgrad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Set·to·1·if·the·input·image·does·not·represent·a·gradient·norm·image</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">float·in·[0,·1)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Relative·gradient·norm·threshold.·The·actual·value·threshold·value·is·thresh·*·(max_grad·-·min_grad)·+·min_grad.·Bassins·separated·by·gradients·with·a·lower·norm·will·be·joined</td></tr></tbody></table></div></div><p·class="plugin">
145 ····</p><h4><a·name="idp17280"></a>Plugin·consumers:</h4><p·class="consumer">145 ····</p><h4><a·name="idp17280"></a>Plugin·consumers:</h4><p·class="consumer">
146 ······<a·class="xref"·href="Secmia2dimagefilter.html"·title="mia-2dimagefilter">mia-2dimagefilter</a>146 ······<a·class="xref"·href="Secmia2dimagefilter.html"·title="mia-2dimagefilter">mia-2dimagefilter</a>
147 ······<a·class="xref"·href="Secmia2dimagefilterstack.html"·title="mia-2dimagefilterstack">mia-2dimagefilterstack</a>147 ······<a·class="xref"·href="Secmia2dimagefilterstack.html"·title="mia-2dimagefilterstack">mia-2dimagefilterstack</a>
148 ······<a·class="xref"·href="Secmia2dsegmentfuzzyw.html"·title="mia-2dsegment-fuzzyw">mia-2dsegment-fuzzyw</a>148 ······<a·class="xref"·href="Secmia2dsegmentfuzzyw.html"·title="mia-2dsegment-fuzzyw">mia-2dsegment-fuzzyw</a>
149 ······<a·class="xref"·href="Secmia2dseries2dordermedian.html"·title="mia-2dseries2dordermedian">mia-2dseries2dordermedian</a>149 ······<a·class="xref"·href="Secmia2dseries2dordermedian.html"·title="mia-2dseries2dordermedian">mia-2dseries2dordermedian</a>
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Offset 65, 15 lines modifiedOffset 65, 15 lines modified
65 combiner65 combiner
66 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to66 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to
67 false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and67 false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and
68 the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the68 the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the
69 moment·the·filter·is·run..·Supported·parameters·are:69 moment·the·filter·is·run..·Supported·parameters·are:
70 ·_____________________________________________________________________________70 ·_____________________________________________________________________________
71 |__Name_|__Type_|______Default___|________________________Description_________|71 |__Name_|__Type_|______Default___|________________________Description_________|
72 |·image·|···io··|(input,required)|second·image·that·is·needed·in·the·combiner.|72 |·image·|···io··|(required,input)|second·image·that·is·needed·in·the·combiner.|
73 |·······|·······|················|For·supported·file·types·see·Plugin_type:···|73 |·······|·······|················|For·supported·file·types·see·Plugin_type:···|
74 |_______|_______|________________|2dimage/io__________________________________|74 |_______|_______|________________|2dimage/io__________________________________|
75 |···op··|factory|····(required)··|Image·combiner·to·be·applied·to·the·images.·|75 |···op··|factory|····(required)··|Image·combiner·to·be·applied·to·the·images.·|
76 |·······|·······|················|For·supported·plug-ins·see·Plugin_type:·····|76 |·······|·······|················|For·supported·plug-ins·see·Plugin_type:·····|
77 |_______|_______|________________|2dimage/combiner____________________________|77 |_______|_______|________________|2dimage/combiner____________________________|
78 |reverse|··bool·|···········0····|reverse·the·order·in·which·the·images·passed|78 |reverse|··bool·|···········0····|reverse·the·order·in·which·the·images·passed|
79 |_______|_______|________________|to_the_combiner_____________________________|79 |_______|_______|________________|to_the_combiner_____________________________|
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174 |··n·|factory|···4n··|Neighborhood·mask·to·describe·connectivity..·For·|174 |··n·|factory|···4n··|Neighborhood·mask·to·describe·connectivity..·For·|
175 |____|_______|_______|supported_plug-ins_see_Plugin_type:_2dimage/shape|175 |____|_______|_______|supported_plug-ins_see_Plugin_type:_2dimage/shape|
176 labelmap176 labelmap
177 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued177 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued
178 intensities/labels..·Supported·parameters·are:178 intensities/labels..·Supported·parameters·are:
179 ·_______________________________________________179 ·_______________________________________________
180 |Name|_Type_|______Default___|_____Description__|180 |Name|_Type_|______Default___|_____Description__|
181 |map_|string|(input,required)|Label_mapping_file|181 |map_|string|(required,input)|Label_mapping_file|
182 labelscale182 labelscale
183 A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input183 A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input
184 image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target184 image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target
185 pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the185 pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the
186 corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same186 corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same
187 count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:187 count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:
188 ·___________________________________________________________________________188 ·___________________________________________________________________________
189 |___Name_|___Type_|__Default_|__________________________Description_________|189 |___Name_|___Type_|__Default_|__________________________Description_________|
190 |out-size|2dbounds|(required)|target_size_given_as_two_coma_separated_values|190 |out-size|2dbounds|(required)|target_size_given_as_two_coma_separated_values|
191 load191 load
192 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the192 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the
193 pipeline..·Supported·parameters·are:193 pipeline..·Supported·parameters·are:
194 ·___________________________________________________________________________194 ·___________________________________________________________________________
195 |Name|Type|______Default___|___________________________Description__________|195 |Name|Type|______Default___|___________________________Description__________|
196 |file|·io·|(input,required)|name·of·the·input·file·to·load·from..·For·······|196 |file|·io·|(required,input)|name·of·the·input·file·to·load·from..·For·······|
197 |____|____|________________|supported_file_types_see_Plugin_type:_2dimage/io|197 |____|____|________________|supported_file_types_see_Plugin_type:_2dimage/io|
198 mask198 mask
199 2D·masking,·one·of·the·two·input·images·must·by·of·type·bit..·Supported199 2D·masking,·one·of·the·two·input·images·must·by·of·type·bit..·Supported
200 parameters·are:200 parameters·are:
201 ·____________________________________________________________________________201 ·____________________________________________________________________________
202 |__Name_|Type|______Default___|__________________________Description_________|202 |__Name_|Type|______Default___|__________________________Description_________|
203 |··fill·|dict|·········min····|·_________________________________________····|203 |··fill·|dict|·········min····|·_________________________________________····|
204 |·······|····|················||fill_style_for_pixels_outside_of_the_mask|···|204 |·······|····|················||fill_style_for_pixels_outside_of_the_mask|···|
205 |·······|····|················||min:·|set·values·outside·the·mask·to·the·|···|205 |·······|····|················||min:·|set·values·outside·the·mask·to·the·|···|
206 |·······|····|················||_____|minimum_value_found_in_the_image.__|···|206 |·······|····|················||_____|minimum_value_found_in_the_image.__|···|
207 |·······|····|················||zero:|set·the·values·outside·the·mask·to·|···|207 |·······|····|················||zero:|set·the·values·outside·the·mask·to·|···|
208 |·······|····|················||_____|zero.______________________________|···|208 |·······|····|················||_____|zero.______________________________|···|
209 |·······|····|················||max:·|set·values·outside·the·mask·to·the·|···|209 |·······|····|················||max:·|set·values·outside·the·mask·to·the·|···|
210 |_______|____|________________||_____|maximum_value_found_in_the_image.._|___|210 |_______|____|________________||_____|maximum_value_found_in_the_image.._|___|
211 |·input·|·io·|(input,required)|second·input·image·file·name.·For·supported···|211 |·input·|·io·|(required,input)|second·input·image·file·name.·For·supported···|
212 |_______|____|________________|file_types_see_Plugin_type:_2dimage/io________|212 |_______|____|________________|file_types_see_Plugin_type:_2dimage/io________|
213 |inverse|bool|···········0····|set·to·true·to·use·the·inverse·of·the·mask·for|213 |inverse|bool|···········0····|set·to·true·to·use·the·inverse·of·the·mask·for|
214 |_______|____|________________|masking_______________________________________|214 |_______|____|________________|masking_______________________________________|
215 maxflow215 maxflow
216 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image216 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image
217 segmentation.·Supported·parameters·are:217 segmentation.·Supported·parameters·are:
218 ·_____________________________________________________________________________218 ·_____________________________________________________________________________
219 |_____Name__|Type|______Default___|________________________Description________|219 |_____Name__|Type|______Default___|________________________Description________|
220 |·sink-flow·|·io·|(input,required)|Image·of·float·type·to·define·the·per-pixel|220 |·sink-flow·|·io·|(required,input)|Image·of·float·type·to·define·the·per-pixel|
221 |···········|····|················|flow·to·the·sink.·For·supported·file·types·|221 |···········|····|················|flow·to·the·sink.·For·supported·file·types·|
222 |___________|____|________________|see_Plugin_type:_2dimage/io________________|222 |___________|____|________________|see_Plugin_type:_2dimage/io________________|
223 |source-flow|·io·|(input,required)|Image·of·float·type·to·define·the·per-pixel|223 |source-flow|·io·|(required,input)|Image·of·float·type·to·define·the·per-pixel|
224 |···········|····|················|flow·to·the·source.·For·supported·file·····|224 |···········|····|················|flow·to·the·source.·For·supported·file·····|
225 |___________|____|________________|types_see_Plugin_type:_2dimage/io__________|225 |___________|____|________________|types_see_Plugin_type:_2dimage/io__________|
226 mean226 mean
227 2D·image·mean·filter.·Supported·parameters·are:227 2D·image·mean·filter.·Supported·parameters·are:
228 ·______________________________________________228 ·______________________________________________
229 |Name|________Type___|Default|____Description__|229 |Name|________Type___|Default|____Description__|
230 |__w_|int_in_[1,_inf)|____1__|half_filter_width|230 |__w_|int_in_[1,_inf)|____1__|half_filter_width|
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309 regiongrow309 regiongrow
310 Region·growing·startin·from·a·seed·until·only·along·increasing·gradients.310 Region·growing·startin·from·a·seed·until·only·along·increasing·gradients.
311 Supported·parameters·are:311 Supported·parameters·are:
312 ·____________________________________________________________________________312 ·____________________________________________________________________________
313 |Name|__Type_|______Default___|__________________________Description_________|313 |Name|__Type_|______Default___|__________________________Description_________|
314 |··n·|factory|··········8n····|Neighborhood·shape.·For·supported·plug-ins·see|314 |··n·|factory|··········8n····|Neighborhood·shape.·For·supported·plug-ins·see|
315 |____|_______|________________|Plugin_type:_2dimage/shape____________________|315 |____|_______|________________|Plugin_type:_2dimage/shape____________________|
316 |seed|···io··|(input,required)|seed·image·(bit·valued).·For·supported·file···|316 |seed|···io··|(required,input)|seed·image·(bit·valued).·For·supported·file···|
317 |____|_______|________________|types_see_Plugin_type:_2dimage/io_____________|317 |____|_______|________________|types_see_Plugin_type:_2dimage/io_____________|
318 sandp318 sandp
319 salt·and·pepper·3d·filter.·Supported·parameters·are:319 salt·and·pepper·3d·filter.·Supported·parameters·are:
320 ·_______________________________________________________320 ·_______________________________________________________
321 |_Name_|_________Type____|Default|________Description___|321 |_Name_|_________Type____|Default|________Description___|
322 |thresh|float_in_(0,_inf)|___100_|thresh_value__________|322 |thresh|float_in_(0,_inf)|___100_|thresh_value__________|
323 |___w__|_int_in_[1,_inf)_|____1__|filter_width_parameter|323 |___w__|_int_in_[1,_inf)_|____1__|filter_width_parameter|
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373 |Name|__Type_|______Default___|___________________________Description_________|373 |Name|__Type_|______Default___|___________________________Description_________|
374 |grad|__bool_|___________0____|Interpret_the_input_image_as_gradient._________|374 |grad|__bool_|___________0____|Interpret_the_input_image_as_gradient._________|
375 |mark|··bool·|···········0····|Mark·the·segmented·watersheds·with·a·special···|375 |mark|··bool·|···········0····|Mark·the·segmented·watersheds·with·a·special···|
376 |____|_______|________________|gray_scale_value_______________________________|376 |____|_______|________________|gray_scale_value_______________________________|
377 |··n·|factory|···[sphere:r=1]·|Neighborhood·for·watershead·region·growing.·For|377 |··n·|factory|···[sphere:r=1]·|Neighborhood·for·watershead·region·growing.·For|
378 |····|·······|················|supported·plug-ins·see·Plugin_type:_2dimage/···|378 |····|·······|················|supported·plug-ins·see·Plugin_type:_2dimage/···|
379 |____|_______|________________|shape__________________________________________|379 |____|_______|________________|shape__________________________________________|
380 |seed|string·|(input,required)|seed·input·image·containing·the·lables·for·the·|380 |seed|string·|(required,input)|seed·input·image·containing·the·lables·for·the·|
381 |____|_______|________________|initial_regions________________________________|381 |____|_______|________________|initial_regions________________________________|
382 tee382 tee
383 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.383 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.
384 Supported·parameters·are:384 Supported·parameters·are:
385 ·___________________________________________________________________________385 ·___________________________________________________________________________
386 |Name|Type|_______Default___|___________________________Description_________|386 |Name|Type|_______Default___|___________________________Description_________|
387 |file|·io·|(required,output)|name·of·the·output·file·to·save·the·image·too..|387 |file|·io·|(required,output)|name·of·the·output·file·to·save·the·image·too..|
Offset 413, 15 lines modifiedOffset 413, 15 lines modified
413 |__t_|_______float___|____0__|Threshold_for_pixels_not_to_take_into_account|413 |__t_|_______float___|____0__|Threshold_for_pixels_not_to_take_into_account|
414 |__w_|int_in_[1,_inf)|____1__|half_filter_width____________________________|414 |__w_|int_in_[1,_inf)|____1__|half_filter_width____________________________|
415 transform415 transform
416 Transform·the·input·image·with·the·given·transformation..·Supported·parameters416 Transform·the·input·image·with·the·given·transformation..·Supported·parameters
417 are:417 are:
418 ·___________________________________________________________________________418 ·___________________________________________________________________________
419 |Name|Type|______Default___|___________________________Description__________|419 |Name|Type|______Default___|___________________________Description__________|
420 |file|·io·|(input,required)|Name·of·the·file·containing·the·transformation..|420 |file|·io·|(required,input)|Name·of·the·file·containing·the·transformation..|
421 |····|····|················|For·supported·file·types·see·Plugin_type:·······|421 |····|····|················|For·supported·file·types·see·Plugin_type:·······|
422 |____|____|________________|2dtransform/io__________________________________|422 |____|____|________________|2dtransform/io__________________________________|
423 ws423 ws
424 basic·watershead·segmentation..·Supported·parameters·are:424 basic·watershead·segmentation..·Supported·parameters·are:
425 ·____________________________________________________________________________425 ·____________________________________________________________________________
426 |___Name_|________Type___|___Default__|____________________Description_______|426 |___Name_|________Type___|___Default__|____________________Description_______|
427 |evalgrad|········bool···|········0···|Set·to·1·if·the·input·image·does·not··|427 |evalgrad|········bool···|········0···|Set·to·1·if·the·input·image·does·not··|
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./usr/share/doc/mia-2.4/userref/SecPlugintype2dstackfilter.html
    
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16 ····</p><p·class="plugin">16 ····</p><p·class="plugin">
17 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugindilate2dstackfilter"></a>dilate</h5></div></div></div><p·class="plugindescr">2D·Stack·morphological·filter·'dilate'.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">17 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugindilate2dstackfilter"></a>dilate</h5></div></div></div><p·class="plugindescr">2D·Stack·morphological·filter·'dilate'.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
18 ····</p><p·class="plugin">18 ····</p><p·class="plugin">
19 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginerode2dstackfilter"></a>erode</h5></div></div></div><p·class="plugindescr">2D·Stack·morphological·filter·'erode'.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">19 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginerode2dstackfilter"></a>erode</h5></div></div></div><p·class="plugindescr">2D·Stack·morphological·filter·'erode'.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
20 ····</p><p·class="plugin">20 ····</p><p·class="plugin">
21 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingauss2dstackfilter"></a>gauss</h5></div></div></div><p·class="plugindescr">Gauss·2D·fifo·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter·(2*w+1)</td></tr></tbody></table></div></div><p·class="plugin">21 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingauss2dstackfilter"></a>gauss</h5></div></div></div><p·class="plugindescr">Gauss·2D·fifo·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter·(2*w+1)</td></tr></tbody></table></div></div><p·class="plugin">
22 ····</p><p·class="plugin">22 ····</p><p·class="plugin">
23 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabel2dstackfilter"></a>label</h5></div></div></div><p·class="plugindescr">Stack·Label·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">Mapfile·to·save·label·numbers·that·are·joined</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">4n</td><td·align="left"·valign="top">2D·neighbourhood·shape·to·define·connectedness.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">23 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabel2dstackfilter"></a>label</h5></div></div></div><p·class="plugindescr">Stack·Label·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">Mapfile·to·save·label·numbers·that·are·joined</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">4n</td><td·align="left"·valign="top">2D·neighbourhood·shape·to·define·connectedness.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimageshape.html"·title="Plugin·type:·2dimage/shape">Plugin·type:·2dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
24 ····</p><p·class="plugin">24 ····</p><p·class="plugin">
25 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmedian2dstackfilter"></a>median</h5></div></div></div><p·class="plugindescr">median·2D·fifo·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">25 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmedian2dstackfilter"></a>median</h5></div></div></div><p·class="plugindescr">median·2D·fifo·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
26 ····</p><p·class="plugin">26 ····</p><p·class="plugin">
27 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmlv2dstackfilter"></a>mlv</h5></div></div></div><p·class="plugindescr">Mean·of·Least·Variance·2D·stack·image·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">27 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmlv2dstackfilter"></a>mlv</h5></div></div></div><p·class="plugindescr">Mean·of·Least·Variance·2D·stack·image·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
28 ····</p><p·class="plugin">28 ····</p><p·class="plugin">
29 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginopen2dstackfilter"></a>open</h5></div></div></div><p·class="plugindescr">2D·Stack·morphological·filter·'open'.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">29 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginopen2dstackfilter"></a>open</h5></div></div></div><p·class="plugindescr">2D·Stack·morphological·filter·'open'.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
30 ····</p><p·class="plugin">30 ····</p><p·class="plugin">
31 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginregiongrow2dstackfilter"></a>regiongrow</h5></div></div></div><p·class="plugindescr">Run·a·region-growing·filter·on·a·stack·of·images·that·comprise·a·3D·image.··The·region·growing·is·based·on·class·probabilities·obtained·from·a·c-means·classification·of·the·pixel·intensities.·One·seed·thresh·is·use·to·initiate·a·region,·and·another·(lower)·threshold·is·used·to·stop·the·region·growing.·By·holding·a·number·of·3D·slices·in·the·working·memory·to·permit·the·region·to·grow·"backwards·"·in·the·stack·a·Quasi-3D·processing·is·achieved.·However,·with·complex·structures·the·region·growing·may·not·properly·be·segmented..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">class</td><td·align="center"·valign="top">int·in·[0,·inf)</td><td·align="center"·valign="top">2</td><td·align="left"·valign="top">class·to·be·segmented</td></tr><tr><td·align="center"·valign="top">depth</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">10</td><td·align="left"·valign="top">number·of·slices·to·keep·during·processing</td></tr><tr><td·align="center"·valign="top">low</td><td·align="center"·valign="top">float·in·(0,·1]</td><td·align="center"·valign="top">0.5</td><td·align="left"·valign="top">low·threshold·for·acceptance·probability</td></tr><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">seed·class·map</td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">float·in·(0,·1]</td><td·align="center"·valign="top">0.98</td><td·align="left"·valign="top">threshold·for·seed·probability</td></tr></tbody></table></div></div><p·class="plugin">31 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginregiongrow2dstackfilter"></a>regiongrow</h5></div></div></div><p·class="plugindescr">Run·a·region-growing·filter·on·a·stack·of·images·that·comprise·a·3D·image.··The·region·growing·is·based·on·class·probabilities·obtained·from·a·c-means·classification·of·the·pixel·intensities.·One·seed·thresh·is·use·to·initiate·a·region,·and·another·(lower)·threshold·is·used·to·stop·the·region·growing.·By·holding·a·number·of·3D·slices·in·the·working·memory·to·permit·the·region·to·grow·"backwards·"·in·the·stack·a·Quasi-3D·processing·is·achieved.·However,·with·complex·structures·the·region·growing·may·not·properly·be·segmented..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">class</td><td·align="center"·valign="top">int·in·[0,·inf)</td><td·align="center"·valign="top">2</td><td·align="left"·valign="top">class·to·be·segmented</td></tr><tr><td·align="center"·valign="top">depth</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">10</td><td·align="left"·valign="top">number·of·slices·to·keep·during·processing</td></tr><tr><td·align="center"·valign="top">low</td><td·align="center"·valign="top">float·in·(0,·1]</td><td·align="center"·valign="top">0.5</td><td·align="left"·valign="top">low·threshold·for·acceptance·probability</td></tr><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">seed·class·map</td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">float·in·(0,·1]</td><td·align="center"·valign="top">0.98</td><td·align="left"·valign="top">threshold·for·seed·probability</td></tr></tbody></table></div></div><p·class="plugin">
32 ····</p><h4><a·name="idp18364"></a>Plugin·consumers:</h4><p·class="consumer">32 ····</p><h4><a·name="idp18364"></a>Plugin·consumers:</h4><p·class="consumer">
33 ······<a·class="xref"·href="Secmia2dstackfilter.html"·title="mia-2dstackfilter">mia-2dstackfilter</a>33 ······<a·class="xref"·href="Secmia2dstackfilter.html"·title="mia-2dstackfilter">mia-2dstackfilter</a>
34 ····</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecPlugintype2dimagetransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="plugins.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecPlugintype2dtransformio.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Plugin·type:·2dimage/transform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Plugin·type:·2dtransform/io</td></tr></table></div></body></html>34 ····</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecPlugintype2dimagetransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="plugins.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecPlugintype2dtransformio.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Plugin·type:·2dimage/transform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Plugin·type:·2dtransform/io</td></tr></table></div></body></html>
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42 ·___________________________________________________________42 ·___________________________________________________________
43 |Name|________Type___|Default|______________Description_____|43 |Name|________Type___|Default|______________Description_____|
44 |__w_|int_in_[1,_inf)|____1__|filter_width_parameter_(2*w+1)|44 |__w_|int_in_[1,_inf)|____1__|filter_width_parameter_(2*w+1)|
45 label45 label
46 Stack·Label·filter.·Supported·parameters·are:46 Stack·Label·filter.·Supported·parameters·are:
47 ·_____________________________________________________________________________47 ·_____________________________________________________________________________
48 |Name|__Type_|______Default___|___________________________Description_________|48 |Name|__Type_|______Default___|___________________________Description_________|
49 |map_|string_|(input,required)|Mapfile_to_save_label_numbers_that_are_joined__|49 |map_|string_|(required,input)|Mapfile_to_save_label_numbers_that_are_joined__|
50 |··n·|factory|··········4n····|2D·neighbourhood·shape·to·define·connectedness.|50 |··n·|factory|··········4n····|2D·neighbourhood·shape·to·define·connectedness.|
51 |····|·······|················|For·supported·plug-ins·see·Plugin_type:········|51 |····|·······|················|For·supported·plug-ins·see·Plugin_type:········|
52 |____|_______|________________|2dimage/shape__________________________________|52 |____|_______|________________|2dimage/shape__________________________________|
53 median53 median
54 median·2D·fifo·filter.·Supported·parameters·are:54 median·2D·fifo·filter.·Supported·parameters·are:
55 ·___________________________________________________55 ·___________________________________________________
56 |Name|________Type___|Default|________Description___|56 |Name|________Type___|Default|________Description___|
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78 ·______________________________________________________________________78 ·______________________________________________________________________
79 |Name_|________Type___|______Default___|_______________Description_____|79 |Name_|________Type___|______Default___|_______________Description_____|
80 |class|int_in_[0,_inf)|___________2____|class_to_be_segmented__________|80 |class|int_in_[0,_inf)|___________2____|class_to_be_segmented__________|
81 |depth|int·in·[1,·inf)|··········10····|number·of·slices·to·keep·during|81 |depth|int·in·[1,·inf)|··········10····|number·of·slices·to·keep·during|
82 |_____|_______________|________________|processing_____________________|82 |_____|_______________|________________|processing_____________________|
83 |·low·|float·in·(0,·1]|·········0.5····|low·threshold·for·acceptance···|83 |·low·|float·in·(0,·1]|·········0.5····|low·threshold·for·acceptance···|
84 |_____|_______________|________________|probability____________________|84 |_____|_______________|________________|probability____________________|
85 |_map_|______string___|(input,required)|seed_class_map_________________|85 |_map_|______string___|(required,input)|seed_class_map_________________|
86 |seed_|float_in_(0,_1]|_________0.98___|threshold_for_seed_probability_|86 |seed_|float_in_(0,_1]|_________0.98___|threshold_for_seed_probability_|
87 Plugin·consumers:87 Plugin·consumers:
88 mia-2dstackfilter88 mia-2dstackfilter
89 ===============================================================================89 ===============================================================================
90 Prev ···························Up························· Next90 Prev ···························Up························· Next
91 Plugin·type:·2dimage/transform Home· Plugin·type:·2dtransform/io91 Plugin·type:·2dimage/transform Home· Plugin·type:·2dtransform/io
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./usr/share/doc/mia-2.4/userref/SecPlugintype3dimagefilter.html
    
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45 ····</p><p·class="plugin">45 ····</p><p·class="plugin">
46 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbandpass3dimagefilter"></a>bandpass</h5></div></div></div><p·class="plugindescr">intensity·bandpass·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·the·band</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·the·band</td></tr></tbody></table></div></div><p·class="plugin">46 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbandpass3dimagefilter"></a>bandpass</h5></div></div></div><p·class="plugindescr">intensity·bandpass·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·the·band</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·the·band</td></tr></tbody></table></div></div><p·class="plugin">
47 ····</p><p·class="plugin">47 ····</p><p·class="plugin">
48 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbinarize3dimagefilter"></a>binarize</h5></div></div></div><p·class="plugindescr">image·binarize·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·accepted·range</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·accepted·range</td></tr></tbody></table></div></div><p·class="plugin">48 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginbinarize3dimagefilter"></a>binarize</h5></div></div></div><p·class="plugindescr">image·binarize·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">max</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">3.40282e+38</td><td·align="left"·valign="top">maximum·of·accepted·range</td></tr><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">minimum·of·accepted·range</td></tr></tbody></table></div></div><p·class="plugin">
49 ····</p><p·class="plugin">49 ····</p><p·class="plugin">
50 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginclose3dimagefilter"></a>close</h5></div></div></div><p·class="plugindescr">morphological·close.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·(black|white)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">50 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginclose3dimagefilter"></a>close</h5></div></div></div><p·class="plugindescr">morphological·close.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·(black|white)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
51 ····</p><p·class="plugin">51 ····</p><p·class="plugin">
52 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincombiner3dimagefilter"></a>combiner</h5></div></div></div><p·class="plugindescr">Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">image</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">second·image·that·is·needed·in·the·combiner.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr><tr><td·align="center"·valign="top">op</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">Image·combiner·to·be·applied·to·the·images.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecombiner.html"·title="Plugin·type:·3dimage/combiner">Plugin·type:·3dimage/combiner</a></td></tr><tr><td·align="center"·valign="top">reverse</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">reverse·the·order·in·which·the·images·passed·to·the·combiner</td></tr></tbody></table></div></div><p·class="plugin">52 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincombiner3dimagefilter"></a>combiner</h5></div></div></div><p·class="plugindescr">Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">image</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">second·image·that·is·needed·in·the·combiner.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr><tr><td·align="center"·valign="top">op</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">Image·combiner·to·be·applied·to·the·images.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecombiner.html"·title="Plugin·type:·3dimage/combiner">Plugin·type:·3dimage/combiner</a></td></tr><tr><td·align="center"·valign="top">reverse</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">reverse·the·order·in·which·the·images·passed·to·the·combiner</td></tr></tbody></table></div></div><p·class="plugin">
53 ····</p><p·class="plugin">53 ····</p><p·class="plugin">
54 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginconvert3dimagefilter"></a>convert</h5></div></div></div><p·class="plugindescr">image·pixel·format·conversion·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">a</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">linear·conversion·parameter·a</td></tr><tr><td·align="center"·valign="top">b</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">linear·conversion·parameter·b</td></tr><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">opt</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">conversion·mapping</td></tr><tr><td·align="left"·valign="top">copy:</td><td·align="left"·valign="top">copy·data·when·converting</td></tr><tr><td·align="left"·valign="top">linear:</td><td·align="left"·valign="top">apply·linear·transformation·x·-&gt;·a*x+b</td></tr><tr><td·align="left"·valign="top">range:</td><td·align="left"·valign="top">apply·linear·transformation·that·maps·the·input·data·type·range·to·the·output·data·type·range</td></tr><tr><td·align="left"·valign="top">opt:</td><td·align="left"·valign="top">apply·a·linear·transformation·that·maps·the·real·input·range·to·the·full·output·range</td></tr><tr><td·align="left"·valign="top">optstat:</td><td·align="left"·valign="top">apply·a·linear·transform·that·maps·based·on·input·mean·and·variation·to·the·full·output·range</td></tr></tbody></table></div></td></tr><tr><td·align="center"·valign="top">repn</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">ubyte</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">output·pixel·type</td></tr><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">54 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginconvert3dimagefilter"></a>convert</h5></div></div></div><p·class="plugindescr">image·pixel·format·conversion·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">a</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">linear·conversion·parameter·a</td></tr><tr><td·align="center"·valign="top">b</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">linear·conversion·parameter·b</td></tr><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">opt</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">conversion·mapping</td></tr><tr><td·align="left"·valign="top">copy:</td><td·align="left"·valign="top">copy·data·when·converting</td></tr><tr><td·align="left"·valign="top">linear:</td><td·align="left"·valign="top">apply·linear·transformation·x·-&gt;·a*x+b</td></tr><tr><td·align="left"·valign="top">range:</td><td·align="left"·valign="top">apply·linear·transformation·that·maps·the·input·data·type·range·to·the·output·data·type·range</td></tr><tr><td·align="left"·valign="top">opt:</td><td·align="left"·valign="top">apply·a·linear·transformation·that·maps·the·real·input·range·to·the·full·output·range</td></tr><tr><td·align="left"·valign="top">optstat:</td><td·align="left"·valign="top">apply·a·linear·transform·that·maps·based·on·input·mean·and·variation·to·the·full·output·range</td></tr></tbody></table></div></td></tr><tr><td·align="center"·valign="top">repn</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">ubyte</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">output·pixel·type</td></tr><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">
55 ····</p><p·class="plugin">55 ····</p><p·class="plugin">
56 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincrop3dimagefilter"></a>crop</h5></div></div></div><p·class="plugindescr">Crop·a·region·of·an·image,·the·region·is·always·clamped·to·the·original·image·size·in·the·sense·that·the·given·range·is·kept..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">end</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[4294967295,4294967295,4294967295]]</td><td·align="left"·valign="top">end·of·cropping·range,·maximum·=·(-1,-1,-1)</td></tr><tr><td·align="center"·valign="top">start</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[0,0,0]]</td><td·align="left"·valign="top">begin·of·cropping·range</td></tr></tbody></table></div></div><p·class="plugin">56 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugincrop3dimagefilter"></a>crop</h5></div></div></div><p·class="plugindescr">Crop·a·region·of·an·image,·the·region·is·always·clamped·to·the·original·image·size·in·the·sense·that·the·given·range·is·kept..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">end</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[4294967295,4294967295,4294967295]]</td><td·align="left"·valign="top">end·of·cropping·range,·maximum·=·(-1,-1,-1)</td></tr><tr><td·align="center"·valign="top">start</td><td·align="center"·valign="top">streamable</td><td·align="center"·valign="top">[[0,0,0]]</td><td·align="left"·valign="top">begin·of·cropping·range</td></tr></tbody></table></div></div><p·class="plugin">
57 ····</p><p·class="plugin">57 ····</p><p·class="plugin">
58 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugindilate3dimagefilter"></a>dilate</h5></div></div></div><p·class="plugindescr">3d·image·stack·dilate·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·(black|white)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">58 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugindilate3dimagefilter"></a>dilate</h5></div></div></div><p·class="plugindescr">3d·image·stack·dilate·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·(black|white)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
59 ····</p><p·class="plugin">59 ····</p><p·class="plugin">
Offset 63, 33 lines modifiedOffset 63, 33 lines modified
63 ····</p><p·class="plugin">63 ····</p><p·class="plugin">
64 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginerode3dimagefilter"></a>erode</h5></div></div></div><p·class="plugindescr">3d·image·stack·erode·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·(black|white)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">64 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginerode3dimagefilter"></a>erode</h5></div></div></div><p·class="plugindescr">3d·image·stack·erode·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">hint</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">black</td><td·align="left"·valign="top">a·hint·at·the·main·image·content·(black|white)</td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=2]</td><td·align="left"·valign="top">structuring·element.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
65 ····</p><p·class="plugin">65 ····</p><p·class="plugin">
66 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingauss3dimagefilter"></a>gauss</h5></div></div></div><p·class="plugindescr">isotropic·3D·gauss·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[0,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">66 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingauss3dimagefilter"></a>gauss</h5></div></div></div><p·class="plugindescr">isotropic·3D·gauss·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[0,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
67 ····</p><p·class="plugin">67 ····</p><p·class="plugin">
68 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingradnorm3dimagefilter"></a>gradnorm</h5></div></div></div><p·class="plugindescr">3D·image·to·gradient·norm·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">68 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingradnorm3dimagefilter"></a>gradnorm</h5></div></div></div><p·class="plugindescr">3D·image·to·gradient·norm·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
69 ····</p><p·class="plugin">69 ····</p><p·class="plugin">
70 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingrowmask3dimagefilter"></a>growmask</h5></div></div></div><p·class="plugindescr">Use·an·input·binary·mask·and·a·reference·gray·scale·image·to·do·region·growing·by·adding·the·neighborhood·pixels·of·an·already·added·pixel·if·the·have·a·lower·intensity·that·is·above·the·given·threshold..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">lower·threshold·for·mask·growing</td></tr><tr><td·align="center"·valign="top">ref</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">reference·image·for·mask·region·growing.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">neighborhood·mask.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">70 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugingrowmask3dimagefilter"></a>growmask</h5></div></div></div><p·class="plugindescr">Use·an·input·binary·mask·and·a·reference·gray·scale·image·to·do·region·growing·by·adding·the·neighborhood·pixels·of·an·already·added·pixel·if·the·have·a·lower·intensity·that·is·above·the·given·threshold..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">min</td><td·align="center"·valign="top">float</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">lower·threshold·for·mask·growing</td></tr><tr><td·align="center"·valign="top">ref</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">reference·image·for·mask·region·growing.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr><tr><td·align="center"·valign="top">shape</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">neighborhood·mask.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
71 ····</p><p·class="plugin">71 ····</p><p·class="plugin">
72 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugininvert3dimagefilter"></a>invert</h5></div></div></div><p·class="plugindescr">intensity·invert·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">72 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugininvert3dimagefilter"></a>invert</h5></div></div></div><p·class="plugindescr">intensity·invert·filter.·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
73 ····</p><p·class="plugin">73 ····</p><p·class="plugin">
74 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginisovoxel3dimagefilter"></a>isovoxel</h5></div></div></div><p·class="plugindescr">This·filter·scales·an·image·to·make·the·voxel·size·isometric·and·its·size·to·correspond·to·the·given·value.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">interp</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[bspline:d=3]</td><td·align="left"·valign="top">interpolation·kernel·to·be·used·.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></td></tr><tr><td·align="center"·valign="top">size</td><td·align="center"·valign="top">float·in·(0,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">isometric·target·voxel·size</td></tr></tbody></table></div></div><p·class="plugin">74 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginisovoxel3dimagefilter"></a>isovoxel</h5></div></div></div><p·class="plugindescr">This·filter·scales·an·image·to·make·the·voxel·size·isometric·and·its·size·to·correspond·to·the·given·value.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">interp</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[bspline:d=3]</td><td·align="left"·valign="top">interpolation·kernel·to·be·used·.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></td></tr><tr><td·align="center"·valign="top">size</td><td·align="center"·valign="top">float·in·(0,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">isometric·target·voxel·size</td></tr></tbody></table></div></div><p·class="plugin">
75 ····</p><p·class="plugin">75 ····</p><p·class="plugin">
76 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginkmeans3dimagefilter"></a>kmeans</h5></div></div></div><p·class="plugindescr">3D·image·k-means·filter.·In·the·output·image·the·pixel·value·represents·the·class·membership·and·the·class·centers·are·stored·as·attribute·in·the·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">c</td><td·align="center"·valign="top">int·in·[2,·inf)</td><td·align="center"·valign="top">3</td><td·align="left"·valign="top">number·of·classes</td></tr></tbody></table></div></div><p·class="plugin">76 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginkmeans3dimagefilter"></a>kmeans</h5></div></div></div><p·class="plugindescr">3D·image·k-means·filter.·In·the·output·image·the·pixel·value·represents·the·class·membership·and·the·class·centers·are·stored·as·attribute·in·the·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">c</td><td·align="center"·valign="top">int·in·[2,·inf)</td><td·align="center"·valign="top">3</td><td·align="left"·valign="top">number·of·classes</td></tr></tbody></table></div></div><p·class="plugin">
77 ····</p><p·class="plugin">77 ····</p><p·class="plugin">
78 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabel3dimagefilter"></a>label</h5></div></div></div><p·class="plugindescr">A·filter·to·label·the··connected·components·of·a·binary·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">neighborhood·mask.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">78 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabel3dimagefilter"></a>label</h5></div></div></div><p·class="plugindescr">A·filter·to·label·the··connected·components·of·a·binary·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">6n</td><td·align="left"·valign="top">neighborhood·mask.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr></tbody></table></div></div><p·class="plugin">
79 ····</p><p·class="plugin">79 ····</p><p·class="plugin">
80 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelmap3dimagefilter"></a>labelmap</h5></div></div></div><p·class="plugindescr">Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">Label·mapping·file</td></tr></tbody></table></div></div><p·class="plugin">80 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelmap3dimagefilter"></a>labelmap</h5></div></div></div><p·class="plugindescr">Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">map</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">Label·mapping·file</td></tr></tbody></table></div></div><p·class="plugin">
81 ····</p><p·class="plugin">81 ····</p><p·class="plugin">
82 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelscale3dimagefilter"></a>labelscale</h5></div></div></div><p·class="plugindescr">A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input·image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target·pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the·corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same·count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">out-size</td><td·align="center"·valign="top">3dbounds</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">target·size·given·as·two·coma·separated·values</td></tr></tbody></table></div></div><p·class="plugin">82 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlabelscale3dimagefilter"></a>labelscale</h5></div></div></div><p·class="plugindescr">A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input·image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target·pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the·corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same·count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">out-size</td><td·align="center"·valign="top">3dbounds</td><td·align="center"·valign="top">(required)</td><td·align="left"·valign="top">target·size·given·as·two·coma·separated·values</td></tr></tbody></table></div></div><p·class="plugin">
83 ····</p><p·class="plugin">83 ····</p><p·class="plugin">
84 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginload3dimagefilter"></a>load</h5></div></div></div><p·class="plugindescr">Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">name·of·the·input·file·to·load·from..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">84 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginload3dimagefilter"></a>load</h5></div></div></div><p·class="plugindescr">Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">name·of·the·input·file·to·load·from..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
85 ····</p><p·class="plugin">85 ····</p><p·class="plugin">
86 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlvdownscale3dimagefilter"></a>lvdownscale</h5></div></div></div><p·class="plugindescr">This·is·a·label·voting·downscale·filter.·It·adownscales·a·3D·image·by·blocks.·For·each·block·the·(non-zero)·label·that·appears·most·times·in·the·block·is·issued·as·output·pixel·in·the·target·image.·If·two·labels·appear·the·same·number·of·times,·the·one·with·the·lower·absolute·value·wins..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">b</td><td·align="center"·valign="top">3dbounds</td><td·align="center"·valign="top">[[1,1,1]]</td><td·align="left"·valign="top">blocksize·for·the·downscaling.·Each·block·will·be·represented·by·one·pixel·in·the·target·image.</td></tr></tbody></table></div></div><p·class="plugin">86 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginlvdownscale3dimagefilter"></a>lvdownscale</h5></div></div></div><p·class="plugindescr">This·is·a·label·voting·downscale·filter.·It·adownscales·a·3D·image·by·blocks.·For·each·block·the·(non-zero)·label·that·appears·most·times·in·the·block·is·issued·as·output·pixel·in·the·target·image.·If·two·labels·appear·the·same·number·of·times,·the·one·with·the·lower·absolute·value·wins..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">b</td><td·align="center"·valign="top">3dbounds</td><td·align="center"·valign="top">[[1,1,1]]</td><td·align="left"·valign="top">blocksize·for·the·downscaling.·Each·block·will·be·represented·by·one·pixel·in·the·target·image.</td></tr></tbody></table></div></div><p·class="plugin">
87 ····</p><p·class="plugin">87 ····</p><p·class="plugin">
88 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmask3dimagefilter"></a>mask</h5></div></div></div><p·class="plugindescr">Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">input</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">second·input·image·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">88 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmask3dimagefilter"></a>mask</h5></div></div></div><p·class="plugindescr">Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">input</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">second·input·image·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
89 ····</p><p·class="plugin">89 ····</p><p·class="plugin">
90 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmean3dimagefilter"></a>mean</h5></div></div></div><p·class="plugindescr">3D·image·mean·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">90 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmean3dimagefilter"></a>mean</h5></div></div></div><p·class="plugindescr">3D·image·mean·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">
91 ····</p><p·class="plugin">91 ····</p><p·class="plugin">
92 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmedian3dimagefilter"></a>median</h5></div></div></div><p·class="plugindescr">median·3d·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">92 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmedian3dimagefilter"></a>median</h5></div></div></div><p·class="plugindescr">median·3d·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
93 ····</p><p·class="plugin">93 ····</p><p·class="plugin">
94 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmlv3dimagefilter"></a>mlv</h5></div></div></div><p·class="plugindescr">Mean·of·Least·Variance·3D·image·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">94 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginmlv3dimagefilter"></a>mlv</h5></div></div></div><p·class="plugindescr">Mean·of·Least·Variance·3D·image·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">filter·width·parameter</td></tr></tbody></table></div></div><p·class="plugin">
95 ····</p><p·class="plugin">95 ····</p><p·class="plugin">
Offset 109, 21 lines modifiedOffset 109, 21 lines modified
109 ····</p><p·class="plugin">109 ····</p><p·class="plugin">
110 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginselectbig3dimagefilter"></a>selectbig</h5></div></div></div><p·class="plugindescr">A·filter·that·creats·a·binary·mask·representing·the·intensity·with·the·highest·pixel·count.The·pixel·value·0·will·be·ignored,·and·if·two·intensities·have·the·same·pixel·count,·then·the·result·is·undefined.·The·input·pixel·must·have·an·integral·pixel·type..·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">110 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginselectbig3dimagefilter"></a>selectbig</h5></div></div></div><p·class="plugindescr">A·filter·that·creats·a·binary·mask·representing·the·intensity·with·the·highest·pixel·count.The·pixel·value·0·will·be·ignored,·and·if·two·intensities·have·the·same·pixel·count,·then·the·result·is·undefined.·The·input·pixel·must·have·an·integral·pixel·type..·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
111 ····</p><p·class="plugin">111 ····</p><p·class="plugin">
112 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsepconv3dimagefilter"></a>sepconv</h5></div></div></div><p·class="plugindescr">3D·image·intensity·separaple·convolution·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">kx</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:w=1]</td><td·align="left"·valign="top">filter·kernel·in·x-direction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dspacialkernel.html"·title="Plugin·type:·1d/spacialkernel">Plugin·type:·1d/spacialkernel</a></td></tr><tr><td·align="center"·valign="top">ky</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:w=1]</td><td·align="left"·valign="top">filter·kernel·in·y-direction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dspacialkernel.html"·title="Plugin·type:·1d/spacialkernel">Plugin·type:·1d/spacialkernel</a></td></tr><tr><td·align="center"·valign="top">kz</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:w=1]</td><td·align="left"·valign="top">filter·kernel·in·z-direction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dspacialkernel.html"·title="Plugin·type:·1d/spacialkernel">Plugin·type:·1d/spacialkernel</a></td></tr></tbody></table></div></div><p·class="plugin">112 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsepconv3dimagefilter"></a>sepconv</h5></div></div></div><p·class="plugindescr">3D·image·intensity·separaple·convolution·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">kx</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:w=1]</td><td·align="left"·valign="top">filter·kernel·in·x-direction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dspacialkernel.html"·title="Plugin·type:·1d/spacialkernel">Plugin·type:·1d/spacialkernel</a></td></tr><tr><td·align="center"·valign="top">ky</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:w=1]</td><td·align="left"·valign="top">filter·kernel·in·y-direction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dspacialkernel.html"·title="Plugin·type:·1d/spacialkernel">Plugin·type:·1d/spacialkernel</a></td></tr><tr><td·align="center"·valign="top">kz</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[gauss:w=1]</td><td·align="left"·valign="top">filter·kernel·in·z-direction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dspacialkernel.html"·title="Plugin·type:·1d/spacialkernel">Plugin·type:·1d/spacialkernel</a></td></tr></tbody></table></div></div><p·class="plugin">
113 ····</p><p·class="plugin">113 ····</p><p·class="plugin">
114 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsobel3dimagefilter"></a>sobel</h5></div></div></div><p·class="plugindescr">The·2D·Sobel·filter·for·gradient·evaluation.·Note·that·the·output·pixel·type·of·the·filtered·image·is·the·same·as·the·input·pixel·type,·so·converting·the·input·beforehand·to·a·floating·point·valued·image·is·recommendable..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">dir</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">x</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">Gradient·direction</td></tr><tr><td·align="left"·valign="top">x:</td><td·align="left"·valign="top">gradient·in·x-direction·</td></tr><tr><td·align="left"·valign="top">y:</td><td·align="left"·valign="top">gradient·in·y-direction·</td></tr><tr><td·align="left"·valign="top">z:</td><td·align="left"·valign="top">gradient·in·z-direction·</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">114 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsobel3dimagefilter"></a>sobel</h5></div></div></div><p·class="plugindescr">The·2D·Sobel·filter·for·gradient·evaluation.·Note·that·the·output·pixel·type·of·the·filtered·image·is·the·same·as·the·input·pixel·type,·so·converting·the·input·beforehand·to·a·floating·point·valued·image·is·recommendable..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">dir</td><td·align="center"·valign="top">dict</td><td·align="center"·valign="top">x</td><td><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·class="sc0"><col·class="sc1"></colgroup><tbody><tr><td·colspan="2"·align="left"·valign="top">Gradient·direction</td></tr><tr><td·align="left"·valign="top">x:</td><td·align="left"·valign="top">gradient·in·x-direction·</td></tr><tr><td·align="left"·valign="top">y:</td><td·align="left"·valign="top">gradient·in·y-direction·</td></tr><tr><td·align="left"·valign="top">z:</td><td·align="left"·valign="top">gradient·in·z-direction·</td></tr></tbody></table></div></td></tr></tbody></table></div></div><p·class="plugin">
115 ····</p><p·class="plugin">115 ····</p><p·class="plugin">
116 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsws3dimagefilter"></a>sws</h5></div></div></div><p·class="plugindescr">seeded·watershead.·The·algorithm·extracts·exactly·so·many·reagions·as·initial·labels·are·given·in·the·seed·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">grad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Interpret·the·input·image·as·gradient.·</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">seed·input·image·containing·the·lables·for·the·initial·regions</td></tr></tbody></table></div></div><p·class="plugin">116 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginsws3dimagefilter"></a>sws</h5></div></div></div><p·class="plugindescr">seeded·watershead.·The·algorithm·extracts·exactly·so·many·reagions·as·initial·labels·are·given·in·the·seed·image..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">grad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Interpret·the·input·image·as·gradient.·</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr><tr><td·align="center"·valign="top">seed</td><td·align="center"·valign="top">string</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">seed·input·image·containing·the·lables·for·the·initial·regions</td></tr></tbody></table></div></div><p·class="plugin">
117 ····</p><p·class="plugin">117 ····</p><p·class="plugin">
118 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintee3dimagefilter"></a>tee</h5></div></div></div><p·class="plugindescr">Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,output)</td><td·align="left"·valign="top">name·of·the·output·file·to·save·the·image·too..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">118 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintee3dimagefilter"></a>tee</h5></div></div></div><p·class="plugindescr">Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,output)</td><td·align="left"·valign="top">name·of·the·output·file·to·save·the·image·too..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></td></tr></tbody></table></div></div><p·class="plugin">
119 ····</p><p·class="plugin">119 ····</p><p·class="plugin">
120 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginthinning3dimagefilter"></a>thinning</h5></div></div></div><p·class="plugindescr">3D·morphological·thinning,··based·on:·Lee·and·Kashyap,·'Building·Skeleton·Models·via·3-D·Medial·Surface/Axis·Thinning·Algorithms',·Graphical·Models·and·Image·Processing,·56(6):462-478,·1994.·This·implementation·only·supports·the·26·neighbourhood..·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">120 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginthinning3dimagefilter"></a>thinning</h5></div></div></div><p·class="plugindescr">3D·morphological·thinning,··based·on:·Lee·and·Kashyap,·'Building·Skeleton·Models·via·3-D·Medial·Surface/Axis·Thinning·Algorithms',·Graphical·Models·and·Image·Processing,·56(6):462-478,·1994.·This·implementation·only·supports·the·26·neighbourhood..·(This·plug-in·doesn't·take·parameters)</p></div><p·class="plugin">
121 ····</p><p·class="plugin">121 ····</p><p·class="plugin">
122 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintransform3dimagefilter"></a>transform</h5></div></div></div><p·class="plugindescr">Transform·the·input·image·with·the·given·transformation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(input,required)</td><td·align="left"·valign="top">Name·of·the·file·containing·the·transformation..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></td></tr><tr><td·align="center"·valign="top">imgboundary</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top"> </td><td·align="left"·valign="top">override·image·interpolation·boundary·conditions.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinebc.html"·title="Plugin·type:·1d/splinebc">Plugin·type:·1d/splinebc</a></td></tr><tr><td·align="center"·valign="top">imgkernel</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top"> </td><td·align="left"·valign="top">override·image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></td></tr></tbody></table></div></div><p·class="plugin">122 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="plugintransform3dimagefilter"></a>transform</h5></div></div></div><p·class="plugindescr">Transform·the·input·image·with·the·given·transformation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">file</td><td·align="center"·valign="top">io</td><td·align="center"·valign="top">(required,input)</td><td·align="left"·valign="top">Name·of·the·file·containing·the·transformation..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></td></tr><tr><td·align="center"·valign="top">imgboundary</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top"> </td><td·align="left"·valign="top">override·image·interpolation·boundary·conditions.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinebc.html"·title="Plugin·type:·1d/splinebc">Plugin·type:·1d/splinebc</a></td></tr><tr><td·align="center"·valign="top">imgkernel</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top"> </td><td·align="left"·valign="top">override·image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></td></tr></tbody></table></div></div><p·class="plugin">
123 ····</p><p·class="plugin">123 ····</p><p·class="plugin">
124 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginvariance3dimagefilter"></a>variance</h5></div></div></div><p·class="plugindescr">3D·image·variance·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">124 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginvariance3dimagefilter"></a>variance</h5></div></div></div><p·class="plugindescr">3D·image·variance·filter.·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">w</td><td·align="center"·valign="top">int·in·[1,·inf)</td><td·align="center"·valign="top">1</td><td·align="left"·valign="top">half·filter·width</td></tr></tbody></table></div></div><p·class="plugin">
125 ····</p><p·class="plugin">125 ····</p><p·class="plugin">
126 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginws3dimagefilter"></a>ws</h5></div></div></div><p·class="plugindescr">basic·watershead·segmentation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">evalgrad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Set·to·1·if·the·input·image·does·not·represent·a·gradient·norm·image</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">float·in·[0,·1)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Relative·gradient·norm·threshold.·The·actual·value·threshold·value·is·thresh·*·(max_grad·-·min_grad)·+·min_grad.·Bassins·separated·by·gradients·with·a·lower·norm·will·be·joined</td></tr></tbody></table></div></div><p·class="plugin">126 ······</p><div·class="sect4"><div·class="titlepage"><div><div><h5·class="title"><a·name="pluginws3dimagefilter"></a>ws</h5></div></div></div><p·class="plugindescr">basic·watershead·segmentation..·Supported·parameters·are:</p><div·class="informaltable"><table·class="informaltable"·width="100%"·border="1"><colgroup><col·width="10%"·class="c1"><col·width="20%"·class="c2"><col·width="10%"·class="c3"></colgroup><thead><tr><th·align="center"·valign="top">Name</th><th·align="center"·valign="top">Type</th><th·align="center"·valign="top">Default</th><th·align="center"·valign="top">Description</th></tr></thead><tbody><tr><td·align="center"·valign="top">evalgrad</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Set·to·1·if·the·input·image·does·not·represent·a·gradient·norm·image</td></tr><tr><td·align="center"·valign="top">mark</td><td·align="center"·valign="top">bool</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Mark·the·segmented·watersheds·with·a·special·gray·scale·value</td></tr><tr><td·align="center"·valign="top">n</td><td·align="center"·valign="top">factory</td><td·align="center"·valign="top">[sphere:r=1]</td><td·align="left"·valign="top">Neighborhood·for·watershead·region·growing.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></td></tr><tr><td·align="center"·valign="top">thresh</td><td·align="center"·valign="top">float·in·[0,·1)</td><td·align="center"·valign="top">0</td><td·align="left"·valign="top">Relative·gradient·norm·threshold.·The·actual·value·threshold·value·is·thresh·*·(max_grad·-·min_grad)·+·min_grad.·Bassins·separated·by·gradients·with·a·lower·norm·will·be·joined</td></tr></tbody></table></div></div><p·class="plugin">
127 ····</p><h4><a·name="idp20158"></a>Plugin·consumers:</h4><p·class="consumer">127 ····</p><h4><a·name="idp20158"></a>Plugin·consumers:</h4><p·class="consumer">
128 ······<a·class="xref"·href="Secmia3dcost.html"·title="mia-3dcost">mia-3dcost</a>128 ······<a·class="xref"·href="Secmia3dcost.html"·title="mia-3dcost">mia-3dcost</a>
129 ······<a·class="xref"·href="Secmia3dimagefilter.html"·title="mia-3dimagefilter">mia-3dimagefilter</a>129 ······<a·class="xref"·href="Secmia3dimagefilter.html"·title="mia-3dimagefilter">mia-3dimagefilter</a>
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Offset 36, 15 lines modifiedOffset 36, 15 lines modified
36 combiner36 combiner
37 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to37 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to
38 false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and38 false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and
39 the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the39 the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the
40 moment·the·filter·is·run..·Supported·parameters·are:40 moment·the·filter·is·run..·Supported·parameters·are:
41 ·_____________________________________________________________________________41 ·_____________________________________________________________________________
42 |__Name_|__Type_|______Default___|________________________Description_________|42 |__Name_|__Type_|______Default___|________________________Description_________|
43 |·image·|···io··|(input,required)|second·image·that·is·needed·in·the·combiner.|43 |·image·|···io··|(required,input)|second·image·that·is·needed·in·the·combiner.|
44 |·······|·······|················|For·supported·file·types·see·Plugin_type:···|44 |·······|·······|················|For·supported·file·types·see·Plugin_type:···|
45 |_______|_______|________________|3dimage/io__________________________________|45 |_______|_______|________________|3dimage/io__________________________________|
46 |···op··|factory|····(required)··|Image·combiner·to·be·applied·to·the·images.·|46 |···op··|factory|····(required)··|Image·combiner·to·be·applied·to·the·images.·|
47 |·······|·······|················|For·supported·plug-ins·see·Plugin_type:·····|47 |·······|·······|················|For·supported·plug-ins·see·Plugin_type:·····|
48 |_______|_______|________________|3dimage/combiner____________________________|48 |_______|_______|________________|3dimage/combiner____________________________|
49 |reverse|··bool·|···········0····|reverse·the·order·in·which·the·images·passed|49 |reverse|··bool·|···········0····|reverse·the·order·in·which·the·images·passed|
50 |_______|_______|________________|to_the_combiner_____________________________|50 |_______|_______|________________|to_the_combiner_____________________________|
Offset 132, 15 lines modifiedOffset 132, 15 lines modified
132 growmask132 growmask
133 Use·an·input·binary·mask·and·a·reference·gray·scale·image·to·do·region·growing133 Use·an·input·binary·mask·and·a·reference·gray·scale·image·to·do·region·growing
134 by·adding·the·neighborhood·pixels·of·an·already·added·pixel·if·the·have·a·lower134 by·adding·the·neighborhood·pixels·of·an·already·added·pixel·if·the·have·a·lower
135 intensity·that·is·above·the·given·threshold..·Supported·parameters·are:135 intensity·that·is·above·the·given·threshold..·Supported·parameters·are:
136 ·_____________________________________________________________________________136 ·_____________________________________________________________________________
137 |Name_|__Type_|______Default___|__________________________Description_________|137 |Name_|__Type_|______Default___|__________________________Description_________|
138 |_min_|_float_|___________1____|lower_threshold_for_mask_growing______________|138 |_min_|_float_|___________1____|lower_threshold_for_mask_growing______________|
139 |·ref·|···io··|(input,required)|reference·image·for·mask·region·growing.·For··|139 |·ref·|···io··|(required,input)|reference·image·for·mask·region·growing.·For··|
140 |·····|·······|················|supported·file·types·see·Plugin_type:_3dimage/|140 |·····|·······|················|supported·file·types·see·Plugin_type:_3dimage/|
141 |_____|_______|________________|io____________________________________________|141 |_____|_______|________________|io____________________________________________|
142 |shape|factory|··········6n····|neighborhood·mask.·For·supported·plug-ins·see·|142 |shape|factory|··········6n····|neighborhood·mask.·For·supported·plug-ins·see·|
143 |_____|_______|________________|Plugin_type:_3dimage/shape____________________|143 |_____|_______|________________|Plugin_type:_3dimage/shape____________________|
144 invert144 invert
145 intensity·invert·filter.·(This·plug-in·doesn't·take·parameters)145 intensity·invert·filter.·(This·plug-in·doesn't·take·parameters)
146 isovoxel146 isovoxel
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167 |··n·|factory|···6n··|neighborhood·mask.·For·supported·plug-ins·see·Plugin|167 |··n·|factory|···6n··|neighborhood·mask.·For·supported·plug-ins·see·Plugin|
168 |____|_______|_______|type:_3dimage/shape_________________________________|168 |____|_______|_______|type:_3dimage/shape_________________________________|
169 labelmap169 labelmap
170 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued170 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued
171 intensities/labels..·Supported·parameters·are:171 intensities/labels..·Supported·parameters·are:
172 ·_______________________________________________172 ·_______________________________________________
173 |Name|_Type_|______Default___|_____Description__|173 |Name|_Type_|______Default___|_____Description__|
174 |map_|string|(input,required)|Label_mapping_file|174 |map_|string|(required,input)|Label_mapping_file|
175 labelscale175 labelscale
176 A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input176 A·filter·that·only·creates·output·voxels·that·are·already·created·in·the·input
177 image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target177 image.·Scaling·is·done·by·using·a·voting·algorithms·that·selects·the·target
178 pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the178 pixel·value·based·on·the·highest·pixel·count·of·a·certain·label·in·the
179 corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same179 corresponding·source·region.·If·the·region·comprises·two·labels·with·the·same
180 count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:180 count,·the·one·with·the·lower·number·wins..·Supported·parameters·are:
181 ·___________________________________________________________________________181 ·___________________________________________________________________________
182 |___Name_|___Type_|__Default_|__________________________Description_________|182 |___Name_|___Type_|__Default_|__________________________Description_________|
183 |out-size|3dbounds|(required)|target_size_given_as_two_coma_separated_values|183 |out-size|3dbounds|(required)|target_size_given_as_two_coma_separated_values|
184 load184 load
185 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the185 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the
186 pipeline..·Supported·parameters·are:186 pipeline..·Supported·parameters·are:
187 ·___________________________________________________________________________187 ·___________________________________________________________________________
188 |Name|Type|______Default___|___________________________Description__________|188 |Name|Type|______Default___|___________________________Description__________|
189 |file|·io·|(input,required)|name·of·the·input·file·to·load·from..·For·······|189 |file|·io·|(required,input)|name·of·the·input·file·to·load·from..·For·······|
190 |____|____|________________|supported_file_types_see_Plugin_type:_3dimage/io|190 |____|____|________________|supported_file_types_see_Plugin_type:_3dimage/io|
191 lvdownscale191 lvdownscale
192 This·is·a·label·voting·downscale·filter.·It·adownscales·a·3D·image·by·blocks.192 This·is·a·label·voting·downscale·filter.·It·adownscales·a·3D·image·by·blocks.
193 For·each·block·the·(non-zero)·label·that·appears·most·times·in·the·block·is193 For·each·block·the·(non-zero)·label·that·appears·most·times·in·the·block·is
194 issued·as·output·pixel·in·the·target·image.·If·two·labels·appear·the·same194 issued·as·output·pixel·in·the·target·image.·If·two·labels·appear·the·same
195 number·of·times,·the·one·with·the·lower·absolute·value·wins..·Supported195 number·of·times,·the·one·with·the·lower·absolute·value·wins..·Supported
196 parameters·are:196 parameters·are:
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202 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from202 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from
203 the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one203 the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one
204 must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline204 must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline
205 are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not205 are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not
206 binary..·Supported·parameters·are:206 binary..·Supported·parameters·are:
207 ·____________________________________________________________________________207 ·____________________________________________________________________________
208 |Name_|Type|______Default___|___________________________Description__________|208 |Name_|Type|______Default___|___________________________Description__________|
209 |input|·io·|(input,required)|second·input·image·file·name.·For·supported·file|209 |input|·io·|(required,input)|second·input·image·file·name.·For·supported·file|
210 |_____|____|________________|types_see_Plugin_type:_3dimage/io_______________|210 |_____|____|________________|types_see_Plugin_type:_3dimage/io_______________|
211 mean211 mean
212 3D·image·mean·filter.·Supported·parameters·are:212 3D·image·mean·filter.·Supported·parameters·are:
213 ·______________________________________________213 ·______________________________________________
214 |Name|________Type___|Default|____Description__|214 |Name|________Type___|Default|____Description__|
215 |__w_|int_in_[1,_inf)|____1__|half_filter_width|215 |__w_|int_in_[1,_inf)|____1__|half_filter_width|
216 median216 median
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330 |Name|__Type_|______Default___|___________________________Description_________|330 |Name|__Type_|______Default___|___________________________Description_________|
331 |grad|__bool_|___________0____|Interpret_the_input_image_as_gradient._________|331 |grad|__bool_|___________0____|Interpret_the_input_image_as_gradient._________|
332 |mark|··bool·|···········0····|Mark·the·segmented·watersheds·with·a·special···|332 |mark|··bool·|···········0····|Mark·the·segmented·watersheds·with·a·special···|
333 |____|_______|________________|gray_scale_value_______________________________|333 |____|_______|________________|gray_scale_value_______________________________|
334 |··n·|factory|···[sphere:r=1]·|Neighborhood·for·watershead·region·growing.·For|334 |··n·|factory|···[sphere:r=1]·|Neighborhood·for·watershead·region·growing.·For|
335 |····|·······|················|supported·plug-ins·see·Plugin_type:_3dimage/···|335 |····|·······|················|supported·plug-ins·see·Plugin_type:_3dimage/···|
336 |____|_______|________________|shape__________________________________________|336 |____|_______|________________|shape__________________________________________|
337 |seed|string·|(input,required)|seed·input·image·containing·the·lables·for·the·|337 |seed|string·|(required,input)|seed·input·image·containing·the·lables·for·the·|
338 |____|_______|________________|initial_regions________________________________|338 |____|_______|________________|initial_regions________________________________|
339 tee339 tee
340 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.340 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter.
341 Supported·parameters·are:341 Supported·parameters·are:
342 ·___________________________________________________________________________342 ·___________________________________________________________________________
343 |Name|Type|_______Default___|___________________________Description_________|343 |Name|Type|_______Default___|___________________________Description_________|
344 |file|·io·|(required,output)|name·of·the·output·file·to·save·the·image·too..|344 |file|·io·|(required,output)|name·of·the·output·file·to·save·the·image·too..|
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350 Processing,·56(6):462-478,·1994.·This·implementation·only·supports·the·26350 Processing,·56(6):462-478,·1994.·This·implementation·only·supports·the·26
351 neighbourhood..·(This·plug-in·doesn't·take·parameters)351 neighbourhood..·(This·plug-in·doesn't·take·parameters)
352 transform352 transform
353 Transform·the·input·image·with·the·given·transformation..·Supported·parameters353 Transform·the·input·image·with·the·given·transformation..·Supported·parameters
354 are:354 are:
355 ·____________________________________________________________________________355 ·____________________________________________________________________________
356 |_____Name__|__Type_|______Default___|_____________________Description_______|356 |_____Name__|__Type_|______Default___|_____________________Description_______|
357 |·····file··|···io··|(input,required)|Name·of·the·file·containing·the········|357 |·····file··|···io··|(required,input)|Name·of·the·file·containing·the········|
358 |···········|·······|················|transformation..·For·supported·file····|358 |···········|·······|················|transformation..·For·supported·file····|
359 |___________|_______|________________|types_see_Plugin_type:_3dtransform/io__|359 |___________|_______|________________|types_see_Plugin_type:_3dtransform/io__|
360 |imgboundary|factory|·········· ····|override·image·interpolation·boundary··|360 |imgboundary|factory|·········· ····|override·image·interpolation·boundary··|
361 |···········|·······|················|conditions.·For·supported·plug-ins·see·|361 |···········|·······|················|conditions.·For·supported·plug-ins·see·|
362 |___________|_______|________________|Plugin_type:_1d/splinebc_______________|362 |___________|_______|________________|Plugin_type:_1d/splinebc_______________|
363 |·imgkernel·|factory|·········· ····|override·image·interpolator·kernel.·For|363 |·imgkernel·|factory|·········· ····|override·image·interpolator·kernel.·For|
364 |···········|·······|················|supported·plug-ins·see·Plugin_type:_1d/|364 |···········|·······|················|supported·plug-ins·see·Plugin_type:_1d/|
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2davgmasked</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="next"·href="Secmia2dbinarycombine.html"·title="mia-2dbinarycombine"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2davgmasked</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dbinarycombine.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2davgmasked"></a>mia-2davgmasked</h3></div></div></div><h4><a·name="idp982"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2davgmasked</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-m·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2davgmasked</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="next"·href="Secmia2dbinarycombine.html"·title="mia-2dbinarycombine"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2davgmasked</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dbinarycombine.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2davgmasked"></a>mia-2davgmasked</h3></div></div></div><h4><a·name="idp982"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2davgmasked</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-m·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp991"></a>Description:</h4><p·class="description">Evaluate·average·intensities·of·an·image·seriesThis·program·is·used·to·evaluate·the·average·intensity·and·its·variation·of·a·series·of·images·in·a·given·masked·region.</p><h4><a·name="idp993"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-files=(input,·required);·io</span></dt><dd><p>input·image(s).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-m,·--mask-file=(input,·requir[·...·truncated·by·diffoscope;·len:·2,·SHA:·9c1623f0d38e28e9594f2ef31a7ec909291c4fdb05a777dccd2e936a7f406011·...·]);·io</span></dt><dd><p>mask·image,·must·be·of·type·byte.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1005"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1056"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1062"></a>Example:</h4><p>3 ········...]</p></div><h4><a·name="idp991"></a>Description:</h4><p·class="description">Evaluate·average·intensities·of·an·image·seriesThis·program·is·used·to·evaluate·the·average·intensity·and·its·variation·of·a·series·of·images·in·a·given·masked·region.</p><h4><a·name="idp993"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-files=(required,·input);·io</span></dt><dd><p>input·image(s).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-m,·--mask-file=(required,·inp[·...·truncated·by·diffoscope;·len:·2,·SHA:·469cc643a19fb75901e5d331b8dc14befa8b98810b246c2fb22fff0c382dc39e·...·]);·io</span></dt><dd><p>mask·image,·must·be·of·type·byte.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1005"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1056"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1062"></a>Example:</h4><p>
4 ····</p><pre·class="screen">mia-2davgmasked·</pre><h4><a·name="idp1065"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dbinarycombine.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Analysis,·filtering,·combining,·and·segmentation·of·2D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dbinarycombine</td></tr></table></div></body></html>4 ····</p><pre·class="screen">mia-2davgmasked·</pre><h4><a·name="idp1065"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dbinarycombine.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Analysis,·filtering,·combining,·and·segmentation·of·2D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dbinarycombine</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-2davgmasked·{-i·io}·{-m·io}·[·options·...]6 mia-2davgmasked·{-i·io}·{-m·io}·[·options·...]
7 Description:7 Description:
8 Evaluate·average·intensities·of·an·image·seriesThis·program·is·used·to·evaluate8 Evaluate·average·intensities·of·an·image·seriesThis·program·is·used·to·evaluate
9 the·average·intensity·and·its·variation·of·a·series·of·images·in·a·given·masked9 the·average·intensity·and·its·variation·of·a·series·of·images·in·a·given·masked
10 region.10 region.
11 Options:11 Options:
12 ··-i,·--in-files=(input,·required);·io12 ··-i,·--in-files=(required,·input);·io
13 ······input·image(s).·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······input·image(s).·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-m,·--mask-file=(input,·required);·io14 ··-m,·--mask-file=(required,·input);·io
15 ······mask·image,·must·be·of·type·byte.·For·supported·file·types·see·Plugin15 ······mask·image,·must·be·of·type·byte.·For·supported·file·types·see·Plugin
16 ······type:_2dimage/io16 ······type:_2dimage/io
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
20 ······Supported·priorities·starting·at·lowest·level·are:20 ······Supported·priorities·starting·at·lowest·level·are:
21 ······trace:···Function·call·trace21 ······trace:···Function·call·trace
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dbinarycombine</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2davgmasked.html"·title="mia-2davgmasked"><link·rel="next"·href="Secmia2ddistance.html"·title="mia-2ddistance"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dbinarycombine</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2davgmasked.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2ddistance.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dbinarycombine"></a>mia-2dbinarycombine</h3></div></div></div><h4><a·name="idp1069"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dbinarycombine</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dbinarycombine</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2davgmasked.html"·title="mia-2davgmasked"><link·rel="next"·href="Secmia2ddistance.html"·title="mia-2ddistance"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dbinarycombine</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2davgmasked.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2ddistance.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dbinarycombine"></a>mia-2dbinarycombine</h3></div></div></div><h4><a·name="idp1069"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dbinarycombine</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp1080"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.</p><h4><a·name="idp1082"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--file1=(input,·required);·io</span></dt><dd><p>input·mask·image·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--file2=(input,·requir[·...·truncated·by·diffoscope;·len:·2,·SHA:·9c1623f0d38e28e9594f2ef31a7ec909291c4fdb05a777dccd2e936a7f406011·...·]);·io</span></dt><dd><p>input·mask·image·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mask·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--operation=nor;·dict</span></dt><dd><p>Operation·to·be·applied</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">or:</td><td·align="left"·valign="top">logocal·or</td></tr><tr><td·align="left"·valign="top">nor:</td><td·align="left"·valign="top">logocal·nor</td></tr><tr><td·align="left"·valign="top">and:</td><td·align="left"·valign="top">logocal·and</td></tr><tr><td·align="left"·valign="top">nand:</td><td·align="left"·valign="top">logocal·nand</td></tr><tr><td·align="left"·valign="top">xor:</td><td·align="left"·valign="top">logocal·xor</td></tr><tr><td·align="left"·valign="top">nxor:</td><td·align="left"·valign="top">logocal·nxor</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp1126"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1177"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1183"></a>Example:</h4><p>Combine·the·binary·images·b1.png·and·b2.png·by·using·the·'nor'·operation·and·store·the·result·in·b1nor2.png.</p><pre·class="screen">mia-2dbinarycombine·-1·b1.png·-2·b2.png·-p·nor·-o·b1nor2.png</pre><h4><a·name="idp1186"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2davgmasked.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2ddistance.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2davgmasked </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2ddistance</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp1080"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.</p><h4><a·name="idp1082"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--file1=(required,·input);·io</span></dt><dd><p>input·mask·image·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--file2=(required,·inp[·...·truncated·by·diffoscope;·len:·2,·SHA:·469cc643a19fb75901e5d331b8dc14befa8b98810b246c2fb22fff0c382dc39e·...·]);·io</span></dt><dd><p>input·mask·image·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mask·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--operation=nor;·dict</span></dt><dd><p>Operation·to·be·applied</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">or:</td><td·align="left"·valign="top">logocal·or</td></tr><tr><td·align="left"·valign="top">nor:</td><td·align="left"·valign="top">logocal·nor</td></tr><tr><td·align="left"·valign="top">and:</td><td·align="left"·valign="top">logocal·and</td></tr><tr><td·align="left"·valign="top">nand:</td><td·align="left"·valign="top">logocal·nand</td></tr><tr><td·align="left"·valign="top">xor:</td><td·align="left"·valign="top">logocal·xor</td></tr><tr><td·align="left"·valign="top">nxor:</td><td·align="left"·valign="top">logocal·nxor</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp1126"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1177"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1183"></a>Example:</h4><p>Combine·the·binary·images·b1.png·and·b2.png·by·using·the·'nor'·operation·and·store·the·result·in·b1nor2.png.</p><pre·class="screen">mia-2dbinarycombine·-1·b1.png·-2·b2.png·-p·nor·-o·b1nor2.png</pre><h4><a·name="idp1186"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2davgmasked.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2ddistance.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2davgmasked </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2ddistance</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dbinarycombine4 mia-2dbinarycombine
5 Sysnopis:5 Sysnopis:
6 mia-2dbinarycombine·{-1·io}·{-2·io}·{-o·io}·[·options·...]6 mia-2dbinarycombine·{-1·io}·{-2·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.8 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.
9 Options:9 Options:
10 ··-1,·--file1=(input,·required);·io10 ··-1,·--file1=(required,·input);·io
11 ······input·mask·image·1.·For·supported·file·types·see·Plugin_type:_2dimage/io11 ······input·mask·image·1.·For·supported·file·types·see·Plugin_type:_2dimage/io
12 ··-2,·--file2=(input,·required);·io12 ··-2,·--file2=(required,·input);·io
13 ······input·mask·image·2.·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······input·mask·image·2.·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·mask·image.·For·supported·file·types·see·Plugin_type:_2dimage/io15 ······output·mask·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
16 ··-p,·--operation=nor;·dict16 ··-p,·--operation=nor;·dict
17 ······Operation·to·be·applied17 ······Operation·to·be·applied
18 ······or:···logocal·or18 ······or:···logocal·or
19 ······nor:··logocal·nor19 ······nor:··logocal·nor
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2ddeform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dcost.html"·title="mia-2dcost"><link·rel="next"·href="Secmia2dfluid.html"·title="mia-2dfluid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2ddeform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dcost.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dfluid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2ddeform"></a>mia-2ddeform</h3></div></div></div><h4><a·name="idp3141"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2ddeform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2ddeform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dcost.html"·title="mia-2dcost"><link·rel="next"·href="Secmia2dfluid.html"·title="mia-2dfluid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2ddeform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dcost.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dfluid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2ddeform"></a>mia-2ddeform</h3></div></div></div><h4><a·name="idp3141"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2ddeform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp3152"></a>Description:</h4><p·class="description">This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.·Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation·formula·is·'x·-&gt;·x·-·v(x)'</p><h4><a·name="idp3154"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output)[·...·truncated·by·diffoscope;·len:·251,·SHA:·3436acba29997d16c8c21c7231ce8330bcbd081c30dbbc6d77036f91549a5262·...·]);·io</span></dt><dd><p>transformation·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dvfio.html"·title="Plugin·type:·2dvf/io">Plugin·type:·2dvf/io</a></p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd></dl></div><h4><a·name="idp3176"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3227"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3233"></a>Example:</h4><p>Deform·image·input.png·by·using·the·transformation·given·in·transform.v·and·store·the·result·in·deformed.png·using·linear·interpolation</p><pre·class="screen">mia-2ddeform·-i·input.png·-t·transform.v·-o·deformed.png·-p·bspline:d=1</pre><h4><a·name="idp3236"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dcost.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dfluid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dcost </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dfluid</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp3152"></a>Description:</h4><p·class="description">This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.·Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation·formula·is·'x·-&gt;·x·-·v(x)'</p><h4><a·name="idp3154"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output)[·...·truncated·by·diffoscope;·len:·251,·SHA:·2dd950b79e268d4c0d8a950f5c06fc061632cf5e5ac3fea13808e39fcfbe2661·...·]);·io</span></dt><dd><p>transformation·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dvfio.html"·title="Plugin·type:·2dvf/io">Plugin·type:·2dvf/io</a></p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd></dl></div><h4><a·name="idp3176"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3227"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3233"></a>Example:</h4><p>Deform·image·input.png·by·using·the·transformation·given·in·transform.v·and·store·the·result·in·deformed.png·using·linear·interpolation</p><pre·class="screen">mia-2ddeform·-i·input.png·-t·transform.v·-o·deformed.png·-p·bspline:d=1</pre><h4><a·name="idp3236"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dcost.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dfluid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dcost </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dfluid</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-2ddeform·{-i·io}·{-o·io}·{-t·io}·[·options·...]6 mia-2ddeform·{-i·io}·{-o·io}·{-t·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.8 This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.
9 Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation9 Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation
10 formula·is·'x·->·x·-·v(x)'10 formula·is·'x·->·x·-·v(x)'
11 Options:11 Options:
12 ··-i,·--in-file=(input,·required);·io12 ··-i,·--in-file=(required,·input);·io
13 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······transformed·image.·For·supported·file·types·see·Plugin_type:_2dimage/io15 ······transformed·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
16 ··-t,·--transformation=(input,·required);·io16 ··-t,·--transformation=(required,·input);·io
17 ······transformation·vector·field.·For·supported·file·types·see·Plugin_type:17 ······transformation·vector·field.·For·supported·file·types·see·Plugin_type:
18 ······2dvf/io18 ······2dvf/io
19 ··-p,·--interpolator=bspline:d=3;·factory19 ··-p,·--interpolator=bspline:d=3;·factory
20 ······image·interpolator·kernel.·For·supported·plug-ins·see·Plugin_type:_1d/20 ······image·interpolator·kernel.·For·supported·plug-ins·see·Plugin_type:_1d/
21 ······splinekernel21 ······splinekernel
22 Help·&·Info22 Help·&·Info
23 ··-V,·--verbose=warning;·dict23 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2ddistance</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dbinarycombine.html"·title="mia-2dbinarycombine"><link·rel="next"·href="Secmia2dfuzzysegment.html"·title="mia-2dfuzzysegment"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2ddistance</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dbinarycombine.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dfuzzysegment.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2ddistance"></a>mia-2ddistance</h3></div></div></div><h4><a·name="idp1190"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2ddistance</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-d·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2ddistance</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dbinarycombine.html"·title="mia-2dbinarycombine"><link·rel="next"·href="Secmia2dfuzzysegment.html"·title="mia-2dfuzzysegment"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2ddistance</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dbinarycombine.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dfuzzysegment.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2ddistance"></a>mia-2ddistance</h3></div></div></div><h4><a·name="idp1190"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2ddistance</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-d·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp1201"></a>Description:</h4><p·class="description">This·program·evaluate·the·average·or·maximum·distance·of·a·mask·given·by·a·binary·image·to·an·image·representing·a·distance·map·and·prints·the·result·to·stdout.·The·distance·map·can·be·obtained·by·running·the·filter·'diatance'·on·a·binary·image.</p><h4><a·name="idp1203"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-d,·--distance-file=(input,·requi[·...·truncated·by·diffoscope;·len:·3,·SHA:·b1f51a511f1da0cd348b8f8598db32e61cb963e5fc69e2b41485bf99590ed75a·...·]);·io</span></dt><dd><p>distance·field·image·(floating·point).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file,·'-':·write·to·stdout</p></dd><dt><span·class="term">-s,·--scale=1;·float</span></dt><dd><p>distance·scaling·factor</p></dd><dt><span·class="term">-m,·--method=avg;·dict</span></dt><dd><p>distance·measuring·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">avg:</td><td·align="left"·valign="top">use·average</td></tr><tr><td·align="left"·valign="top">max:</td><td·align="left"·valign="top">use·maximum</td></tr><tr><td·align="left"·valign="top">raw:</td><td·align="left"·valign="top">collect·raw·values·as·vector</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp1241"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1292"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1298"></a>Example:</h4><p>Evaluate·the·maximum·distance·of·mask·m.v·by·using·the·distance·field·distance.v·and·scale·by·factor·2.0.·The·result·is·written·to·stdout</p><pre·class="screen">mia-2ddistance·-i·m.v·-d·distance.v·-s·2.0·-m·max</pre><h4><a·name="idp1301"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dbinarycombine.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dfuzzysegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dbinarycombine </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dfuzzysegment</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp1201"></a>Description:</h4><p·class="description">This·program·evaluate·the·average·or·maximum·distance·of·a·mask·given·by·a·binary·image·to·an·image·representing·a·distance·map·and·prints·the·result·to·stdout.·The·distance·map·can·be·obtained·by·running·the·filter·'diatance'·on·a·binary·image.</p><h4><a·name="idp1203"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-d,·--distance-file=(required,·in[·...·truncated·by·diffoscope;·len:·3,·SHA:·373cb2c6d4fe2778441d4f0266505b699fa518d002e5793b87f9b48836de3f62·...·]);·io</span></dt><dd><p>distance·field·image·(floating·point).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file,·'-':·write·to·stdout</p></dd><dt><span·class="term">-s,·--scale=1;·float</span></dt><dd><p>distance·scaling·factor</p></dd><dt><span·class="term">-m,·--method=avg;·dict</span></dt><dd><p>distance·measuring·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">avg:</td><td·align="left"·valign="top">use·average</td></tr><tr><td·align="left"·valign="top">max:</td><td·align="left"·valign="top">use·maximum</td></tr><tr><td·align="left"·valign="top">raw:</td><td·align="left"·valign="top">collect·raw·values·as·vector</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp1241"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1292"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1298"></a>Example:</h4><p>Evaluate·the·maximum·distance·of·mask·m.v·by·using·the·distance·field·distance.v·and·scale·by·factor·2.0.·The·result·is·written·to·stdout</p><pre·class="screen">mia-2ddistance·-i·m.v·-d·distance.v·-s·2.0·-m·max</pre><h4><a·name="idp1301"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dbinarycombine.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dfuzzysegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dbinarycombine </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dfuzzysegment</td></tr></table></div></body></html>
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6 mia-2ddistance·{-i·io}·{-d·io}·{-o·string}·[·options·...]6 mia-2ddistance·{-i·io}·{-d·io}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·evaluate·the·average·or·maximum·distance·of·a·mask·given·by·a8 This·program·evaluate·the·average·or·maximum·distance·of·a·mask·given·by·a
9 binary·image·to·an·image·representing·a·distance·map·and·prints·the·result·to9 binary·image·to·an·image·representing·a·distance·map·and·prints·the·result·to
10 stdout.·The·distance·map·can·be·obtained·by·running·the·filter·'diatance'·on·a10 stdout.·The·distance·map·can·be·obtained·by·running·the·filter·'diatance'·on·a
11 binary·image.11 binary·image.
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io14 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
15 ··-d,·--distance-file=(input,·required);·io15 ··-d,·--distance-file=(required,·input);·io
16 ······distance·field·image·(floating·point).·For·supported·file·types·see16 ······distance·field·image·(floating·point).·For·supported·file·types·see
17 ······Plugin_type:_2dimage/io17 ······Plugin_type:_2dimage/io
18 ··-o,·--out-file=(required,·output);·string18 ··-o,·--out-file=(required,·output);·string
19 ······output·file,·'-':·write·to·stdout19 ······output·file,·'-':·write·to·stdout
20 ··-s,·--scale=1;·float20 ··-s,·--scale=1;·float
21 ······distance·scaling·factor21 ······distance·scaling·factor
22 ··-m,·--method=avg;·dict22 ··-m,·--method=avg;·dict
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14 ··style=sparse···#storage·style·(sparse|grid)·14 ··style=sparse···#storage·style·(sparse|grid)·
15 ··repn=float32···#representation·of·values·15 ··repn=float32···#representation·of·values·
16 ··size=1000·1000·#grid·size·of·the·transformation16 ··size=1000·1000·#grid·size·of·the·transformation
17 ··endian=low·····#endianess·of·binary·data·(low|big)·17 ··endian=low·····#endianess·of·binary·data·(low|big)·
18 }18 }
  
19 This·example·header·has·to·be·interpreted·like·follows:·two-dimensional·data,·each·entry·consists·of·7·values·the·values·etry·consists·of·a·2D·vector,·a·scalar,·and·a·2x2·matrix·(saved·in·row-major·format).The·data·records·represent·strain·tensors,·and·only·a·sparse·set·of·points·is·given.·The·values·are·given·as·single·floating·point·(32·bit).·The·original·transformation·field·corresponds·to·images·of·1000x1000·pixels·and·the·binary·data·is·stored·in·low·endian·format.</p><h4><a·name="idp6191"></a>Options:</h4><h4><a·name="idp6192"></a>19 This·example·header·has·to·be·interpreted·like·follows:·two-dimensional·data,·each·entry·consists·of·7·values·the·values·etry·consists·of·a·2D·vector,·a·scalar,·and·a·2x2·matrix·(saved·in·row-major·format).The·data·records·represent·strain·tensors,·and·only·a·sparse·set·of·points·is·given.·The·values·are·given·as·single·floating·point·(32·bit).·The·original·transformation·field·corresponds·to·images·of·1000x1000·pixels·and·the·binary·data·is·stored·in·low·endian·format.</p><h4><a·name="idp6191"></a>Options:</h4><h4><a·name="idp6192"></a>
20 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.</p></dd><dt><span·class="term">-o,[·...·truncated·by·diffoscope;·len:·182,·SHA:·0385e007b62cac577a714c6f9d599d1675684c2211ebeee086b4aad8bdee5711·...·]);·io</span></dt><dd><p>transformation·of·which·the·quantity·will·be·evaluated..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp6207"></a>20 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.</p></dd><dt><span·class="term">-o,[·...·truncated·by·diffoscope;·len:·182,·SHA:·aa136f4cfc01592a4a5178c8f86a57266aade3f2b29e0257de13a29980332aaf·...·]);·io</span></dt><dd><p>transformation·of·which·the·quantity·will·be·evaluated..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp6207"></a>
21 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-q,·--quantity=strain;·dict</span></dt><dd><p>Specify·the·quantity·to·be·evaluated·at·the·given·points</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">derivative:</td><td·align="left"·valign="top">Evaluate·the·transformation·derivative·at·the·given·points</td></tr><tr><td·align="left"·valign="top">strain:</td><td·align="left"·valign="top">Evaluate·the·strain·tensor·at·the·given·points</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp6224"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6275"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6281"></a>Example:</h4><p>Derivative·of·the·transformation·change.v2df·for·each··point·given·in·input.csv·are·evaluated·and·written·to·output.s.</p><pre·class="screen">mia-2deval-transformquantity·-i·input.csv·-o·output.s·--transformation·change.v2df</pre><h4><a·name="idp6284"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecToolsfortheAnalysisof2Dimageseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof2Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dtrackpixelmovement.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Tools·for·the·Analysis·of·2D·image·series </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dtrackpixelmovement</td></tr></table></div></body></html>21 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-q,·--quantity=strain;·dict</span></dt><dd><p>Specify·the·quantity·to·be·evaluated·at·the·given·points</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">derivative:</td><td·align="left"·valign="top">Evaluate·the·transformation·derivative·at·the·given·points</td></tr><tr><td·align="left"·valign="top">strain:</td><td·align="left"·valign="top">Evaluate·the·strain·tensor·at·the·given·points</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp6224"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6275"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6281"></a>Example:</h4><p>Derivative·of·the·transformation·change.v2df·for·each··point·given·in·input.csv·are·evaluated·and·written·to·output.s.</p><pre·class="screen">mia-2deval-transformquantity·-i·input.csv·-o·output.s·--transformation·change.v2df</pre><h4><a·name="idp6284"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecToolsfortheAnalysisof2Dimageseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof2Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dtrackpixelmovement.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Tools·for·the·Analysis·of·2D·image·series </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dtrackpixelmovement</td></tr></table></div></body></html>
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20 of·a·2D·vector,·a·scalar,·and·a·2x2·matrix·(saved·in·row-major·format).The·data20 of·a·2D·vector,·a·scalar,·and·a·2x2·matrix·(saved·in·row-major·format).The·data
21 records·represent·strain·tensors,·and·only·a·sparse·set·of·points·is·given.·The21 records·represent·strain·tensors,·and·only·a·sparse·set·of·points·is·given.·The
22 values·are·given·as·single·floating·point·(32·bit).·The·original·transformation22 values·are·given·as·single·floating·point·(32·bit).·The·original·transformation
23 field·corresponds·to·images·of·1000x1000·pixels·and·the·binary·data·is·stored23 field·corresponds·to·images·of·1000x1000·pixels·and·the·binary·data·is·stored
24 in·low·endian·format.24 in·low·endian·format.
25 Options:25 Options:
26 ·File-IO26 ·File-IO
27 ··-i,·--in-file=(input,·required);·string27 ··-i,·--in-file=(required,·input);·string
28 ······input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the28 ······input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the
29 ······quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid29 ······quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid
30 ······point·of·the·transformation·range.30 ······point·of·the·transformation·range.
31 ··-o,·--out-file=(required,·output);·string31 ··-o,·--out-file=(required,·output);·string
32 ······output·strains·file,·for·a·format·description·see·above.32 ······output·strains·file,·for·a·format·description·see·above.
33 ··-t,·--transformation=(input,·required);·io33 ··-t,·--transformation=(required,·input);·io
34 ······transformation·of·which·the·quantity·will·be·evaluated..·For·supported34 ······transformation·of·which·the·quantity·will·be·evaluated..·For·supported
35 ······file·types·see·Plugin_type:_2dtransform/io35 ······file·types·see·Plugin_type:_2dtransform/io
36 ·Parameters36 ·Parameters
37 ··-q,·--quantity=strain;·dict37 ··-q,·--quantity=strain;·dict
38 ······Specify·the·quantity·to·be·evaluated·at·the·given·points38 ······Specify·the·quantity·to·be·evaluated·at·the·given·points
39 ······derivative:·Evaluate·the·transformation·derivative·at·the·given·points39 ······derivative:·Evaluate·the·transformation·derivative·at·the·given·points
40 ······strain:·····Evaluate·the·strain·tensor·at·the·given·points40 ······strain:·····Evaluate·the·strain·tensor·at·the·given·points
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dfluid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2ddeform.html"·title="mia-2ddeform"><link·rel="next"·href="Secmia2dfluidsynregistration.html"·title="mia-2dfluid-syn-registration"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dfluid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2ddeform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dfluidsynregistration.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dfluid"></a>mia-2dfluid</h3></div></div></div><h4><a·name="idp3240"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dfluid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dfluid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2ddeform.html"·title="mia-2ddeform"><link·rel="next"·href="Secmia2dfluidsynregistration.html"·title="mia-2dfluid-syn-registration"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dfluid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2ddeform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dfluidsynregistration.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dfluid"></a>mia-2dfluid</h3></div></div></div><h4><a·name="idp3240"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dfluid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp3249"></a>Description:</h4><p·class="description">This·program·is·used·for·non-rigid·registration·based·on·fluid·dynamics.·For·reference·see·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/TMI.2002.803113"·target="_top">Wollny,·G.·and·Kruggel,·F.,·'Computational·cost·of·non-rigid·registration·algorithms··based·on·fluid·dynamics',·IEEE·Transactions·on·Medical·Imaging,·11(8),·pp.·946-952,·2002.</a></p><p·class="description">It·uses·SSD·as·the·sole·registration·criterion.</p><h4><a·name="idp3253"></a>Options:</h4><h4><a·name="idp3254"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>input·(test)·image·to·be·registered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref[·...·truncated·by·diffoscope;·len:·23,·SHA:·976994bcd74e031805e41c1c7287b79043e1ca4e26ef54fc05fd886f3057d0c6·...·]);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-transformation=(output);·io</span></dt><dd><p>output·transformation·comprising·the·registration.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dvfio.html"·title="Plugin·type:·2dvf/io">Plugin·type:·2dvf/io</a></p></dd><dt><span·class="term">-d,·--out-image=(output);·io</span></dt><dd><p>output·image·deformed·according·to·the·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp3276"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3327"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3333"></a>Registration·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-m,·--mgstart=16;·uint</span></dt><dd><p>multigrid·start·size</p></dd><dt><span·class="term">-e,·--epsilon=0.001;·float</span></dt><dd><p>optimization·breaking·condition</p></dd><dt><span·class="term">--mu=1;·float</span></dt><dd><p>elasticity·parameter</p></dd><dt><span·class="term">--lambda=1;·float</span></dt><dd><p>elasticity·parameter</p></dd><dt><span·class="term">--elastic</span></dt><dd><p>use·elastic·registration</p></dd></dl></div><h4><a·name="idp3355"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·and·write·the·deformation·vector·field·regfield.v.·Start·registration·at·the·smallest·size·above·16·pixel.</p><pre·class="screen">mia-2dfluid·-i·test.v·-r·ref.v·-o·regfield.v·-s·16</pre><h4><a·name="idp3358"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2ddeform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dfluidsynregistration.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2ddeform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dfluid-syn-registration</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp3249"></a>Description:</h4><p·class="description">This·program·is·used·for·non-rigid·registration·based·on·fluid·dynamics.·For·reference·see·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/TMI.2002.803113"·target="_top">Wollny,·G.·and·Kruggel,·F.,·'Computational·cost·of·non-rigid·registration·algorithms··based·on·fluid·dynamics',·IEEE·Transactions·on·Medical·Imaging,·11(8),·pp.·946-952,·2002.</a></p><p·class="description">It·uses·SSD·as·the·sole·registration·criterion.</p><h4><a·name="idp3253"></a>Options:</h4><h4><a·name="idp3254"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>input·(test)·image·to·be·registered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref[·...·truncated·by·diffoscope;·len:·23,·SHA:·d8cff23466c0688127f76ed31bc7fb8fdfe59d34c3fcf1ecbc5f7daa30f89ec5·...·]);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-transformation=(output);·io</span></dt><dd><p>output·transformation·comprising·the·registration.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dvfio.html"·title="Plugin·type:·2dvf/io">Plugin·type:·2dvf/io</a></p></dd><dt><span·class="term">-d,·--out-image=(output);·io</span></dt><dd><p>output·image·deformed·according·to·the·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp3276"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3327"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3333"></a>Registration·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-m,·--mgstart=16;·uint</span></dt><dd><p>multigrid·start·size</p></dd><dt><span·class="term">-e,·--epsilon=0.001;·float</span></dt><dd><p>optimization·breaking·condition</p></dd><dt><span·class="term">--mu=1;·float</span></dt><dd><p>elasticity·parameter</p></dd><dt><span·class="term">--lambda=1;·float</span></dt><dd><p>elasticity·parameter</p></dd><dt><span·class="term">--elastic</span></dt><dd><p>use·elastic·registration</p></dd></dl></div><h4><a·name="idp3355"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·and·write·the·deformation·vector·field·regfield.v.·Start·registration·at·the·smallest·size·above·16·pixel.</p><pre·class="screen">mia-2dfluid·-i·test.v·-r·ref.v·-o·regfield.v·-s·16</pre><h4><a·name="idp3358"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2ddeform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dfluidsynregistration.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2ddeform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dfluid-syn-registration</td></tr></table></div></body></html>
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9 reference·see9 reference·see
10 Wollny,_G._and_Kruggel,_F.,_'Computational_cost_of_non-rigid_registration10 Wollny,_G._and_Kruggel,_F.,_'Computational_cost_of_non-rigid_registration
11 algorithms_based_on_fluid_dynamics',_IEEE_Transactions_on_Medical_Imaging,_1111 algorithms_based_on_fluid_dynamics',_IEEE_Transactions_on_Medical_Imaging,_11
12 (8),_pp._946-952,_2002.12 (8),_pp._946-952,_2002.
13 It·uses·SSD·as·the·sole·registration·criterion.13 It·uses·SSD·as·the·sole·registration·criterion.
14 Options:14 Options:
15 File-IO15 File-IO
16 ··-i,·--in-image=(input,·required);·io16 ··-i,·--in-image=(required,·input);·io
17 ······input·(test)·image·to·be·registered.·For·supported·file·types·see·Plugin17 ······input·(test)·image·to·be·registered.·For·supported·file·types·see·Plugin
18 ······type:_2dimage/io18 ······type:_2dimage/io
19 ··-r,·--ref-image=(input,·required);·io19 ··-r,·--ref-image=(required,·input);·io
20 ······reference·image.·For·supported·file·types·see·Plugin_type:_2dimage/io20 ······reference·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
21 ··-o,·--out-transformation=(output);·io21 ··-o,·--out-transformation=(output);·io
22 ······output·transformation·comprising·the·registration.·For·supported·file22 ······output·transformation·comprising·the·registration.·For·supported·file
23 ······types·see·Plugin_type:_2dvf/io23 ······types·see·Plugin_type:_2dvf/io
24 ··-d,·--out-image=(output);·io24 ··-d,·--out-image=(output);·io
25 ······output·image·deformed·according·to·the·transformation.·For·supported·file25 ······output·image·deformed·according·to·the·transformation.·For·supported·file
26 ······types·see·Plugin_type:_2dimage/io26 ······types·see·Plugin_type:_2dimage/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dfluid-syn-registration</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dfluid.html"·title="mia-2dfluid"><link·rel="next"·href="Secmia2dforce.html"·title="mia-2dforce"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dfluid-syn-registration</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dfluid.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dforce.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dfluidsynregistration"></a>mia-2dfluid-syn-registration</h3></div></div></div><h4><a·name="idp3362"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dfluid-syn-registration</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-O·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dfluid-syn-registration</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dfluid.html"·title="mia-2dfluid"><link·rel="next"·href="Secmia2dforce.html"·title="mia-2dforce"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dfluid-syn-registration</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dfluid.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dforce.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dfluidsynregistration"></a>mia-2dfluid-syn-registration</h3></div></div></div><h4><a·name="idp3362"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dfluid-syn-registration</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-O·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp3375"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·2D·images.·The·transformation·applied·is·a·symmeric·diffeomorpic·fluid·dynamic·registration.·To·work·most·efficiently,·this·program·makes·a·few·assumptions·about·the·imput·data,·i.e.·the·image·must·be·of·the·same·size,·have·the·same·voxel·spacing,·and·any·intensity·range·normalization·or·equalization·should·also·be·done·before·calling·this·program.</p><h4><a·name="idp3377"></a>Options:</h4><h4><a·name="idp3378"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3429"></a>IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(input,·required);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--transform=(required,·output);·io</span></dt><dd><p>output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd><dt><span·class="term">-O,·--inverse-transform=(required,·output);·io</span></dt><dd><p>inverse·output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp3451"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3457"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--mg-levels=3;·uint</span></dt><dd><p>Number·of·multi-resolution·levels·to·run·the·registration·on.·Not·that·some·registration·parameters·can·be·given·as·a·coma·seperated·list·to·indicate·per·level·values.·In·these·cases··if·the·number·of·given·values·is·smaller·than·the·number·of·multi-resolution·levels·(this·parameter),·the·the·last·given·value·is·used·for·all·subsequest·multi-resolution·levels.</p></dd><dt><span·class="term">-S,·--step=0.25;·float·in·(0,·0.5]</span></dt><dd><p>Initial·step·size·for·all·levels</p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>Image·similarity·function·to·be·minimized.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagecost.html"·title="Plugin·type:·2dimage/cost">Plugin·type:·2dimage/cost</a></p></dd><dt><span·class="term">-R,·--regularizer=sor:kernel=fluid,maxiter=50;·factory</span></dt><dd><p>Regularization·for·the·force·to·transformation·update.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dvfregularizer.html"·title="Plugin·type:·2dvf/regularizer">Plugin·type:·2dvf/regularizer</a></p></dd><dt><span·class="term">-T,·--conv-test-interval=·in·[4,·40]</span></dt><dd><p>Convergence·test·interations·intervall:·In·order·to·measure·convergence·the·cost·function·value·is·averaged·over·this·amount·of·iterations,·and·the·decline·rate·is·evaluated·based·on·the·linare·regression·of·the·cost·function·values·in·this·intervall.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-D,·--stop-decline-rate=·in·[0,·inf)</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·decline·rate.·If·the·rate·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-C,·--stop-cost=</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·value.·If·the·cost·drops·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-I,·--iter=·in·[4,·inf)</span></dt><dd><p>Naximum·number·if·iterations·done·on·each·multi-resolution·level.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd></dl></div><h4><a·name="idp3493"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·saving·the·transformation·to·transform.v·and·the·inverse·transform·to·inverse-transform.v.·Use·three·multiresolution·levels,·ssd·as·image·cost·function.</p><pre·class="screen">mia-2dfluid-syn-registration·-i·test.v·-r·ref.v·-t·transform.v·-T·inverse-transform.v··-l·3·ssd</pre><h4><a·name="idp3496"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dfluid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dforce.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dfluid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dforce</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp3375"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·2D·images.·The·transformation·applied·is·a·symmeric·diffeomorpic·fluid·dynamic·registration.·To·work·most·efficiently,·this·program·makes·a·few·assumptions·about·the·imput·data,·i.e.·the·image·must·be·of·the·same·size,·have·the·same·voxel·spacing,·and·any·intensity·range·normalization·or·equalization·should·also·be·done·before·calling·this·program.</p><h4><a·name="idp3377"></a>Options:</h4><h4><a·name="idp3378"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3429"></a>IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(required,·input);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--transform=(required,·output);·io</span></dt><dd><p>output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd><dt><span·class="term">-O,·--inverse-transform=(required,·output);·io</span></dt><dd><p>inverse·output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp3451"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3457"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--mg-levels=3;·uint</span></dt><dd><p>Number·of·multi-resolution·levels·to·run·the·registration·on.·Not·that·some·registration·parameters·can·be·given·as·a·coma·seperated·list·to·indicate·per·level·values.·In·these·cases··if·the·number·of·given·values·is·smaller·than·the·number·of·multi-resolution·levels·(this·parameter),·the·the·last·given·value·is·used·for·all·subsequest·multi-resolution·levels.</p></dd><dt><span·class="term">-S,·--step=0.25;·float·in·(0,·0.5]</span></dt><dd><p>Initial·step·size·for·all·levels</p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>Image·similarity·function·to·be·minimized.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagecost.html"·title="Plugin·type:·2dimage/cost">Plugin·type:·2dimage/cost</a></p></dd><dt><span·class="term">-R,·--regularizer=sor:kernel=fluid,maxiter=50;·factory</span></dt><dd><p>Regularization·for·the·force·to·transformation·update.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dvfregularizer.html"·title="Plugin·type:·2dvf/regularizer">Plugin·type:·2dvf/regularizer</a></p></dd><dt><span·class="term">-T,·--conv-test-interval=·in·[4,·40]</span></dt><dd><p>Convergence·test·interations·intervall:·In·order·to·measure·convergence·the·cost·function·value·is·averaged·over·this·amount·of·iterations,·and·the·decline·rate·is·evaluated·based·on·the·linare·regression·of·the·cost·function·values·in·this·intervall.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-D,·--stop-decline-rate=·in·[0,·inf)</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·decline·rate.·If·the·rate·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-C,·--stop-cost=</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·value.·If·the·cost·drops·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-I,·--iter=·in·[4,·inf)</span></dt><dd><p>Naximum·number·if·iterations·done·on·each·multi-resolution·level.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd></dl></div><h4><a·name="idp3493"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·saving·the·transformation·to·transform.v·and·the·inverse·transform·to·inverse-transform.v.·Use·three·multiresolution·levels,·ssd·as·image·cost·function.</p><pre·class="screen">mia-2dfluid-syn-registration·-i·test.v·-r·ref.v·-t·transform.v·-T·inverse-transform.v··-l·3·ssd</pre><h4><a·name="idp3496"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dfluid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dforce.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dfluid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dforce</td></tr></table></div></body></html>
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29 ··-h,·--help=();·bool29 ··-h,·--help=();·bool
30 ······print·this·help30 ······print·this·help
31 ··-?,·--usage=();·bool31 ··-?,·--usage=();·bool
32 ······print·a·short·help32 ······print·a·short·help
33 ··--version=();·bool33 ··--version=();·bool
34 ······print·the·version·number·and·exit34 ······print·the·version·number·and·exit
35 IO35 IO
36 ··-i,·--in-image=(input,·required);·io36 ··-i,·--in-image=(required,·input);·io
37 ······test·image.·For·supported·file·types·see·Plugin_type:_2dimage/io37 ······test·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
38 ··-r,·--ref-image=(input,·required);·io38 ··-r,·--ref-image=(required,·input);·io
39 ······reference·image.·For·supported·file·types·see·Plugin_type:_2dimage/io39 ······reference·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
40 ··-o,·--transform=(required,·output);·io40 ··-o,·--transform=(required,·output);·io
41 ······output·transformation.·For·supported·file·types·see·Plugin_type:41 ······output·transformation.·For·supported·file·types·see·Plugin_type:
42 ······2dtransform/io42 ······2dtransform/io
43 ··-O,·--inverse-transform=(required,·output);·io43 ··-O,·--inverse-transform=(required,·output);·io
44 ······inverse·output·transformation.·For·supported·file·types·see·Plugin_type:44 ······inverse·output·transformation.·For·supported·file·types·see·Plugin_type:
45 ······2dtransform/io45 ······2dtransform/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dforce</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dfluidsynregistration.html"·title="mia-2dfluid-syn-registration"><link·rel="next"·href="Secmia2dimageregistration.html"·title="mia-2dimageregistration"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dforce</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dfluidsynregistration.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimageregistration.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dforce"></a>mia-2dforce</h3></div></div></div><h4><a·name="idp3500"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dforce</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-c·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dforce</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dfluidsynregistration.html"·title="mia-2dfluid-syn-registration"><link·rel="next"·href="Secmia2dimageregistration.html"·title="mia-2dimageregistration"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dforce</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dfluidsynregistration.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimageregistration.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dforce"></a>mia-2dforce</h3></div></div></div><h4><a·name="idp3500"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dforce</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-c·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp3513"></a>Description:</h4><p·class="description">This·image·evaluate·the·force·field·between·two·images·based·on·a·given·cost·function.</p><h4><a·name="idp3515"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--src-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-file=(input,·required);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·force·norm·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-c,·--cost=(required);·string</span></dt><dd><p>cost·function·to·use</p></dd></dl></div><h4><a·name="idp3536"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3587"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3593"></a>Example:</h4><p>Evaluate·the·force·between·test.v·and·reference.v·by·using·SSD·ans·save·the·norm·of·the·force·to·forcenorm.v</p><pre·class="screen">mia-2dforce·-i·test.v·-r·reference.v·-c·ssd·-o·forcenorm.v</pre><h4><a·name="idp3596"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dfluidsynregistration.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimageregistration.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dfluid-syn-registration </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimageregistration</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp3513"></a>Description:</h4><p·class="description">This·image·evaluate·the·force·field·between·two·images·based·on·a·given·cost·function.</p><h4><a·name="idp3515"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--src-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-file=(required,·input);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·force·norm·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-c,·--cost=(required);·string</span></dt><dd><p>cost·function·to·use</p></dd></dl></div><h4><a·name="idp3536"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3587"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3593"></a>Example:</h4><p>Evaluate·the·force·between·test.v·and·reference.v·by·using·SSD·ans·save·the·norm·of·the·force·to·forcenorm.v</p><pre·class="screen">mia-2dforce·-i·test.v·-r·reference.v·-c·ssd·-o·forcenorm.v</pre><h4><a·name="idp3596"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dfluidsynregistration.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimageregistration.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dfluid-syn-registration </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimageregistration</td></tr></table></div></body></html>
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4 mia-2dforce4 mia-2dforce
5 Sysnopis:5 Sysnopis:
6 mia-2dforce·{-i·io}·{-r·io}·{-o·io}·{-c·string}·[·options·...]6 mia-2dforce·{-i·io}·{-r·io}·{-o·io}·{-c·string}·[·options·...]
7 Description:7 Description:
8 This·image·evaluate·the·force·field·between·two·images·based·on·a·given·cost8 This·image·evaluate·the·force·field·between·two·images·based·on·a·given·cost
9 function.9 function.
10 Options:10 Options:
11 ··-i,·--src-file=(input,·required);·io11 ··-i,·--src-file=(required,·input);·io
12 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io12 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
13 ··-r,·--ref-file=(input,·required);·io13 ··-r,·--ref-file=(required,·input);·io
14 ······reference·image.·For·supported·file·types·see·Plugin_type:_2dimage/io14 ······reference·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
15 ··-o,·--out-file=(required,·output);·io15 ··-o,·--out-file=(required,·output);·io
16 ······output·force·norm·image.·For·supported·file·types·see·Plugin_type:16 ······output·force·norm·image.·For·supported·file·types·see·Plugin_type:
17 ······2dimage/io17 ······2dimage/io
18 ··-c,·--cost=(required);·string18 ··-c,·--cost=(required);·string
19 ······cost·function·to·use19 ······cost·function·to·use
20 Help·&·Info20 Help·&·Info
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./usr/share/doc/mia-2.4/userref/Secmia2dfuzzysegment.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dfuzzysegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2ddistance.html"·title="mia-2ddistance"><link·rel="next"·href="Secmia2dgrayimagecombinetorgb.html"·title="mia-2dgrayimage-combine-to-rgb"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dfuzzysegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2ddistance.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dgrayimagecombinetorgb.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dfuzzysegment"></a>mia-2dfuzzysegment</h3></div></div></div><h4><a·name="idp1305"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dfuzzysegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dfuzzysegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2ddistance.html"·title="mia-2ddistance"><link·rel="next"·href="Secmia2dgrayimagecombinetorgb.html"·title="mia-2dgrayimage-combine-to-rgb"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dfuzzysegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2ddistance.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dgrayimagecombinetorgb.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dfuzzysegment"></a>mia-2dfuzzysegment</h3></div></div></div><h4><a·name="idp1305"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dfuzzysegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp1312"></a>Description:</h4><p·class="description">This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·fuzzy·segmentation·of·2D·image.·cf·D.L.·Pham·and·J.L.Prince,·"An·adaptive·fuzzy·C-means·algorithm·for·image·segmentation·in·the·presence·of·intensity·inhomogeneities",·Pat.·Rec.·Let.,·20:57-68,1999</p><h4><a·name="idp1314"></a>Options:</h4><h4><a·name="idp1315"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·segmenetd.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-c,·--cls-file=(output);·io</span></dt><dd><p>output·class·probability·images·(floating·point·values·and·multi-image).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--b0-file=(output);·io</span></dt><dd><p>image·corrected·for·intensity·non-uniformity.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-g,·--gain-file=(output);·io</span></dt><dd><p>gain·field·(floating·point·valued).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1337"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1388"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-r,·--residuum=0.1;·float</span></dt><dd><p>relative·residuum</p></dd><dt><span·class="term">--l1=200000;·float</span></dt><dd><p>Penalize·magnitude·of·intensity·inhomogeinity·correction</p></dd><dt><span·class="term">--l2=2e+06;·float</span></dt><dd><p>Smoothness·of·intensity·inhomogeinity·correction</p></dd></dl></div><h4><a·name="idp1406"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1412"></a>Example:</h4><p>Run·a·5-class·segmentation·over·input·image·input.v·and·store·the·class·probability·images·in·cls.v·and·the·B0-field·corrected·image·in·b0.v.</p><pre·class="screen">mia-2dfuzzysegment·-i·input.v·-c·5·-o·b0.v·-c·cls.v</pre><h4><a·name="idp1415"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2ddistance.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dgrayimagecombinetorgb.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2ddistance </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dgrayimage-combine-to-rgb</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp1312"></a>Description:</h4><p·class="description">This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·fuzzy·segmentation·of·2D·image.·cf·D.L.·Pham·and·J.L.Prince,·"An·adaptive·fuzzy·C-means·algorithm·for·image·segmentation·in·the·presence·of·intensity·inhomogeneities",·Pat.·Rec.·Let.,·20:57-68,1999</p><h4><a·name="idp1314"></a>Options:</h4><h4><a·name="idp1315"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·segmenetd.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-c,·--cls-file=(output);·io</span></dt><dd><p>output·class·probability·images·(floating·point·values·and·multi-image).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--b0-file=(output);·io</span></dt><dd><p>image·corrected·for·intensity·non-uniformity.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-g,·--gain-file=(output);·io</span></dt><dd><p>gain·field·(floating·point·valued).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1337"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1388"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-r,·--residuum=0.1;·float</span></dt><dd><p>relative·residuum</p></dd><dt><span·class="term">--l1=200000;·float</span></dt><dd><p>Penalize·magnitude·of·intensity·inhomogeinity·correction</p></dd><dt><span·class="term">--l2=2e+06;·float</span></dt><dd><p>Smoothness·of·intensity·inhomogeinity·correction</p></dd></dl></div><h4><a·name="idp1406"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1412"></a>Example:</h4><p>Run·a·5-class·segmentation·over·input·image·input.v·and·store·the·class·probability·images·in·cls.v·and·the·B0-field·corrected·image·in·b0.v.</p><pre·class="screen">mia-2dfuzzysegment·-i·input.v·-c·5·-o·b0.v·-c·cls.v</pre><h4><a·name="idp1415"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2ddistance.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dgrayimagecombinetorgb.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2ddistance </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dgrayimage-combine-to-rgb</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to8 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to
9 facilitate·a·fuzzy·segmentation·of·2D·image.·cf·D.L.·Pham·and·J.L.Prince,·"An9 facilitate·a·fuzzy·segmentation·of·2D·image.·cf·D.L.·Pham·and·J.L.Prince,·"An
10 adaptive·fuzzy·C-means·algorithm·for·image·segmentation·in·the·presence·of10 adaptive·fuzzy·C-means·algorithm·for·image·segmentation·in·the·presence·of
11 intensity·inhomogeneities",·Pat.·Rec.·Let.,·20:57-68,199911 intensity·inhomogeneities",·Pat.·Rec.·Let.,·20:57-68,1999
12 Options:12 Options:
13 File-IO13 File-IO
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······input·image(s)·to·be·segmenetd.·For·supported·file·types·see·Plugin_type:15 ······input·image(s)·to·be·segmenetd.·For·supported·file·types·see·Plugin_type:
16 ······2dimage/io16 ······2dimage/io
17 ··-c,·--cls-file=(output);·io17 ··-c,·--cls-file=(output);·io
18 ······output·class·probability·images·(floating·point·values·and·multi-image).18 ······output·class·probability·images·(floating·point·values·and·multi-image).
19 ······For·supported·file·types·see·Plugin_type:_2dimage/io19 ······For·supported·file·types·see·Plugin_type:_2dimage/io
20 ··-o,·--b0-file=(output);·io20 ··-o,·--b0-file=(output);·io
21 ······image·corrected·for·intensity·non-uniformity.·For·supported·file·types21 ······image·corrected·for·intensity·non-uniformity.·For·supported·file·types
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dgroundtruthreg</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="next"·href="Secmia2dmany2onenonrigid.html"·title="mia-2dmany2one-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dgroundtruthreg</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof2Dimages.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmany2onenonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dgroundtruthreg"></a>mia-2dgroundtruthreg</h3></div></div></div><h4><a·name="idp4145"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dgroundtruthreg</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-A·<em·class="replaceable"><code>double</code></em>}·{-B·<em·class="replaceable"><code>double</code></em>}·{-R·<em·class="replaceable"><code>double</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dgroundtruthreg</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="next"·href="Secmia2dmany2onenonrigid.html"·title="mia-2dmany2one-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dgroundtruthreg</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof2Dimages.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmany2onenonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dgroundtruthreg"></a>mia-2dgroundtruthreg</h3></div></div></div><h4><a·name="idp4145"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dgroundtruthreg</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-A·<em·class="replaceable"><code>double</code></em>}·{-B·<em·class="replaceable"><code>double</code></em>}·{-R·<em·class="replaceable"><code>double</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp4160"></a>Description:</h4><p·class="description">This·program·implements·the·non-linear·registration·based·on·Pseudo·Ground·Thruth·for·motion·compensation·of·series·of·myocardial·perfusion·images·as·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1007/978-3-642-04268-3_21"·target="_top">Chao·Li·and·Ying·Sun,·'Nonrigid·Registration·of·Myocardial·Perfusion·MRI·Using·Pseudo·Ground·Truth'·,·In·Proc.·Medical·Image·Computing·and·Computer-Assisted·Intervention·MICCAI·2009,·165-172,·2009.</a></p><p·class="description">·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.</p><h4><a·name="idp4164"></a>Options:</h4><h4><a·name="idp4165"></a>3 ········...]</p></div><h4><a·name="idp4160"></a>Description:</h4><p·class="description">This·program·implements·the·non-linear·registration·based·on·Pseudo·Ground·Thruth·for·motion·compensation·of·series·of·myocardial·perfusion·images·as·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1007/978-3-642-04268-3_21"·target="_top">Chao·Li·and·Ying·Sun,·'Nonrigid·Registration·of·Myocardial·Perfusion·MRI·Using·Pseudo·Ground·Truth'·,·In·Proc.·Medical·Image·Computing·and·Computer-Assisted·Intervention·MICCAI·2009,·165-172,·2009.</a></p><p·class="description">·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.</p><h4><a·name="idp4164"></a>Options:</h4><h4><a·name="idp4165"></a>
4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·files</p></dd></dl></div><h4><a·name="idp4179"></a>4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·files</p></dd></dl></div><h4><a·name="idp4179"></a>
5 Preconditions</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-P,·--passes=4;·ulong</span></dt><dd><p>number·of·registration·passes</p></dd></dl></div><h4><a·name="idp4189"></a>5 Preconditions</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-P,·--passes=4;·ulong</span></dt><dd><p>number·of·registration·passes</p></dd></dl></div><h4><a·name="idp4189"></a>
6 Pseudo-Ground-Thruth</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-A,·--alpha=(required);·double</span></dt><dd><p>spacial·neighborhood·penalty·weight</p></dd><dt><span·class="term">-B,·--beta=(required);·double</span></dt><dd><p>temporal·second·derivative·penalty·weight</p></dd><dt><span·class="term">-R,·--rho_thresh=(required);·double</span></dt><dd><p>correlation·threshold·for·neighborhood·analysis</p></dd></dl></div><h4><a·name="idp4203"></a>6 Pseudo-Ground-Thruth</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-A,·--alpha=(required);·double</span></dt><dd><p>spacial·neighborhood·penalty·weight</p></dd><dt><span·class="term">-B,·--beta=(required);·double</span></dt><dd><p>temporal·second·derivative·penalty·weight</p></dd><dt><span·class="term">-R,·--rho_thresh=(required);·double</span></dt><dd><p>correlation·threshold·for·neighborhood·analysis</p></dd></dl></div><h4><a·name="idp4203"></a>
7 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">-l,·--mr-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-d,·--divcurl=20;·double</span></dt><dd><p>divcurl·regularization·weight</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-a,·--start-c-rate=32;·ulong</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-w,·--imageweight=1;·double</span></dt><dd><p>image·cost·weight</p></dd></dl></div><h4><a·name="idp4239"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4290"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4296"></a>Example:</h4><p>Register·the·perfusion·series·given·by·images·imageXXXX.exr·by·using·Pseudo·Ground·Truth·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·images·to··'regXXXX.exr'.</p><pre·class="screen">mia-2dgroundtruthreg·-i·imageXXXX.exr·-o·regXXXX.exr·-k·2</pre><h4><a·name="idp4299"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof2Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmany2onenonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Registration·of·series·of·2D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmany2one-nonrigid</td></tr></table></div></body></html>7 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">-l,·--mr-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-d,·--divcurl=20;·double</span></dt><dd><p>divcurl·regularization·weight</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-a,·--start-c-rate=32;·ulong</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-w,·--imageweight=1;·double</span></dt><dd><p>image·cost·weight</p></dd></dl></div><h4><a·name="idp4239"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4290"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4296"></a>Example:</h4><p>Register·the·perfusion·series·given·by·images·imageXXXX.exr·by·using·Pseudo·Ground·Truth·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·images·to··'regXXXX.exr'.</p><pre·class="screen">mia-2dgroundtruthreg·-i·imageXXXX.exr·-o·regXXXX.exr·-k·2</pre><h4><a·name="idp4299"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof2Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmany2onenonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Registration·of·series·of·2D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmany2one-nonrigid</td></tr></table></div></body></html>
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12 Chao_Li_and_Ying_Sun,_'Nonrigid_Registration_of_Myocardial_Perfusion_MRI_Using12 Chao_Li_and_Ying_Sun,_'Nonrigid_Registration_of_Myocardial_Perfusion_MRI_Using
13 Pseudo_Ground_Truth'_,_In_Proc._Medical_Image_Computing_and_Computer-Assisted13 Pseudo_Ground_Truth'_,_In_Proc._Medical_Image_Computing_and_Computer-Assisted
14 Intervention_MICCAI_2009,_165-172,_2009.14 Intervention_MICCAI_2009,_165-172,_2009.
15 Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration15 Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration
16 step·is·usually·required.16 step·is·usually·required.
17 Options:17 Options:
18 ·File-IO18 ·File-IO
19 ··-i,·--in-file=(input,·required);·string19 ··-i,·--in-file=(required,·input);·string
20 ······input·perfusion·data·set20 ······input·perfusion·data·set
21 ··-o,·--out-file=(required,·output);·string21 ··-o,·--out-file=(required,·output);·string
22 ······output·perfusion·data·set22 ······output·perfusion·data·set
23 ··-r,·--registered=reg;·stringSTRING23 ··-r,·--registered=reg;·stringSTRING
24 ······file·name·base·for·registered·files24 ······file·name·base·for·registered·files
25 ·Preconditions25 ·Preconditions
26 ··-s,·--skip=2;·ulong26 ··-s,·--skip=2;·ulong
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagecombine-dice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dgrayimagecombinetorgb.html"·title="mia-2dgrayimage-combine-to-rgb"><link·rel="next"·href="Secmia2dimagecombiner.html"·title="mia-2dimagecombiner"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagecombine-dice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dgrayimagecombinetorgb.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecombiner.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagecombinedice"></a>mia-2dimagecombine-dice</h3></div></div></div><h4><a·name="idp1514"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagecombine-dice</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagecombine-dice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dgrayimagecombinetorgb.html"·title="mia-2dgrayimage-combine-to-rgb"><link·rel="next"·href="Secmia2dimagecombiner.html"·title="mia-2dimagecombiner"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagecombine-dice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dgrayimagecombinetorgb.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecombiner.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagecombinedice"></a>mia-2dimagecombine-dice</h3></div></div></div><h4><a·name="idp1514"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagecombine-dice</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp1523"></a>Description:</h4><p·class="description">This·program·evaluate·the·dice·index·of·two·binary·masks·given·as·binary·images.·The·result·is·written·to·stdout.</p><h4><a·name="idp1525"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--in-file-1=(input,·required);·io</span></dt><dd><p>input·image·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--in-file-2=(input,·require[·...·truncated·by·diffoscope;·len:·1,·SHA:·18ac3e7343f016890c510e93f935261169d9e3f565436429830faf0934f4f8e4·...·]);·io</span></dt><dd><p>input·image·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1537"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1588"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1594"></a>Example:</h4><p>Evaluate·the·dice·index·of·maks1.png·and·mask2.png</p><pre·class="screen">mia-2dimagecombine-dice·-1·mask1.png·-2·mask2.png</pre><h4><a·name="idp1597"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dgrayimagecombinetorgb.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecombiner.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dgrayimage-combine-to-rgb </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagecombiner</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp1523"></a>Description:</h4><p·class="description">This·program·evaluate·the·dice·index·of·two·binary·masks·given·as·binary·images.·The·result·is·written·to·stdout.</p><h4><a·name="idp1525"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--in-file-1=(required,·input);·io</span></dt><dd><p>input·image·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--in-file-2=(required,·inpu[·...·truncated·by·diffoscope;·len:·1,·SHA:·e3b98a4da31a127d4bde6e43033f66ba274cab0eb7eb1c70ec41402bf6273dd8·...·]);·io</span></dt><dd><p>input·image·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1537"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1588"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1594"></a>Example:</h4><p>Evaluate·the·dice·index·of·maks1.png·and·mask2.png</p><pre·class="screen">mia-2dimagecombine-dice·-1·mask1.png·-2·mask2.png</pre><h4><a·name="idp1597"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dgrayimagecombinetorgb.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecombiner.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dgrayimage-combine-to-rgb </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagecombiner</td></tr></table></div></body></html>
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4 mia-2dimagecombine-dice4 mia-2dimagecombine-dice
5 Sysnopis:5 Sysnopis:
6 mia-2dimagecombine-dice·{-1·io}·{-2·io}·[·options·...]6 mia-2dimagecombine-dice·{-1·io}·{-2·io}·[·options·...]
7 Description:7 Description:
8 This·program·evaluate·the·dice·index·of·two·binary·masks·given·as·binary8 This·program·evaluate·the·dice·index·of·two·binary·masks·given·as·binary
9 images.·The·result·is·written·to·stdout.9 images.·The·result·is·written·to·stdout.
10 Options:10 Options:
11 ··-1,·--in-file-1=(input,·required);·io11 ··-1,·--in-file-1=(required,·input);·io
12 ······input·image·1.·For·supported·file·types·see·Plugin_type:_2dimage/io12 ······input·image·1.·For·supported·file·types·see·Plugin_type:_2dimage/io
13 ··-2,·--in-file-2=(input,·required);·io13 ··-2,·--in-file-2=(required,·input);·io
14 ······input·image·2.·For·supported·file·types·see·Plugin_type:_2dimage/io14 ······input·image·2.·For·supported·file·types·see·Plugin_type:_2dimage/io
15 Help·&·Info15 Help·&·Info
16 ··-V,·--verbose=warning;·dict16 ··-V,·--verbose=warning;·dict
17 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.17 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
18 ······Supported·priorities·starting·at·lowest·level·are:18 ······Supported·priorities·starting·at·lowest·level·are:
19 ······trace:···Function·call·trace19 ······trace:···Function·call·trace
20 ······debug:···Debug·output20 ······debug:···Debug·output
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagecombiner</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagecombinedice.html"·title="mia-2dimagecombine-dice"><link·rel="next"·href="Secmia2dimagecreator.html"·title="mia-2dimagecreator"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagecombiner</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagecombinedice.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecreator.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagecombiner"></a>mia-2dimagecombiner</h3></div></div></div><h4><a·name="idp1601"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagecombiner</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagecombiner</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagecombinedice.html"·title="mia-2dimagecombine-dice"><link·rel="next"·href="Secmia2dimagecreator.html"·title="mia-2dimagecreator"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagecombiner</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagecombinedice.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecreator.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagecombiner"></a>mia-2dimagecombiner</h3></div></div></div><h4><a·name="idp1601"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagecombiner</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp1612"></a>Description:</h4><p·class="description">Combine·two·image·by·a·given·operation.</p><h4><a·name="idp1614"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--in-file-1=(input,·required);·io</span></dt><dd><p>first·input·image·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--in-fil[·...·truncated·by·diffoscope;·len:·20,·SHA:·081be03456b4d482b60c8dcd019d1c0a6b2d1d4fcb166a83fe8e5ea474d1d67c·...·]);·io</span></dt><dd><p>second·input·image·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--operation=absdiff;·factory</span></dt><dd><p>operation·to·be·applied.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagecombiner.html"·title="Plugin·type:·2dimage/combiner">Plugin·type:·2dimage/combiner</a></p></dd></dl></div><h4><a·name="idp1636"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1687"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1693"></a>Example:</h4><p>Combine·image·A.exr·and·image·B.exr··by·adding·the·intensity·values·and·save·the·output·to·sum.exr.</p><pre·class="screen">mia-2dimagecombiner·-i·A.exr·-r·B.exr·-o·sum.exr·-p·add</pre><h4><a·name="idp1696"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagecombinedice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecreator.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagecombine-dice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagecreator</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp1612"></a>Description:</h4><p·class="description">Combine·two·image·by·a·given·operation.</p><h4><a·name="idp1614"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--in-file-1=(required,·input);·io</span></dt><dd><p>first·input·image·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--in-fil[·...·truncated·by·diffoscope;·len:·20,·SHA:·4d5f05e8370392544ac3a63808b9aa434464729622442772025c496196f4d09e·...·]);·io</span></dt><dd><p>second·input·image·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--operation=absdiff;·factory</span></dt><dd><p>operation·to·be·applied.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagecombiner.html"·title="Plugin·type:·2dimage/combiner">Plugin·type:·2dimage/combiner</a></p></dd></dl></div><h4><a·name="idp1636"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1687"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1693"></a>Example:</h4><p>Combine·image·A.exr·and·image·B.exr··by·adding·the·intensity·values·and·save·the·output·to·sum.exr.</p><pre·class="screen">mia-2dimagecombiner·-i·A.exr·-r·B.exr·-o·sum.exr·-p·add</pre><h4><a·name="idp1696"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagecombinedice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagecreator.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagecombine-dice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagecreator</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dimagecombiner4 mia-2dimagecombiner
5 Sysnopis:5 Sysnopis:
6 mia-2dimagecombiner·{-1·io}·{-2·io}·{-o·io}·[·options·...]6 mia-2dimagecombiner·{-1·io}·{-2·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Combine·two·image·by·a·given·operation.8 Combine·two·image·by·a·given·operation.
9 Options:9 Options:
10 ··-1,·--in-file-1=(input,·required);·io10 ··-1,·--in-file-1=(required,·input);·io
11 ······first·input·image·to·be·combined.·For·supported·file·types·see·Plugin11 ······first·input·image·to·be·combined.·For·supported·file·types·see·Plugin
12 ······type:_2dimage/io12 ······type:_2dimage/io
13 ··-2,·--in-file-2=(input,·required);·io13 ··-2,·--in-file-2=(required,·input);·io
14 ······second·input·image·to·be·combined.·For·supported·file·types·see·Plugin14 ······second·input·image·to·be·combined.·For·supported·file·types·see·Plugin
15 ······type:_2dimage/io15 ······type:_2dimage/io
16 ··-o,·--out-file=(required,·output);·io16 ··-o,·--out-file=(required,·output);·io
17 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see17 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see
18 ······Plugin_type:_2dimage/io18 ······Plugin_type:_2dimage/io
19 ··-p,·--operation=absdiff;·factory19 ··-p,·--operation=absdiff;·factory
20 ······operation·to·be·applied.·For·supported·plug-ins·see·Plugin_type:_2dimage/20 ······operation·to·be·applied.·For·supported·plug-ins·see·Plugin_type:_2dimage/
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2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp1848"></a>Description:</h4><p·class="description">This·program·runs·a·series·filters·on·a·given·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·Ware·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run7 ········...]</p></div><h4><a·name="idp1848"></a>Description:</h4><p·class="description">This·program·runs·a·series·filters·on·a·given·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·Ware·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run
8 ···'mia-plugin-help·filter/2dimage'8 ···'mia-plugin-help·filter/2dimage'
9 from·the·command·line</p><h4><a·name="idp1850"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1862"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1913"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1919"></a>Example:</h4><p>Run·a·kmeans·classification·of·5·classes·on·input.png·and·then·a·binarization·of·the·4th·class·and·store·the·result·in·result.png</p><pre·class="screen">mia-2dimagefilter·-i·input.png·-o·result.png·kmeans:c=5·binarize:min=4,max=4</pre><h4><a·name="idp1922"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagecreator.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagefilterstack.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagecreator </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagefilterstack</td></tr></table></div></body></html>9 from·the·command·line</p><h4><a·name="idp1850"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp1862"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp1913"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp1919"></a>Example:</h4><p>Run·a·kmeans·classification·of·5·classes·on·input.png·and·then·a·binarization·of·the·4th·class·and·store·the·result·in·result.png</p><pre·class="screen">mia-2dimagefilter·-i·input.png·-o·result.png·kmeans:c=5·binarize:min=4,max=4</pre><h4><a·name="idp1922"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagecreator.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagefilterstack.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagecreator </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagefilterstack</td></tr></table></div></body></html>
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7 ...]7 ...]
8 Description:8 Description:
9 This·program·runs·a·series·filters·on·a·given·input·image.·The·filters·are9 This·program·runs·a·series·filters·on·a·given·input·image.·The·filters·are
10 given·as·extra·parameters·on·the·command·line·and·Ware·run·in·the·order·in10 given·as·extra·parameters·on·the·command·line·and·Ware·run·in·the·order·in
11 which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run·'mia-11 which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run·'mia-
12 plugin-help·filter/2dimage'·from·the·command·line12 plugin-help·filter/2dimage'·from·the·command·line
13 Options:13 Options:
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:15 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
16 ······2dimage/io16 ······2dimage/io
17 ··-o,·--out-file=(required,·output);·io17 ··-o,·--out-file=(required,·output);·io
18 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see18 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see
19 ······Plugin_type:_2dimage/io19 ······Plugin_type:_2dimage/io
20 Help·&·Info20 Help·&·Info
21 ··-V,·--verbose=warning;·dict21 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagefilterstack</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagefilter.html"·title="mia-2dimagefilter"><link·rel="next"·href="Secmia2dimagefullstats.html"·title="mia-2dimagefullstats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagefilterstack</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilter.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimagefullstats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagefilterstack"></a>mia-2dimagefilterstack</h3></div></div></div><h4><a·name="idp1926"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagefilterstack</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagefilterstack</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagefilter.html"·title="mia-2dimagefilter"><link·rel="next"·href="Secmia2dimagefullstats.html"·title="mia-2dimagefullstats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagefilterstack</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilter.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimagefullstats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagefilterstack"></a>mia-2dimagefilterstack</h3></div></div></div><h4><a·name="idp1926"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagefilterstack</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp1938"></a>Description:</h4><p·class="description">This·program·runs·a·series·filters·on·a·series·of·consecutive·numbered·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.</p><h4><a·name="idp1940"></a>Options:</h4><h4><a·name="idp1941"></a>File·IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--type=</span></dt><dd><p>output·file·type,·if·not·given·the·input·type·is·used<td·align="left"·valign="top">·Supported·values·are:(-,·@,·BMP,·DCM,·EXR,·JPEG,·JPG,·PNG,·RAW,·TIF,·TIFF,·V,·VISTA,·bmp,·dcm,·exr,·jpeg,·jpg,·png,·raw,·tif,·tiff,·v,·vista,·)</td></p></dd></dl></div><h4><a·name="idp1958"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2009"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2015"></a>Processing1</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--start=0;·ulong</span></dt><dd><p>first·possible·number·of·file·number·range·to·be·filtered</p></dd><dt><span·class="term">-e,·--end=2147483647;·ulong</span></dt><dd><p>last·possible·number·of·file·number·range·to·be·filtered</p></dd></dl></div><h4><a·name="idp2025"></a>Example:</h4><p>Run·a·kmeans·classification·of·5·classes·on·images·inputXXXX.png·(X·being·digits)·and·then·a·binarization·of·the·4th·class·and·store·the·result·in·resultXXXX.png</p><pre·class="screen">mia-2dimagefilterstack·-i·input0000.png·-o·result·-t·png·kmeans:c=5·binarize:min=4,max=4</pre><h4><a·name="idp2028"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilter.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagefullstats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagefilter </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagefullstats</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp1938"></a>Description:</h4><p·class="description">This·program·runs·a·series·filters·on·a·series·of·consecutive·numbered·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.</p><h4><a·name="idp1940"></a>Options:</h4><h4><a·name="idp1941"></a>File·IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--type=</span></dt><dd><p>output·file·type,·if·not·given·the·input·type·is·used<td·align="left"·valign="top">·Supported·values·are:(-,·@,·BMP,·DCM,·EXR,·JPEG,·JPG,·PNG,·RAW,·TIF,·TIFF,·V,·VISTA,·bmp,·dcm,·exr,·jpeg,·jpg,·png,·raw,·tif,·tiff,·v,·vista,·)</td></p></dd></dl></div><h4><a·name="idp1958"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2009"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2015"></a>Processing1</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--start=0;·ulong</span></dt><dd><p>first·possible·number·of·file·number·range·to·be·filtered</p></dd><dt><span·class="term">-e,·--end=2147483647;·ulong</span></dt><dd><p>last·possible·number·of·file·number·range·to·be·filtered</p></dd></dl></div><h4><a·name="idp2025"></a>Example:</h4><p>Run·a·kmeans·classification·of·5·classes·on·images·inputXXXX.png·(X·being·digits)·and·then·a·binarization·of·the·4th·class·and·store·the·result·in·resultXXXX.png</p><pre·class="screen">mia-2dimagefilterstack·-i·input0000.png·-o·result·-t·png·kmeans:c=5·binarize:min=4,max=4</pre><h4><a·name="idp2028"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilter.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimagefullstats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagefilter </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimagefullstats</td></tr></table></div></body></html>
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagefullstats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagefilterstack.html"·title="mia-2dimagefilterstack"><link·rel="next"·href="Secmia2dimageseriesmaximumintensityprojection.html"·title="mia-2dimageseries-maximum-intensity-projection"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagefullstats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilterstack.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimageseriesmaximumintensityprojection.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagefullstats"></a>mia-2dimagefullstats</h3></div></div></div><h4><a·name="idp2032"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagefullstats</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagefullstats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagefilterstack.html"·title="mia-2dimagefilterstack"><link·rel="next"·href="Secmia2dimageseriesmaximumintensityprojection.html"·title="mia-2dimageseries-maximum-intensity-projection"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagefullstats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilterstack.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dimageseriesmaximumintensityprojection.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagefullstats"></a>mia-2dimagefullstats</h3></div></div></div><h4><a·name="idp2032"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagefullstats</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2039"></a>Description:</h4><p·class="description">This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·Min·and·Max·of·the·intensity·values.</p><h4><a·name="idp2041"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2048"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2099"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2105"></a>Example:</h4><p>Evaluate·the·statistics·of·image·input.png</p><pre·class="screen">mia-2dimagefullstats·-i·input.png</pre><h4><a·name="idp2108"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilterstack.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimageseriesmaximumintensityprojection.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagefilterstack </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimageseries-maximum-intensity-projection</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2039"></a>Description:</h4><p·class="description">This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·Min·and·Max·of·the·intensity·values.</p><h4><a·name="idp2041"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2048"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2099"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2105"></a>Example:</h4><p>Evaluate·the·statistics·of·image·input.png</p><pre·class="screen">mia-2dimagefullstats·-i·input.png</pre><h4><a·name="idp2108"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagefilterstack.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dimageseriesmaximumintensityprojection.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagefilterstack </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dimageseries-maximum-intensity-projection</td></tr></table></div></body></html>
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4 mia-2dimagefullstats4 mia-2dimagefullstats
5 Sysnopis:5 Sysnopis:
6 mia-2dimagefullstats·{-i·io}·[·options·...]6 mia-2dimagefullstats·{-i·io}·[·options·...]
7 Description:7 Description:
8 This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,8 This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,
9 Variation,·Median,·Min·and·Max·of·the·intensity·values.9 Variation,·Median,·Min·and·Max·of·the·intensity·values.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io12 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
13 Help·&·Info13 Help·&·Info
14 ··-V,·--verbose=warning;·dict14 ··-V,·--verbose=warning;·dict
15 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.15 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
16 ······Supported·priorities·starting·at·lowest·level·are:16 ······Supported·priorities·starting·at·lowest·level·are:
17 ······trace:···Function·call·trace17 ······trace:···Function·call·trace
18 ······debug:···Debug·output18 ······debug:···Debug·output
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimageregistration</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dforce.html"·title="mia-2dforce"><link·rel="next"·href="Secmia2dmultiforce.html"·title="mia-2dmulti-force"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimageregistration</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dforce.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiforce.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimageregistration"></a>mia-2dimageregistration</h3></div></div></div><h4><a·name="idp3600"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimageregistration</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimageregistration</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dforce.html"·title="mia-2dforce"><link·rel="next"·href="Secmia2dmultiforce.html"·title="mia-2dmulti-force"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimageregistration</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dforce.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiforce.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimageregistration"></a>mia-2dimageregistration</h3></div></div></div><h4><a·name="idp3600"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimageregistration</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp3614"></a>Description:</h4><p·class="description">This·program·runs·registration·of·two·images·optimizing·a·transformation·of·the·given·transformation·model·by·optimizing·certain·cost·measures·that·are·given·as·free·parameters.</p><h4><a·name="idp3616"></a>Options:</h4><h4><a·name="idp3617"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>test·image·to·be·registered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=([·...·truncated·by·diffoscope;·len:·15,·SHA:·33a12c838e1abf52415f9c322e9e81a06a6559539e51d2d8f6d85a0bf28cf702·...·]);·io</span></dt><dd><p>reference·image·to·be·registered·to.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(output);·io</span></dt><dd><p>registered·output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--transformation=(required,·output);·io</span></dt><dd><p>output·transformation·comprising·the·registration.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp3639"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3690"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-R,·--refiner=</span></dt><dd><p>optimizer·used·for·refinement·after·the·main·optimizer·was·called.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd></dl></div><h4><a·name="idp3711"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3717"></a>Example:</h4><p>Register·the·image·'moving.png'·to·the·image·'reference.png'·by·using·a·rigid·transformation·model··and·ssd·as·cost·function.·Write·the·result·to·output.png</p><pre·class="screen">mia-2dimageregistration···-i·moving.png·-r·reference.png·-o·output.png·-f·rigid·image:cost=ssd</pre><h4><a·name="idp3720"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dforce.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiforce.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dforce </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmulti-force</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp3614"></a>Description:</h4><p·class="description">This·program·runs·registration·of·two·images·optimizing·a·transformation·of·the·given·transformation·model·by·optimizing·certain·cost·measures·that·are·given·as·free·parameters.</p><h4><a·name="idp3616"></a>Options:</h4><h4><a·name="idp3617"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>test·image·to·be·registered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=([·...·truncated·by·diffoscope;·len:·15,·SHA:·da8a98fed43ed2f2e7a321d4877b5e3db55241e0cc72373a2f7ee9015f12dce3·...·]);·io</span></dt><dd><p>reference·image·to·be·registered·to.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(output);·io</span></dt><dd><p>registered·output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--transformation=(required,·output);·io</span></dt><dd><p>output·transformation·comprising·the·registration.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp3639"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3690"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-R,·--refiner=</span></dt><dd><p>optimizer·used·for·refinement·after·the·main·optimizer·was·called.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd></dl></div><h4><a·name="idp3711"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3717"></a>Example:</h4><p>Register·the·image·'moving.png'·to·the·image·'reference.png'·by·using·a·rigid·transformation·model··and·ssd·as·cost·function.·Write·the·result·to·output.png</p><pre·class="screen">mia-2dimageregistration···-i·moving.png·-r·reference.png·-o·output.png·-f·rigid·image:cost=ssd</pre><h4><a·name="idp3720"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dforce.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiforce.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dforce </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmulti-force</td></tr></table></div></body></html>
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7 2dimage/fullcost·...]7 2dimage/fullcost·...]
8 Description:8 Description:
9 This·program·runs·registration·of·two·images·optimizing·a·transformation·of·the9 This·program·runs·registration·of·two·images·optimizing·a·transformation·of·the
10 given·transformation·model·by·optimizing·certain·cost·measures·that·are·given10 given·transformation·model·by·optimizing·certain·cost·measures·that·are·given
11 as·free·parameters.11 as·free·parameters.
12 Options:12 Options:
13 File-IO13 File-IO
14 ··-i,·--in-image=(input,·required);·io14 ··-i,·--in-image=(required,·input);·io
15 ······test·image·to·be·registered.·For·supported·file·types·see·Plugin_type:15 ······test·image·to·be·registered.·For·supported·file·types·see·Plugin_type:
16 ······2dimage/io16 ······2dimage/io
17 ··-r,·--ref-image=(input,·required);·io17 ··-r,·--ref-image=(required,·input);·io
18 ······reference·image·to·be·registered·to.·For·supported·file·types·see·Plugin18 ······reference·image·to·be·registered·to.·For·supported·file·types·see·Plugin
19 ······type:_2dimage/io19 ······type:_2dimage/io
20 ··-o,·--out-image=(output);·io20 ··-o,·--out-image=(output);·io
21 ······registered·output·image.·For·supported·file·types·see·Plugin_type:21 ······registered·output·image.·For·supported·file·types·see·Plugin_type:
22 ······2dimage/io22 ······2dimage/io
23 ··-t,·--transformation=(required,·output);·io23 ··-t,·--transformation=(required,·output);·io
24 ······output·transformation·comprising·the·registration.·For·supported·file24 ······output·transformation·comprising·the·registration.·For·supported·file
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimageselect</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="next"·href="Secmia2dmultiimageto3d.html"·title="mia-2dmultiimageto3d"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimageselect</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecImageconversion.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimageto3d.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimageselect"></a>mia-2dimageselect</h3></div></div></div><h4><a·name="idp53"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimageselect</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimageselect</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="next"·href="Secmia2dmultiimageto3d.html"·title="mia-2dmultiimageto3d"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimageselect</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecImageconversion.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimageto3d.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimageselect"></a>mia-2dimageselect</h3></div></div></div><h4><a·name="idp53"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimageselect</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp62"></a>Description:</h4><p·class="description">This·program·is·used·to·select·one·2D·images·from·a·multi-image·file.</p><h4><a·name="idp64"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-n,·--number=0;·ulong</span></dt><dd><p>image·number·to·be·selected</p></dd></dl></div><h4><a·name="idp80"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp131"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp137"></a>Example:</h4><p>Store·the·third·image·in·multiimage.v·to·image.v·(note:·counting·starts·with·zero).</p><pre·class="screen">mia-2dimageselect·-i·multiimage.v·-o·image.v·-n·2</pre><h4><a·name="idp140"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecImageconversion.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimageto3d.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Image·conversion </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmultiimageto3d</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp62"></a>Description:</h4><p·class="description">This·program·is·used·to·select·one·2D·images·from·a·multi-image·file.</p><h4><a·name="idp64"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-n,·--number=0;·ulong</span></dt><dd><p>image·number·to·be·selected</p></dd></dl></div><h4><a·name="idp80"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp131"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp137"></a>Example:</h4><p>Store·the·third·image·in·multiimage.v·to·image.v·(note:·counting·starts·with·zero).</p><pre·class="screen">mia-2dimageselect·-i·multiimage.v·-o·image.v·-n·2</pre><h4><a·name="idp140"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecImageconversion.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimageto3d.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Image·conversion </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmultiimageto3d</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dimageselect4 mia-2dimageselect
5 Sysnopis:5 Sysnopis:
6 mia-2dimageselect·{-i·io}·{-o·io}·[·options·...]6 mia-2dimageselect·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·select·one·2D·images·from·a·multi-image·file.8 This·program·is·used·to·select·one·2D·images·from·a·multi-image·file.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·images.·For·supported·file·types·see·Plugin_type:_2dimage/io11 ······input·images.·For·supported·file·types·see·Plugin_type:_2dimage/io
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·image.·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······output·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-n,·--number=0;·ulong14 ··-n,·--number=0;·ulong
15 ······image·number·to·be·selected15 ······image·number·to·be·selected
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagestack-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="next"·href="Secmia2dstackcmeanspresegment.html"·title="mia-2dstack-cmeans-presegment"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagestack-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dstackcmeanspresegment.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagestackcmeans"></a>mia-2dimagestack-cmeans</h3></div></div></div><h4><a·name="idp8554"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagestack-cmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagestack-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="next"·href="Secmia2dstackcmeanspresegment.html"·title="mia-2dstack-cmeans-presegment"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagestack-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dstackcmeanspresegment.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagestackcmeans"></a>mia-2dimagestack-cmeans</h3></div></div></div><h4><a·name="idp8554"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagestack-cmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8563"></a>Description:</h4><p·class="description">This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram·and·then·writes·the·probability·mapping·for·thr·original·intensity·values</p><h4><a·name="idp8565"></a>Options:</h4><h4><a·name="idp8566"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-probmap=(required,·output);·string</span></dt><dd><p>Save·probability·map·to·this·file</p></dd></dl></div><h4><a·name="idp8577"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8628"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--histogram-thresh=5;·float·in·[0,·50]</span></dt><dd><p>Percent·of·the·extrem·parts·of·the·histogram·to·be·collapsed·into·the·respective·last·histogram·bin.</p></dd><dt><span·class="term">-C,·--classes=kmeans:nc=3;·factory</span></dt><dd><p>C-means·class·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd></dl></div><h4><a·name="idp8639"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8645"></a>Example:</h4><p>Run·the·program·over·images·imageXXXX.png·with·the·sparse·histogram,·threshold·the·lower·5%·bins·(if·available),·run·cmeans·with·three·classes·on·the·non-zero·pixels.</p><pre·class="screen">mia-2dimagestack-cmeans·-i·image0000.png·-o·cmeans,txt·--histogram-tresh=5·--classes·3</pre><h4><a·name="idp8648"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dstackcmeanspresegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core) </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dstack-cmeans-presegment</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8563"></a>Description:</h4><p·class="description">This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram·and·then·writes·the·probability·mapping·for·thr·original·intensity·values</p><h4><a·name="idp8565"></a>Options:</h4><h4><a·name="idp8566"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-probmap=(required,·output);·string</span></dt><dd><p>Save·probability·map·to·this·file</p></dd></dl></div><h4><a·name="idp8577"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8628"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--histogram-thresh=5;·float·in·[0,·50]</span></dt><dd><p>Percent·of·the·extrem·parts·of·the·histogram·to·be·collapsed·into·the·respective·last·histogram·bin.</p></dd><dt><span·class="term">-C,·--classes=kmeans:nc=3;·factory</span></dt><dd><p>C-means·class·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd></dl></div><h4><a·name="idp8639"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8645"></a>Example:</h4><p>Run·the·program·over·images·imageXXXX.png·with·the·sparse·histogram,·threshold·the·lower·5%·bins·(if·available),·run·cmeans·with·three·classes·on·the·non-zero·pixels.</p><pre·class="screen">mia-2dimagestack-cmeans·-i·image0000.png·-o·cmeans,txt·--histogram-tresh=5·--classes·3</pre><h4><a·name="idp8648"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dstackcmeanspresegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core) </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dstack-cmeans-presegment</td></tr></table></div></body></html>
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6 mia-2dimagestack-cmeans·{-i·io}·{-o·string}·[·options·...]6 mia-2dimagestack-cmeans·{-i·io}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then8 This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then
9 runs·a·c-means·classification·over·the·histogram·and·then·writes·the9 runs·a·c-means·classification·over·the·histogram·and·then·writes·the
10 probability·mapping·for·thr·original·intensity·values10 probability·mapping·for·thr·original·intensity·values
11 Options:11 Options:
12 File-IO12 File-IO
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:14 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
15 ······2dimage/io15 ······2dimage/io
16 ··-o,·--out-probmap=(required,·output);·string16 ··-o,·--out-probmap=(required,·output);·string
17 ······Save·probability·map·to·this·file17 ······Save·probability·map·to·this·file
18 Help·&·Info18 Help·&·Info
19 ··-V,·--verbose=warning;·dict19 ··-V,·--verbose=warning;·dict
20 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.20 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagestats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimageseriesmaximumintensityprojection.html"·title="mia-2dimageseries-maximum-intensity-projection"><link·rel="next"·href="Secmia2dlerp.html"·title="mia-2dlerp"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagestats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimageseriesmaximumintensityprojection.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dlerp.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagestats"></a>mia-2dimagestats</h3></div></div></div><h4><a·name="idp2192"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagestats</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dimagestats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimageseriesmaximumintensityprojection.html"·title="mia-2dimageseries-maximum-intensity-projection"><link·rel="next"·href="Secmia2dlerp.html"·title="mia-2dlerp"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dimagestats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimageseriesmaximumintensityprojection.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dlerp.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dimagestats"></a>mia-2dimagestats</h3></div></div></div><h4><a·name="idp2192"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dimagestats</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2199"></a>Description:</h4><p·class="description">This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·and·Median·Average·Distance·of·the·intensity·values.·The·program·allows·one·to·set·a·lower·threshold·and·to·cut·off·a·percentage·of·the·high·intensity·pixels</p><h4><a·name="idp2201"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image·to·be·analyzed.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--thresh=10;·float</span></dt><dd><p>intensity·thresh·to·ignore</p></dd><dt><span·class="term">-g,·--high-thresh=0.05;·float</span></dt><dd><p>upper·histogram·percentage·to·ignore</p></dd><dt><span·class="term">--use-histogram</span></dt><dd><p>Use·a·histogram·to·accumulate·statistics</p></dd></dl></div><h4><a·name="idp2220"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2271"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2277"></a>Example:</h4><p>Evaluate·the·statistics·of·image·input.png.·Don't·include·the·upper·1%·of·intensities·in·the·statistics.·The·result·is·written·to·stdout</p><pre·class="screen">mia-2dimagestats·-i·input.png·-g·1</pre><h4><a·name="idp2280"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimageseriesmaximumintensityprojection.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dlerp.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimageseries-maximum-intensity-projection </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dlerp</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2199"></a>Description:</h4><p·class="description">This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·and·Median·Average·Distance·of·the·intensity·values.·The·program·allows·one·to·set·a·lower·threshold·and·to·cut·off·a·percentage·of·the·high·intensity·pixels</p><h4><a·name="idp2201"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image·to·be·analyzed.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--thresh=10;·float</span></dt><dd><p>intensity·thresh·to·ignore</p></dd><dt><span·class="term">-g,·--high-thresh=0.05;·float</span></dt><dd><p>upper·histogram·percentage·to·ignore</p></dd><dt><span·class="term">--use-histogram</span></dt><dd><p>Use·a·histogram·to·accumulate·statistics</p></dd></dl></div><h4><a·name="idp2220"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2271"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2277"></a>Example:</h4><p>Evaluate·the·statistics·of·image·input.png.·Don't·include·the·upper·1%·of·intensities·in·the·statistics.·The·result·is·written·to·stdout</p><pre·class="screen">mia-2dimagestats·-i·input.png·-g·1</pre><h4><a·name="idp2280"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimageseriesmaximumintensityprojection.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dlerp.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimageseries-maximum-intensity-projection </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dlerp</td></tr></table></div></body></html>
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6 mia-2dimagestats·{-i·io}·[·options·...]6 mia-2dimagestats·{-i·io}·[·options·...]
7 Description:7 Description:
8 This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,8 This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,
9 Variation,·Median,·and·Median·Average·Distance·of·the·intensity·values.·The9 Variation,·Median,·and·Median·Average·Distance·of·the·intensity·values.·The
10 program·allows·one·to·set·a·lower·threshold·and·to·cut·off·a·percentage·of·the10 program·allows·one·to·set·a·lower·threshold·and·to·cut·off·a·percentage·of·the
11 high·intensity·pixels11 high·intensity·pixels
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·image·to·be·analyzed.·For·supported·file·types·see·Plugin_type:14 ······input·image·to·be·analyzed.·For·supported·file·types·see·Plugin_type:
15 ······2dimage/io15 ······2dimage/io
16 ··-t,·--thresh=10;·float16 ··-t,·--thresh=10;·float
17 ······intensity·thresh·to·ignore17 ······intensity·thresh·to·ignore
18 ··-g,·--high-thresh=0.05;·float18 ··-g,·--high-thresh=0.05;·float
19 ······upper·histogram·percentage·to·ignore19 ······upper·histogram·percentage·to·ignore
20 ··--use-histogram20 ··--use-histogram
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dlerp</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagestats.html"·title="mia-2dimagestats"><link·rel="next"·href="Secmia2dmultiimagevar.html"·title="mia-2dmultiimagevar"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dlerp</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagestats.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimagevar.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dlerp"></a>mia-2dlerp</h3></div></div></div><h4><a·name="idp2284"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dlerp</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-p·<em·class="replaceable"><code>vfloat</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dlerp</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dimagestats.html"·title="mia-2dimagestats"><link·rel="next"·href="Secmia2dmultiimagevar.html"·title="mia-2dmultiimagevar"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dlerp</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagestats.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimagevar.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dlerp"></a>mia-2dlerp</h3></div></div></div><h4><a·name="idp2284"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dlerp</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-p·<em·class="replaceable"><code>vfloat</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2297"></a>Description:</h4><p·class="description">Merge·two·images·by·pixel-wise·linearly·combining·their·intensities.</p><h4><a·name="idp2299"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--first=(input,·required);·io</span></dt><dd><p>first·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--second=(input,·requi[·...·truncated·by·diffoscope;·len:·3,·SHA:·b1f51a511f1da0cd348b8f8598db32e61cb963e5fc69e2b41485bf99590ed75a·...·]);·io</span></dt><dd><p>second·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--positions=(required);·vfloat</span></dt><dd><p>image·series·positions·(first,·target,·second)</p></dd></dl></div><h4><a·name="idp2320"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2371"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2377"></a>Test</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--selftest=(</span></dt><dd><p>run·a·self·test·of·the·program</p></dd></dl></div><h4><a·name="idp2383"></a>Example:</h4><p>Combine·image·inputA.v·and·inputB.v·by·using·position·coordinates·4,·7,·and·9.·This·means·the·output·pixel·values·will·be·evaluated·according·to3 ········...]</p></div><h4><a·name="idp2297"></a>Description:</h4><p·class="description">Merge·two·images·by·pixel-wise·linearly·combining·their·intensities.</p><h4><a·name="idp2299"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--first=(required,·input);·io</span></dt><dd><p>first·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-2,·--second=(required,·in[·...·truncated·by·diffoscope;·len:·3,·SHA:·373cb2c6d4fe2778441d4f0266505b699fa518d002e5793b87f9b48836de3f62·...·]);·io</span></dt><dd><p>second·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--positions=(required);·vfloat</span></dt><dd><p>image·series·positions·(first,·target,·second)</p></dd></dl></div><h4><a·name="idp2320"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2371"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2377"></a>Test</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--selftest=(</span></dt><dd><p>run·a·self·test·of·the·program</p></dd></dl></div><h4><a·name="idp2383"></a>Example:</h4><p>Combine·image·inputA.v·and·inputB.v·by·using·position·coordinates·4,·7,·and·9.·This·means·the·output·pixel·values·will·be·evaluated·according·to
  
4 ····(9-7)/(9-4)·*·A·+·(7-4)/(9-4)·*·B··4 ····(9-7)/(9-4)·*·A·+·(7-4)/(9-4)·*·B··
  
5 The·result·image·will·be·written·to·output.v</p><pre·class="screen">mia-2dlerp·-1·inputA.v·-2·inputB.v·-p·4,7,9·-o·output.v</pre><h4><a·name="idp2386"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagestats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimagevar.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagestats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmultiimagevar</td></tr></table></div></body></html>5 The·result·image·will·be·written·to·output.v</p><pre·class="screen">mia-2dlerp·-1·inputA.v·-2·inputB.v·-p·4,7,9·-o·output.v</pre><h4><a·name="idp2386"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagestats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmultiimagevar.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagestats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmultiimagevar</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dlerp4 mia-2dlerp
5 Sysnopis:5 Sysnopis:
6 mia-2dlerp·{-1·io}·{-2·io}·{-o·io}·{-p·vfloat}·[·options·...]6 mia-2dlerp·{-1·io}·{-2·io}·{-o·io}·{-p·vfloat}·[·options·...]
7 Description:7 Description:
8 Merge·two·images·by·pixel-wise·linearly·combining·their·intensities.8 Merge·two·images·by·pixel-wise·linearly·combining·their·intensities.
9 Options:9 Options:
10 ··-1,·--first=(input,·required);·io10 ··-1,·--first=(required,·input);·io
11 ······first·input·image·.·For·supported·file·types·see·Plugin_type:_2dimage/io11 ······first·input·image·.·For·supported·file·types·see·Plugin_type:_2dimage/io
12 ··-2,·--second=(input,·required);·io12 ··-2,·--second=(required,·input);·io
13 ······second·input·image·.·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······second·input·image·.·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·vector·field.·For·supported·file·types·see·Plugin_type:_2dimage/io15 ······output·vector·field.·For·supported·file·types·see·Plugin_type:_2dimage/io
16 ··-p,·--positions=(required);·vfloat16 ··-p,·--positions=(required);·vfloat
17 ······image·series·positions·(first,·target,·second)17 ······image·series·positions·(first,·target,·second)
18 Help·&·Info18 Help·&·Info
19 ··-V,·--verbose=warning;·dict19 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmany2one-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dgroundtruthreg.html"·title="mia-2dgroundtruthreg"><link·rel="next"·href="Secmia2dmyoicafull.html"·title="mia-2dmyoica-full"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmany2one-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dgroundtruthreg.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicafull.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmany2onenonrigid"></a>mia-2dmany2one-nonrigid</h3></div></div></div><h4><a·name="idp4303"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmany2one-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmany2one-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dgroundtruthreg.html"·title="mia-2dgroundtruthreg"><link·rel="next"·href="Secmia2dmyoicafull.html"·title="mia-2dmyoica-full"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmany2one-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dgroundtruthreg.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicafull.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmany2onenonrigid"></a>mia-2dmany2one-nonrigid</h3></div></div></div><h4><a·name="idp4303"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmany2one-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp4315"></a>Description:</h4><p·class="description">This·program·registers·all·images·of·a·conscutively·numbered·set·of·images·to·one·common·user·defined·reference.</p><h4><a·name="idp4317"></a>Options:</h4><h4><a·name="idp4318"></a>7 ········...]</p></div><h4><a·name="idp4315"></a>Description:</h4><p·class="description">This·program·registers·all·images·of·a·conscutively·numbered·set·of·images·to·one·common·user·defined·reference.</p><h4><a·name="idp4317"></a>Options:</h4><h4><a·name="idp4318"></a>
8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>file·name·for·registered·images,·numbering·and·pattern·are·deducted·from·the·input·data</p></dd></dl></div><h4><a·name="idp4328"></a>8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>file·name·for·registered·images,·numbering·and·pattern·are·deducted·from·the·input·data</p></dd></dl></div><h4><a·name="idp4328"></a>
9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·registration·of·these·images·at·the·beginning·of·the·series</p></dd></dl></div><h4><a·name="idp4351"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4402"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4408"></a>Example:</h4><p>Register·the·image·series·given·by·images·'inputXXXX.png'·to·reference·image·30.·Skip·two·images·at·the·beginning·and·using·mutual·information·as·cost·function,·and·penalize·the·transformation·by·divcurl·with·weight·5.·Store·the·result·in·'registeredXXXX.png'.</p><pre·class="screen">mia-2dmany2one-nonrigid···-i·input0000.png·-o·registered%04d.png·-k·2·-r·30·image:cost=mi·divcurl:weight=5</pre><h4><a·name="idp4411"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dgroundtruthreg.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicafull.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dgroundtruthreg </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-full</td></tr></table></div></body></html>9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·registration·of·these·images·at·the·beginning·of·the·series</p></dd></dl></div><h4><a·name="idp4351"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4402"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4408"></a>Example:</h4><p>Register·the·image·series·given·by·images·'inputXXXX.png'·to·reference·image·30.·Skip·two·images·at·the·beginning·and·using·mutual·information·as·cost·function,·and·penalize·the·transformation·by·divcurl·with·weight·5.·Store·the·result·in·'registeredXXXX.png'.</p><pre·class="screen">mia-2dmany2one-nonrigid···-i·input0000.png·-o·registered%04d.png·-k·2·-r·30·image:cost=mi·divcurl:weight=5</pre><h4><a·name="idp4411"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dgroundtruthreg.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicafull.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dgroundtruthreg </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-full</td></tr></table></div></body></html>
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6 mia-2dmany2one-nonrigid·{-i·string}·{-o·string}·[·options·...]·[·Plugin_type:6 mia-2dmany2one-nonrigid·{-i·string}·{-o·string}·[·options·...]·[·Plugin_type:
7 2dimage/fullcost·...]7 2dimage/fullcost·...]
8 Description:8 Description:
9 This·program·registers·all·images·of·a·conscutively·numbered·set·of·images·to9 This·program·registers·all·images·of·a·conscutively·numbered·set·of·images·to
10 one·common·user·defined·reference.10 one·common·user·defined·reference.
11 Options:11 Options:
12 ·File-IO12 ·File-IO
13 ··-i,·--in-file=(input,·required);·string13 ··-i,·--in-file=(required,·input);·string
14 ······input·perfusion·data·set14 ······input·perfusion·data·set
15 ··-o,·--out-file=(required,·output);·string15 ··-o,·--out-file=(required,·output);·string
16 ······file·name·for·registered·images,·numbering·and·pattern·are·deducted·from16 ······file·name·for·registered·images,·numbering·and·pattern·are·deducted·from
17 ······the·input·data17 ······the·input·data
18 ·Registration18 ·Registration
19 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING19 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING
20 ······Optimizer·used·for·minimization20 ······Optimizer·used·for·minimization
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmultiimageto3d</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia2dimageselect.html"·title="mia-2dimageselect"><link·rel="next"·href="Secmia2dto3dimage.html"·title="mia-2dto3dimage"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmultiimageto3d</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimageselect.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimage.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmultiimageto3d"></a>mia-2dmultiimageto3d</h3></div></div></div><h4><a·name="idp144"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmultiimageto3d</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmultiimageto3d</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia2dimageselect.html"·title="mia-2dimageselect"><link·rel="next"·href="Secmia2dto3dimage.html"·title="mia-2dto3dimage"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmultiimageto3d</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimageselect.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimage.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmultiimageto3d"></a>mia-2dmultiimageto3d</h3></div></div></div><h4><a·name="idp144"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmultiimageto3d</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp153"></a>Description:</h4><p·class="description">This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image.</p><h4><a·name="idp155"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp167"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp218"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp224"></a>Example:</h4><p>Convert·an·series·of·images·stored·in·a·2D·image·container·multiimage2d.v·to·a·3D·image·image3d.v.</p><pre·class="screen">mia-2dmultiimageto3d·-i·multiimage2d.v·-o·image3d.v</pre><h4><a·name="idp227"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimageselect.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimage.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimageselect </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dto3dimage</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp153"></a>Description:</h4><p·class="description">This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image.</p><h4><a·name="idp155"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp167"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp218"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp224"></a>Example:</h4><p>Convert·an·series·of·images·stored·in·a·2D·image·container·multiimage2d.v·to·a·3D·image·image3d.v.</p><pre·class="screen">mia-2dmultiimageto3d·-i·multiimage2d.v·-o·image3d.v</pre><h4><a·name="idp227"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimageselect.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimage.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimageselect </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dto3dimage</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dmultiimageto3d4 mia-2dmultiimageto3d
5 Sysnopis:5 Sysnopis:
6 mia-2dmultiimageto3d·{-i·io}·{-o·io}·[·options·...]6 mia-2dmultiimageto3d·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image.8 This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·images.·For·supported·file·types·see·Plugin_type:_2dimage/io11 ······input·images.·For·supported·file·types·see·Plugin_type:_2dimage/io
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·image.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······output·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 Help·&·Info14 Help·&·Info
15 ··-V,·--verbose=warning;·dict15 ··-V,·--verbose=warning;·dict
16 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.16 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
17 ······Supported·priorities·starting·at·lowest·level·are:17 ······Supported·priorities·starting·at·lowest·level·are:
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./usr/share/doc/mia-2.4/userref/Secmia2dmyocardica.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyocard-ica</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="next"·href="Secmia2dmyocardicaseries.html"·title="mia-2dmyocard-icaseries"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyocard-ica</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecToolsforMyocardialPerfusionAnalysis.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyocardicaseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyocardica"></a>mia-2dmyocard-ica</h3></div></div></div><h4><a·name="idp6455"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyocard-ica</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyocard-ica</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="next"·href="Secmia2dmyocardicaseries.html"·title="mia-2dmyocard-icaseries"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyocard-ica</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecToolsforMyocardialPerfusionAnalysis.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyocardicaseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyocardica"></a>mia-2dmyocard-ica</h3></div></div></div><h4><a·name="idp6455"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyocard-ica</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp6462"></a>Description:</h4><p·class="description">This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·to·create·a·segmentation·set·and·use·mia-2dmyoica-nonrigid.·If·the·input·data·is·given·by·means·of·a·segmentation·set,·then·on·can·also·use·mia-2dmyocard-icaseries.3 ········...]</p></div><h4><a·name="idp6462"></a>Description:</h4><p·class="description">This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·to·create·a·segmentation·set·and·use·mia-2dmyoica-nonrigid.·If·the·input·data·is·given·by·means·of·a·segmentation·set,·then·on·can·also·use·mia-2dmyocard-icaseries.
4 This·program·is·essentially·used·to·test·different·options·on·how·to·run·the·ICA·forreference·image·creation.</p><h4><a·name="idp6464"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-base=(input,·required);·io</span></dt><dd><p>input·file·name·ofolloing·pattern·nameXXXX.ext·X=numbers.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">--coefs=STRING</span></dt><dd><p>output·mixing·coefficients·to·this·file</p></dd><dt><span·class="term">-o,·--out-base=(output);·string</span></dt><dd><p>output·file·name·base</p></dd><dt><span·class="term">-t,·--type=exr;·set</span></dt><dd><p>output·file·type<td·align="left"·valign="top">·Supported·values·are:(-,·@,·BMP,·DCM,·EXR,·JPEG,·JPG,·PNG,·RAW,·TIF,·TIFF,·V,·VISTA,·bmp,·dcm,·exr,·jpeg,·jpg,·png,·raw,·tif,·tiff,·v,·vista,·)</td></p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-e,·--end=60;·ulong</span></dt><dd><p>last·image·in·series</p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>nr.·of·components,·0=estimate·automatically</p></dd><dt><span·class="term">-m,·--strip-mean</span></dt><dd><p>strip·mean·image·from·series</p></dd><dt><span·class="term">-f,·--save-features=STRING</span></dt><dd><p>save·feature·image</p></dd><dt><span·class="term">-p,·--strip-periodic</span></dt><dd><p>strip·only·periodic·component</p></dd><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-x,·--max-ica-iterations=0;·int</span></dt><dd><p>max·ICA·solver·iterations</p></dd><dt><span·class="term">-n,·--ica-normalize</span></dt><dd><p>ica_normalize·feature·images</p></dd><dt><span·class="term">--all-features=STRING</span></dt><dd><p>save·all·feature·images·to</p></dd><dt><span·class="term">-L,·--LV-crop-amp=0;·float</span></dt><dd><p>LV·crop·mask·amplification,·0.0·=·don't·crop</p></dd></dl></div><h4><a·name="idp6529"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6580"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6586"></a>Example:</h4><p>Evaluate·the·synthetic·references·from·images·imageXXXX.exr·and·save·them·to·refXXXX.exr·by·using·five·independend·components,·mean·stripping,·normalizing,·and·skipping·2·images.</p><pre·class="screen">mia-2dmyocard-ica·-i·imageXXXX.exr·-o·ref·-k·2·-C·5·-m·-n</pre><h4><a·name="idp6589"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecToolsforMyocardialPerfusionAnalysis.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyocardicaseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Tools·for·Myocardial·Perfusion·Analysis </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyocard-icaseries</td></tr></table></div></body></html>4 This·program·is·essentially·used·to·test·different·options·on·how·to·run·the·ICA·forreference·image·creation.</p><h4><a·name="idp6464"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-base=(required,·input);·io</span></dt><dd><p>input·file·name·ofolloing·pattern·nameXXXX.ext·X=numbers.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">--coefs=STRING</span></dt><dd><p>output·mixing·coefficients·to·this·file</p></dd><dt><span·class="term">-o,·--out-base=(output);·string</span></dt><dd><p>output·file·name·base</p></dd><dt><span·class="term">-t,·--type=exr;·set</span></dt><dd><p>output·file·type<td·align="left"·valign="top">·Supported·values·are:(-,·@,·BMP,·DCM,·EXR,·JPEG,·JPG,·PNG,·RAW,·TIF,·TIFF,·V,·VISTA,·bmp,·dcm,·exr,·jpeg,·jpg,·png,·raw,·tif,·tiff,·v,·vista,·)</td></p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-e,·--end=60;·ulong</span></dt><dd><p>last·image·in·series</p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>nr.·of·components,·0=estimate·automatically</p></dd><dt><span·class="term">-m,·--strip-mean</span></dt><dd><p>strip·mean·image·from·series</p></dd><dt><span·class="term">-f,·--save-features=STRING</span></dt><dd><p>save·feature·image</p></dd><dt><span·class="term">-p,·--strip-periodic</span></dt><dd><p>strip·only·periodic·component</p></dd><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-x,·--max-ica-iterations=0;·int</span></dt><dd><p>max·ICA·solver·iterations</p></dd><dt><span·class="term">-n,·--ica-normalize</span></dt><dd><p>ica_normalize·feature·images</p></dd><dt><span·class="term">--all-features=STRING</span></dt><dd><p>save·all·feature·images·to</p></dd><dt><span·class="term">-L,·--LV-crop-amp=0;·float</span></dt><dd><p>LV·crop·mask·amplification,·0.0·=·don't·crop</p></dd></dl></div><h4><a·name="idp6529"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6580"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6586"></a>Example:</h4><p>Evaluate·the·synthetic·references·from·images·imageXXXX.exr·and·save·them·to·refXXXX.exr·by·using·five·independend·components,·mean·stripping,·normalizing,·and·skipping·2·images.</p><pre·class="screen">mia-2dmyocard-ica·-i·imageXXXX.exr·-o·ref·-k·2·-C·5·-m·-n</pre><h4><a·name="idp6589"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecToolsforMyocardialPerfusionAnalysis.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyocardicaseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Tools·for·Myocardial·Perfusion·Analysis </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyocard-icaseries</td></tr></table></div></body></html>
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyocard-icaseries</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyocardica.html"·title="mia-2dmyocard-ica"><link·rel="next"·href="Secmia2dmyoseriescompdice.html"·title="mia-2dmyoseries-compdice"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyocard-icaseries</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardica.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriescompdice.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyocardicaseries"></a>mia-2dmyocard-icaseries</h3></div></div></div><h4><a·name="idp6593"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyocard-icaseries</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyocard-icaseries</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyocardica.html"·title="mia-2dmyocard-ica"><link·rel="next"·href="Secmia2dmyoseriescompdice.html"·title="mia-2dmyoseries-compdice"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyocard-icaseries</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardica.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriescompdice.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyocardicaseries"></a>mia-2dmyocard-icaseries</h3></div></div></div><h4><a·name="idp6593"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyocard-icaseries</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp6600"></a>Description:</h4><p·class="description">This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this·program·is·essentially·the·same·without·the·registration·bits.</p><h4><a·name="idp6602"></a>Options:</h4><h4><a·name="idp6603"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-r,·--references=(output);·string</span></dt><dd><p>File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images.</p></dd><dt><span·class="term">-c,·--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·the·features·images·resulting·from·the·ICA·and·some·intermediate·images·used·for·the·RV-LV·segmentation·with·the·given·file·name·base·to·PNG·files.·Also·save·the·coefficients·of·the·initial·best·and·the·final·IC·mixing·matrix.</p></dd></dl></div><h4><a·name="idp6621"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6672"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=1.4;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp6721"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6727"></a>Example:</h4><p>Evaluate·the·synthetic·references·from·set·segment.set·and·save·them·to·refXXXX.???·by·using·five·independend·components,·and·skipping·2·images.·Per·default·a·bounding·box·around·the·LV·will·be·segmented·and·scaled·by·1.4·and·the·cropped·images·will·be·saved·to·cropXXXX.???·and·a·segmentation·set·cropped.set··is·created.·The·image·file·type·???·is·deducted·from·the·input·images·in·segment.set.</p><pre·class="screen">mia-2dmyocard-icaseries·-i·segment.set·-r·ref·-o·ref·-k·2·-C·5</pre><h4><a·name="idp6730"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardica.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriescompdice.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyocard-ica </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoseries-compdice</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp6600"></a>Description:</h4><p·class="description">This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this·program·is·essentially·the·same·without·the·registration·bits.</p><h4><a·name="idp6602"></a>Options:</h4><h4><a·name="idp6603"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-r,·--references=(output);·string</span></dt><dd><p>File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images.</p></dd><dt><span·class="term">-c,·--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·the·features·images·resulting·from·the·ICA·and·some·intermediate·images·used·for·the·RV-LV·segmentation·with·the·given·file·name·base·to·PNG·files.·Also·save·the·coefficients·of·the·initial·best·and·the·final·IC·mixing·matrix.</p></dd></dl></div><h4><a·name="idp6621"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6672"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=1.4;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp6721"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6727"></a>Example:</h4><p>Evaluate·the·synthetic·references·from·set·segment.set·and·save·them·to·refXXXX.???·by·using·five·independend·components,·and·skipping·2·images.·Per·default·a·bounding·box·around·the·LV·will·be·segmented·and·scaled·by·1.4·and·the·cropped·images·will·be·saved·to·cropXXXX.???·and·a·segmentation·set·cropped.set··is·created.·The·image·file·type·???·is·deducted·from·the·input·images·in·segment.set.</p><pre·class="screen">mia-2dmyocard-icaseries·-i·segment.set·-r·ref·-o·ref·-k·2·-C·5</pre><h4><a·name="idp6730"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardica.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriescompdice.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyocard-ica </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoseries-compdice</td></tr></table></div></body></html>
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8 This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images8 This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images
9 given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be9 given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be
10 used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full10 used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full
11 motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this11 motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this
12 program·is·essentially·the·same·without·the·registration·bits.12 program·is·essentially·the·same·without·the·registration·bits.
13 Options:13 Options:
14 File-IO14 File-IO
15 ··-i,·--in-file=(input,·required);·string15 ··-i,·--in-file=(required,·input);·string
16 ······input·perfusion·data·set16 ······input·perfusion·data·set
17 ··-r,·--references=(output);·string17 ··-r,·--references=(output);·string
18 ······File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme18 ······File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme
19 ······are·taken·from·the·input·images.19 ······are·taken·from·the·input·images.
20 ··-c,·--save-cropped=(output);·string20 ··-c,·--save-cropped=(output);·string
21 ······save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will21 ······save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will
22 ······use·the·stem·of·the·name·as·file·name·base22 ······use·the·stem·of·the·name·as·file·name·base
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyocard-segment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecWorkinprogress.html"·title="Work·in·progress"><link·rel="prev"·href="SecWorkinprogress.html"·title="Work·in·progress"><link·rel="next"·href="plugins.html"·title="Chapter 3. Plugin·Reference"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyocard-segment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecWorkinprogress.html">Prev</a> </td><th·width="60%"·align="center">Work·in·progress</th><td·width="20%"·align="right"> <a·accesskey="n"·href="plugins.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyocardsegment"></a>mia-2dmyocard-segment</h3></div></div></div><h4><a·name="idp15159"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyocard-segment</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyocard-segment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecWorkinprogress.html"·title="Work·in·progress"><link·rel="prev"·href="SecWorkinprogress.html"·title="Work·in·progress"><link·rel="next"·href="plugins.html"·title="Chapter 3. Plugin·Reference"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyocard-segment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecWorkinprogress.html">Prev</a> </td><th·width="60%"·align="center">Work·in·progress</th><td·width="20%"·align="right"> <a·accesskey="n"·href="plugins.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyocardsegment"></a>mia-2dmyocard-segment</h3></div></div></div><h4><a·name="idp15159"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyocard-segment</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp15168"></a>Description:</h4><p·class="description">This·program·is·work·in·progress</p><h4><a·name="idp15170"></a>Options:</h4><h4><a·name="idp15171"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·myocardial·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-f,·--save-features=(output);·string</span></dt><dd><p>save·ICA·features·to·files·with·this·name·base</p></dd></dl></div><h4><a·name="idp15186"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp15237"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation·testing·4·and·5</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd></dl></div><h4><a·name="idp15264"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp15270"></a>Example:</h4><p>Example</p><pre·class="screen">mia-2dmyocard-segment·Example</pre><h4><a·name="idp15273"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecWorkinprogress.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecWorkinprogress.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="plugins.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Work·in·progress </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Chapter 3. Plugin·Reference</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp15168"></a>Description:</h4><p·class="description">This·program·is·work·in·progress</p><h4><a·name="idp15170"></a>Options:</h4><h4><a·name="idp15171"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·myocardial·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-f,·--save-features=(output);·string</span></dt><dd><p>save·ICA·features·to·files·with·this·name·base</p></dd></dl></div><h4><a·name="idp15186"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp15237"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation·testing·4·and·5</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd></dl></div><h4><a·name="idp15264"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp15270"></a>Example:</h4><p>Example</p><pre·class="screen">mia-2dmyocard-segment·Example</pre><h4><a·name="idp15273"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecWorkinprogress.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecWorkinprogress.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="plugins.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Work·in·progress </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Chapter 3. Plugin·Reference</td></tr></table></div></body></html>
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4 mia-2dmyocard-segment4 mia-2dmyocard-segment
5 Sysnopis:5 Sysnopis:
6 mia-2dmyocard-segment·{-i·string}·{-o·io}·[·options·...]6 mia-2dmyocard-segment·{-i·string}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·work·in·progress8 This·program·is·work·in·progress
9 Options:9 Options:
10 File-IO10 File-IO
11 ··-i,·--in-file=(input,·required);·string11 ··-i,·--in-file=(required,·input);·string
12 ······input·perfusion·data·set12 ······input·perfusion·data·set
13 ··-o,·--out-file=(required,·output);·io13 ··-o,·--out-file=(required,·output);·io
14 ······output·myocardial·mask.·For·supported·file·types·see·Plugin_type:14 ······output·myocardial·mask.·For·supported·file·types·see·Plugin_type:
15 ······2dimage/io15 ······2dimage/io
16 ··-f,·--save-features=(output);·string16 ··-f,·--save-features=(output);·string
17 ······save·ICA·features·to·files·with·this·name·base17 ······save·ICA·features·to·files·with·this·name·base
18 Help·&·Info18 Help·&·Info
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-full</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmany2onenonrigid.html"·title="mia-2dmany2one-nonrigid"><link·rel="next"·href="Secmia2dmyoicanonrigid.html"·title="mia-2dmyoica-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-full</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmany2onenonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicafull"></a>mia-2dmyoica-full</h3></div></div></div><h4><a·name="idp4415"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-full</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-full</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmany2onenonrigid.html"·title="mia-2dmany2one-nonrigid"><link·rel="next"·href="Secmia2dmyoicanonrigid.html"·title="mia-2dmyoica-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-full</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmany2onenonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicafull"></a>mia-2dmyoica-full</h3></div></div></div><h4><a·name="idp4415"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-full</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp4424"></a>Description:</h4><p·class="description">This·program·implements·the·2D·version·of·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis",·Medical·Image·Analysis,·2012.</a></p><p·class="description">·The·software·may·first·run·a·linear·registration·and·then·a·non-linear·registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all·registrations·in·parallel.</p><h4><a·name="idp4428"></a>Options:</h4><h4><a·name="idp4429"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=STRING</span></dt><dd><p>File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.</p></dd><dt><span·class="term">--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd><dt><span·class="term">--save-refs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·the·reference·images·to·files·with·the·given·name·base</p></dd><dt><span·class="term">--save-regs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp4459"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4510"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.·A·value·0.0·forces·the·series·to·be·identified·as·acquired·with·initial·breath·hold.</p></dd></dl></div><h4><a·name="idp4563"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4569"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-L,·--linear-optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization·of·the·linear·registration·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">--linear-transform=affine;·factory</span></dt><dd><p>linear·transform·to·be·used·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-O,·--non-linear-optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization·in·the·non-linear·registration.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass.</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>Cofficient·rate·divider·for·each·pass.</p></dd><dt><span·class="term">-d,·--start-divcurl=10000;·double</span></dt><dd><p>Start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass.</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>Divcurl·weight·scaling·with·each·new·pass.</p></dd><dt><span·class="term">-R,·--reference=-1;·int</span></dt><dd><p>Global·reference·all·image·should·be·aligned·to.·If·set·to·a·non-negative·value,·the·images·will·be·aligned·to·this·references,·and·the·cropped·output·image·date·will·be·injected·into·the·original·images.·Leave·at·-1·if·you·don't·care.·In·this·case·all·images·with·be·registered·to·a·mean·position·of·the·movement</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost,·do·not·specify·the·src·and·ref·parameters,·these·will·be·set·by·the·program.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-p,·--linear-passes=3;·ulong</span></dt><dd><p>linear·registration·passes·(0·to·disable)</p></dd><dt><span·class="term">-P,·--nonlinear-passes=3;·ulong</span></dt><dd><p>non-linear·registration·passes·(0·to·disable)</p></dd></dl></div><h4><a·name="idp4623"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-full···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp4626"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmany2onenonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmany2one-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-nonrigid</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp4424"></a>Description:</h4><p·class="description">This·program·implements·the·2D·version·of·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis",·Medical·Image·Analysis,·2012.</a></p><p·class="description">·The·software·may·first·run·a·linear·registration·and·then·a·non-linear·registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all·registrations·in·parallel.</p><h4><a·name="idp4428"></a>Options:</h4><h4><a·name="idp4429"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=STRING</span></dt><dd><p>File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.</p></dd><dt><span·class="term">--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd><dt><span·class="term">--save-refs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·the·reference·images·to·files·with·the·given·name·base</p></dd><dt><span·class="term">--save-regs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp4459"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4510"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.·A·value·0.0·forces·the·series·to·be·identified·as·acquired·with·initial·breath·hold.</p></dd></dl></div><h4><a·name="idp4563"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4569"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-L,·--linear-optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization·of·the·linear·registration·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">--linear-transform=affine;·factory</span></dt><dd><p>linear·transform·to·be·used·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-O,·--non-linear-optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization·in·the·non-linear·registration.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass.</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>Cofficient·rate·divider·for·each·pass.</p></dd><dt><span·class="term">-d,·--start-divcurl=10000;·double</span></dt><dd><p>Start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass.</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>Divcurl·weight·scaling·with·each·new·pass.</p></dd><dt><span·class="term">-R,·--reference=-1;·int</span></dt><dd><p>Global·reference·all·image·should·be·aligned·to.·If·set·to·a·non-negative·value,·the·images·will·be·aligned·to·this·references,·and·the·cropped·output·image·date·will·be·injected·into·the·original·images.·Leave·at·-1·if·you·don't·care.·In·this·case·all·images·with·be·registered·to·a·mean·position·of·the·movement</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost,·do·not·specify·the·src·and·ref·parameters,·these·will·be·set·by·the·program.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-p,·--linear-passes=3;·ulong</span></dt><dd><p>linear·registration·passes·(0·to·disable)</p></dd><dt><span·class="term">-P,·--nonlinear-passes=3;·ulong</span></dt><dd><p>non-linear·registration·passes·(0·to·disable)</p></dd></dl></div><h4><a·name="idp4623"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-full···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp4626"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmany2onenonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmany2one-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-nonrigid</td></tr></table></div></body></html>
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11 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using11 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using
12 Independent_Component_Analysis",_Medical_Image_Analysis,_2012.12 Independent_Component_Analysis",_Medical_Image_Analysis,_2012.
13 The·software·may·first·run·a·linear·registration·and·then·a·non-linear13 The·software·may·first·run·a·linear·registration·and·then·a·non-linear
14 registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all14 registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all
15 registrations·in·parallel.15 registrations·in·parallel.
16 Options:16 Options:
17 File-IO17 File-IO
18 ··-i,·--in-file=(input,·required);·string18 ··-i,·--in-file=(required,·input);·string
19 ······input·perfusion·data·set19 ······input·perfusion·data·set
20 ··-o,·--out-file=(required,·output);·string20 ··-o,·--out-file=(required,·output);·string
21 ······output·perfusion·data·set21 ······output·perfusion·data·set
22 ··-r,·--registered=STRING22 ··-r,·--registered=STRING
23 ······File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme23 ······File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme
24 ······are·taken·from·the·input·images·as·given·in·the·input·data·set.24 ······are·taken·from·the·input·images·as·given·in·the·input·data·set.
25 ··--save-cropped=(output);·string25 ··--save-cropped=(output);·string
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicafull.html"·title="mia-2dmyoica-full"><link·rel="next"·href="Secmia2dmyoicanonrigidparallel.html"·title="mia-2dmyoica-nonrigid-parallel"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicafull.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigidparallel.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicanonrigid"></a>mia-2dmyoica-nonrigid</h3></div></div></div><h4><a·name="idp4630"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicafull.html"·title="mia-2dmyoica-full"><link·rel="next"·href="Secmia2dmyoicanonrigidparallel.html"·title="mia-2dmyoica-nonrigid-parallel"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicafull.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigidparallel.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicanonrigid"></a>mia-2dmyoica-nonrigid</h3></div></div></div><h4><a·name="idp4630"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp4639"></a>Description:</h4><p·class="description">This·program·implements·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.</a></p><h4><a·name="idp4643"></a>Options:</h4><h4><a·name="idp4644"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd><dt><span·class="term">--save-cropped=STRING</span></dt><dd><p>save·cropped·set·to·this·file</p></dd><dt><span·class="term">--save-feature=STRING</span></dt><dd><p>save·the·features·images·resulting·from·the·ICA·and·some·intermediate·images·used·for·the·RV-LV·segmentation·with·the·given·file·name·base·to·PNG·files.·Also·save·the·coefficients·of·the·initial·best·and·the·final·IC·mixing·matrix.</p></dd><dt><span·class="term">--save-refs=STRING</span></dt><dd><p>save·synthetic·reference·images</p></dd><dt><span·class="term">--save-regs=STRING</span></dt><dd><p>save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp4674"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4725"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.</p></dd></dl></div><h4><a·name="idp4778"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4784"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-R,·--refiner=</span></dt><dd><p>optimizer·used·for·refinement·after·the·main·optimizer·was·called.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=10;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=5;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp4825"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-nonrigid···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp4828"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicafull.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigidparallel.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-full </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-nonrigid-parallel</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp4639"></a>Description:</h4><p·class="description">This·program·implements·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.</a></p><h4><a·name="idp4643"></a>Options:</h4><h4><a·name="idp4644"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd><dt><span·class="term">--save-cropped=STRING</span></dt><dd><p>save·cropped·set·to·this·file</p></dd><dt><span·class="term">--save-feature=STRING</span></dt><dd><p>save·the·features·images·resulting·from·the·ICA·and·some·intermediate·images·used·for·the·RV-LV·segmentation·with·the·given·file·name·base·to·PNG·files.·Also·save·the·coefficients·of·the·initial·best·and·the·final·IC·mixing·matrix.</p></dd><dt><span·class="term">--save-refs=STRING</span></dt><dd><p>save·synthetic·reference·images</p></dd><dt><span·class="term">--save-regs=STRING</span></dt><dd><p>save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp4674"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4725"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.</p></dd></dl></div><h4><a·name="idp4778"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4784"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-R,·--refiner=</span></dt><dd><p>optimizer·used·for·refinement·after·the·main·optimizer·was·called.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=10;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=5;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp4825"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-nonrigid···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp4828"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicafull.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigidparallel.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-full </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-nonrigid-parallel</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·implements·the·motion·compensation·algorithm·described·in8 This·program·implements·the·motion·compensation·algorithm·described·in
9 Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion9 Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion
10 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using10 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using
11 Independent_Component_Analysis"_Medical_Image_Analysis,_2012.11 Independent_Component_Analysis"_Medical_Image_Analysis,_2012.
12 Options:12 Options:
13 File-IO13 File-IO
14 ··-i,·--in-file=(input,·required);·string14 ··-i,·--in-file=(required,·input);·string
15 ······input·perfusion·data·set15 ······input·perfusion·data·set
16 ··-o,·--out-file=(required,·output);·string16 ··-o,·--out-file=(required,·output);·string
17 ······output·perfusion·data·set17 ······output·perfusion·data·set
18 ··-r,·--registered=reg;·stringSTRING18 ··-r,·--registered=reg;·stringSTRING
19 ······file·name·base·for·registered·fiels19 ······file·name·base·for·registered·fiels
20 ··--save-cropped=STRING20 ··--save-cropped=STRING
21 ······save·cropped·set·to·this·file21 ······save·cropped·set·to·this·file
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid2</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicanonrigidparallel.html"·title="mia-2dmyoica-nonrigid-parallel"><link·rel="next"·href="Secmia2dmyoicapgt.html"·title="mia-2dmyoicapgt"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-nonrigid2</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigidparallel.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicapgt.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicanonrigid2"></a>mia-2dmyoica-nonrigid2</h3></div></div></div><h4><a·name="idp5029"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-nonrigid2</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid2</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicanonrigidparallel.html"·title="mia-2dmyoica-nonrigid-parallel"><link·rel="next"·href="Secmia2dmyoicapgt.html"·title="mia-2dmyoicapgt"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-nonrigid2</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigidparallel.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicapgt.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicanonrigid2"></a>mia-2dmyoica-nonrigid2</h3></div></div></div><h4><a·name="idp5029"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-nonrigid2</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp5038"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·perfusion·image·series.In·each·pass,·first·an·ICA·analysis·is·run·to·estimate·and·eliminate·the·periodic·movement·and·create·reference·images·with·intensities·similar·to·the·corresponding·original·image.·Then·non-rigid·registration·is·run·using·the·an·"ssd·+·divcurl"·cost·model.·The·B-spline·c-rate·and·the·divcurl·cost·weight·are·changed·in·each·pass·according·to·given·parameters.In·the·first·pass·a·bounding·box·around·the·LV·myocardium·may·be·extractedto·speed·up·computation3 ········...]</p></div><h4><a·name="idp5038"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·perfusion·image·series.In·each·pass,·first·an·ICA·analysis·is·run·to·estimate·and·eliminate·the·periodic·movement·and·create·reference·images·with·intensities·similar·to·the·corresponding·original·image.·Then·non-rigid·registration·is·run·using·the·an·"ssd·+·divcurl"·cost·model.·The·B-spline·c-rate·and·the·divcurl·cost·weight·are·changed·in·each·pass·according·to·given·parameters.In·the·first·pass·a·bounding·box·around·the·LV·myocardium·may·be·extractedto·speed·up·computation
4 Special·note·to·this·implemnentation:·the·registration·is·always·run·from·the·original·images·to·avoid·the·accumulation·of·interpolation·errors.</p><h4><a·name="idp5040"></a>Options:</h4><h4><a·name="idp5041"></a>4 Special·note·to·this·implemnentation:·the·registration·is·always·run·from·the·original·images·to·avoid·the·accumulation·of·interpolation·errors.</p><h4><a·name="idp5040"></a>Options:</h4><h4><a·name="idp5041"></a>
5 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd><dt><span·class="term">--save-cropped=STRING</span></dt><dd><p>save·cropped·set·to·this·file</p></dd><dt><span·class="term">--save-feature=STRING</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd></dl></div><h4><a·name="idp5063"></a>5 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd><dt><span·class="term">--save-cropped=STRING</span></dt><dd><p>save·cropped·set·to·this·file</p></dd><dt><span·class="term">--save-feature=STRING</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd></dl></div><h4><a·name="idp5063"></a>
6 ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>don't·normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp5112"></a>6 ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>don't·normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp5112"></a>
7 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=32;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=20;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imageweight=1;·double</span></dt><dd><p>image·cost·weight</p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5152"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5203"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5209"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-nonrigid2···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5212"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigidparallel.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicapgt.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-nonrigid-parallel </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoicapgt</td></tr></table></div></body></html>7 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=32;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=20;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imageweight=1;·double</span></dt><dd><p>image·cost·weight</p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5152"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5203"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5209"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-nonrigid2···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5212"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigidparallel.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicapgt.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-nonrigid-parallel </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoicapgt</td></tr></table></div></body></html>
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12 "ssd·+·divcurl"·cost·model.·The·B-spline·c-rate·and·the·divcurl·cost·weight·are12 "ssd·+·divcurl"·cost·model.·The·B-spline·c-rate·and·the·divcurl·cost·weight·are
13 changed·in·each·pass·according·to·given·parameters.In·the·first·pass·a·bounding13 changed·in·each·pass·according·to·given·parameters.In·the·first·pass·a·bounding
14 box·around·the·LV·myocardium·may·be·extractedto·speed·up·computation·Special14 box·around·the·LV·myocardium·may·be·extractedto·speed·up·computation·Special
15 note·to·this·implemnentation:·the·registration·is·always·run·from·the·original15 note·to·this·implemnentation:·the·registration·is·always·run·from·the·original
16 images·to·avoid·the·accumulation·of·interpolation·errors.16 images·to·avoid·the·accumulation·of·interpolation·errors.
17 Options:17 Options:
18 ·File-IO18 ·File-IO
19 ··-i,·--in-file=(input,·required);·string19 ··-i,·--in-file=(required,·input);·string
20 ······input·perfusion·data·set20 ······input·perfusion·data·set
21 ··-o,·--out-file=(required,·output);·string21 ··-o,·--out-file=(required,·output);·string
22 ······output·perfusion·data·set22 ······output·perfusion·data·set
23 ··-r,·--registered=reg;·stringSTRING23 ··-r,·--registered=reg;·stringSTRING
24 ······file·name·base·for·registered·fiels24 ······file·name·base·for·registered·fiels
25 ··--save-cropped=STRING25 ··--save-cropped=STRING
26 ······save·cropped·set·to·this·file26 ······save·cropped·set·to·this·file
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid-parallel</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicanonrigid.html"·title="mia-2dmyoica-nonrigid"><link·rel="next"·href="Secmia2dmyoicanonrigid2.html"·title="mia-2dmyoica-nonrigid2"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-nonrigid-parallel</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid2.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicanonrigidparallel"></a>mia-2dmyoica-nonrigid-parallel</h3></div></div></div><h4><a·name="idp4832"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-nonrigid-parallel</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoica-nonrigid-parallel</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicanonrigid.html"·title="mia-2dmyoica-nonrigid"><link·rel="next"·href="Secmia2dmyoicanonrigid2.html"·title="mia-2dmyoica-nonrigid2"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoica-nonrigid-parallel</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid2.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicanonrigidparallel"></a>mia-2dmyoica-nonrigid-parallel</h3></div></div></div><h4><a·name="idp4832"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoica-nonrigid-parallel</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp4841"></a>Description:</h4><p·class="description">This·program·implements·the·2D·version·of·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.</a></p><p·class="description">This·version·of·the·program·runs·all·registrations·in·parallel.</p><h4><a·name="idp4845"></a>Options:</h4><h4><a·name="idp4846"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.</p></dd><dt><span·class="term">--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd><dt><span·class="term">--save-refs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·the·reference·images·to·files·with·the·given·name·base</p></dd><dt><span·class="term">--save-regs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp4876"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4927"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.</p></dd></dl></div><h4><a·name="idp4980"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4986"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass.</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>Cofficient·rate·divider·for·each·pass.</p></dd><dt><span·class="term">-d,·--start-divcurl=10000;·double</span></dt><dd><p>Start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass.</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>Divcurl·weight·scaling·with·each·new·pass.</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost,·do·not·specify·the·src·and·ref·parameters,·these·will·be·set·by·the·program.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5022"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-nonrigid-parallel···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5025"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid2.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-nonrigid2</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp4841"></a>Description:</h4><p·class="description">This·program·implements·the·2D·version·of·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.</a></p><p·class="description">This·version·of·the·program·runs·all·registrations·in·parallel.</p><h4><a·name="idp4845"></a>Options:</h4><h4><a·name="idp4846"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.</p></dd><dt><span·class="term">--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd><dt><span·class="term">--save-refs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·the·reference·images·to·files·with·the·given·name·base</p></dd><dt><span·class="term">--save-regs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp4876"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4927"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.</p></dd></dl></div><h4><a·name="idp4980"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4986"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass.</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>Cofficient·rate·divider·for·each·pass.</p></dd><dt><span·class="term">-d,·--start-divcurl=10000;·double</span></dt><dd><p>Start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass.</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>Divcurl·weight·scaling·with·each·new·pass.</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost,·do·not·specify·the·src·and·ref·parameters,·these·will·be·set·by·the·program.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5022"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoica-nonrigid-parallel···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5025"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoicanonrigid2.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoica-nonrigid2</td></tr></table></div></body></html>
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9 described·in9 described·in
10 Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion10 Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion
11 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using11 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using
12 Independent_Component_Analysis"_Medical_Image_Analysis,_2012.12 Independent_Component_Analysis"_Medical_Image_Analysis,_2012.
13 This·version·of·the·program·runs·all·registrations·in·parallel.13 This·version·of·the·program·runs·all·registrations·in·parallel.
14 Options:14 Options:
15 File-IO15 File-IO
16 ··-i,·--in-file=(input,·required);·string16 ··-i,·--in-file=(required,·input);·string
17 ······input·perfusion·data·set17 ······input·perfusion·data·set
18 ··-o,·--out-file=(required,·output);·string18 ··-o,·--out-file=(required,·output);·string
19 ······output·perfusion·data·set19 ······output·perfusion·data·set
20 ··-r,·--registered=reg;·stringSTRING20 ··-r,·--registered=reg;·stringSTRING
21 ······File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme21 ······File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme
22 ······are·taken·from·the·input·images·as·given·in·the·input·data·set.22 ······are·taken·from·the·input·images·as·given·in·the·input·data·set.
23 ··--save-cropped=(output);·string23 ··--save-cropped=(output);·string
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoicapgt</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicanonrigid2.html"·title="mia-2dmyoica-nonrigid2"><link·rel="next"·href="Secmia2dmyomilles.html"·title="mia-2dmyomilles"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoicapgt</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid2.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyomilles.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicapgt"></a>mia-2dmyoicapgt</h3></div></div></div><h4><a·name="idp5216"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoicapgt</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoicapgt</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicanonrigid2.html"·title="mia-2dmyoica-nonrigid2"><link·rel="next"·href="Secmia2dmyomilles.html"·title="mia-2dmyomilles"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoicapgt</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid2.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyomilles.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoicapgt"></a>mia-2dmyoicapgt</h3></div></div></div><h4><a·name="idp5216"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoicapgt</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp5225"></a>Description:</h4><p·class="description">This·program·implements·a·two·passs·motion·compensation·algorithm.·First·a·linear·registration·is·run·based·on·a·variation·of·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.acra.2010.06.015"·target="_top">Gupta·et~al.·"Fully·automatic·registration·and·segmentation·of·first-pass·myocardial·perfusion·MR·image·sequences",·Academic·Radiology·17,·1375-1385</a></p><p·class="description">·as·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/DOI:10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis",·Medical·Image·Analysis,·2012,</a></p><p·class="description">followed·by·a·non-linear·registration·based·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1007/978-3-642-04268-3_21"·target="_top">Chao·Li·and·Ying·Sun,·"Nonrigid·Registration·of·Myocardial·Perfusion·MRI·Using·Pseudo·Ground·Truth",·In·Proc.·Medical·Image·Computing·and·Computer-Assisted·Intervention·MICCAI·2009,·165-172,·2009.</a></p><p·class="description">·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.·This·version·of·the·program·may·run·all·registrations·in·parallel.</p><h4><a·name="idp5233"></a>Options:</h4><h4><a·name="idp5234"></a>3 ········...]</p></div><h4><a·name="idp5225"></a>Description:</h4><p·class="description">This·program·implements·a·two·passs·motion·compensation·algorithm.·First·a·linear·registration·is·run·based·on·a·variation·of·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.acra.2010.06.015"·target="_top">Gupta·et~al.·"Fully·automatic·registration·and·segmentation·of·first-pass·myocardial·perfusion·MR·image·sequences",·Academic·Radiology·17,·1375-1385</a></p><p·class="description">·as·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/DOI:10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis",·Medical·Image·Analysis,·2012,</a></p><p·class="description">followed·by·a·non-linear·registration·based·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1007/978-3-642-04268-3_21"·target="_top">Chao·Li·and·Ying·Sun,·"Nonrigid·Registration·of·Myocardial·Perfusion·MRI·Using·Pseudo·Ground·Truth",·In·Proc.·Medical·Image·Computing·and·Computer-Assisted·Intervention·MICCAI·2009,·165-172,·2009.</a></p><p·class="description">·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.·This·version·of·the·program·may·run·all·registrations·in·parallel.</p><h4><a·name="idp5233"></a>Options:</h4><h4><a·name="idp5234"></a>
4 Pseudo·Ground·Thruth·estimation</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-A,·--alpha=0.1;·double</span></dt><dd><p>spacial·neighborhood·penalty·weight</p></dd><dt><span·class="term">-B,·--beta=4;·double</span></dt><dd><p>temporal·second·derivative·penalty·weight</p></dd><dt><span·class="term">-T,·--rho-thresh=0.85;·double</span></dt><dd><p>correlation·threshold·for·neighborhood·analysis</p></dd></dl></div><h4><a·name="idp5248"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=STRING</span></dt><dd><p>File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.</p></dd><dt><span·class="term">--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd><dt><span·class="term">--save-refs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·the·reference·images·to·files·with·the·given·name·base</p></dd><dt><span·class="term">--save-regs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp5278"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5329"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.·A·value·0.0·forces·the·series·to·be·identified·as·acquired·with·initial·breath·hold.</p></dd></dl></div><h4><a·name="idp5382"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5388"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-L,·--linear-optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization·of·the·linear·registration·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">--linear-transform=affine;·factory</span></dt><dd><p>linear·transform·to·be·used·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-O,·--non-linear-optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization·in·the·non-linear·registration.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass.</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>Cofficient·rate·divider·for·each·pass.</p></dd><dt><span·class="term">-d,·--start-divcurl=10000;·double</span></dt><dd><p>Start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass.</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>Divcurl·weight·scaling·with·each·new·pass.</p></dd><dt><span·class="term">-R,·--reference=-1;·int</span></dt><dd><p>Global·reference·all·image·should·be·aligned·to.·If·set·to·a·non-negative·value,·the·images·will·be·aligned·to·this·references,·and·the·cropped·output·image·date·will·be·injected·into·the·original·images.·Leave·at·-1·if·you·don't·care.·In·this·case·all·images·with·be·registered·to·a·mean·position·of·the·movement</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost,·do·not·specify·the·src·and·ref·parameters,·these·will·be·set·by·the·program.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-p,·--linear-passes=3;·ulong</span></dt><dd><p>linear·registration·passes·(0·to·disable)</p></dd><dt><span·class="term">-P,·--nonlinear-passes=3;·ulong</span></dt><dd><p>non-linear·registration·passes·(0·to·disable)</p></dd></dl></div><h4><a·name="idp5442"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·first·using·automatic·ICA·estimation·to·run·the·linear·registration·and·then·the·PGT·registration.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoicapgt···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5445"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid2.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyomilles.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-nonrigid2 </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyomilles</td></tr></table></div></body></html>4 Pseudo·Ground·Thruth·estimation</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-A,·--alpha=0.1;·double</span></dt><dd><p>spacial·neighborhood·penalty·weight</p></dd><dt><span·class="term">-B,·--beta=4;·double</span></dt><dd><p>temporal·second·derivative·penalty·weight</p></dd><dt><span·class="term">-T,·--rho-thresh=0.85;·double</span></dt><dd><p>correlation·threshold·for·neighborhood·analysis</p></dd></dl></div><h4><a·name="idp5248"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=STRING</span></dt><dd><p>File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.</p></dd><dt><span·class="term">--save-cropped=(output);·string</span></dt><dd><p>save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base</p></dd><dt><span·class="term">--save-feature=(output);·string</span></dt><dd><p>save·segmentation·feature·images·and·initial·ICA·mixing·matrix</p></dd><dt><span·class="term">--save-refs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·the·reference·images·to·files·with·the·given·name·base</p></dd><dt><span·class="term">--save-regs=(output);·string</span></dt><dd><p>for·each·registration·pass·save·intermediate·registered·images</p></dd></dl></div><h4><a·name="idp5278"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5329"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-s,·--segscale=0;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--min-breathing-frequency=-1;·float</span></dt><dd><p>minimal·mean·frequency·a·mixing·curve·can·have·to·be·considered·to·stem·from·brething.·A·healthy·rest·breating·rate·is·12·per·minute.·A·negative·value·disables·the·test.·A·value·0.0·forces·the·series·to·be·identified·as·acquired·with·initial·breath·hold.</p></dd></dl></div><h4><a·name="idp5382"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5388"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-L,·--linear-optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization·of·the·linear·registration·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">--linear-transform=affine;·factory</span></dt><dd><p>linear·transform·to·be·used·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-O,·--non-linear-optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization·in·the·non-linear·registration.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=16;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass.</p></dd><dt><span·class="term">--c-rate-divider=2;·double</span></dt><dd><p>Cofficient·rate·divider·for·each·pass.</p></dd><dt><span·class="term">-d,·--start-divcurl=10000;·double</span></dt><dd><p>Start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass.</p></dd><dt><span·class="term">--divcurl-divider=2;·double</span></dt><dd><p>Divcurl·weight·scaling·with·each·new·pass.</p></dd><dt><span·class="term">-R,·--reference=-1;·int</span></dt><dd><p>Global·reference·all·image·should·be·aligned·to.·If·set·to·a·non-negative·value,·the·images·will·be·aligned·to·this·references,·and·the·cropped·output·image·date·will·be·injected·into·the·original·images.·Leave·at·-1·if·you·don't·care.·In·this·case·all·images·with·be·registered·to·a·mean·position·of·the·movement</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd;·factory</span></dt><dd><p>image·cost,·do·not·specify·the·src·and·ref·parameters,·these·will·be·set·by·the·program.·The·string·value·will·be·used·to·construct·a·plug-in..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-p,·--linear-passes=3;·ulong</span></dt><dd><p>linear·registration·passes·(0·to·disable)</p></dd><dt><span·class="term">-P,·--nonlinear-passes=3;·ulong</span></dt><dd><p>non-linear·registration·passes·(0·to·disable)</p></dd></dl></div><h4><a·name="idp5442"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·first·using·automatic·ICA·estimation·to·run·the·linear·registration·and·then·the·PGT·registration.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyoicapgt···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5445"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicanonrigid2.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyomilles.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoica-nonrigid2 </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyomilles</td></tr></table></div></body></html>
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25 ··-A,·--alpha=0.1;·double25 ··-A,·--alpha=0.1;·double
26 ······spacial·neighborhood·penalty·weight26 ······spacial·neighborhood·penalty·weight
27 ··-B,·--beta=4;·double27 ··-B,·--beta=4;·double
28 ······temporal·second·derivative·penalty·weight28 ······temporal·second·derivative·penalty·weight
29 ··-T,·--rho-thresh=0.85;·double29 ··-T,·--rho-thresh=0.85;·double
30 ······correlation·threshold·for·neighborhood·analysis30 ······correlation·threshold·for·neighborhood·analysis
31 File-IO31 File-IO
32 ··-i,·--in-file=(input,·required);·string32 ··-i,·--in-file=(required,·input);·string
33 ······input·perfusion·data·set33 ······input·perfusion·data·set
34 ··-o,·--out-file=(required,·output);·string34 ··-o,·--out-file=(required,·output);·string
35 ······output·perfusion·data·set35 ······output·perfusion·data·set
36 ··-r,·--registered=STRING36 ··-r,·--registered=STRING
37 ······File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme37 ······File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme
38 ······are·taken·from·the·input·images·as·given·in·the·input·data·set.38 ······are·taken·from·the·input·images·as·given·in·the·input·data·set.
39 ··--save-cropped=(output);·string39 ··--save-cropped=(output);·string
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyomilles</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicapgt.html"·title="mia-2dmyoicapgt"><link·rel="next"·href="Secmia2dmyoperiodicnonrigid.html"·title="mia-2dmyoperiodic-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyomilles</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicapgt.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoperiodicnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyomilles"></a>mia-2dmyomilles</h3></div></div></div><h4><a·name="idp5449"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyomilles</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyomilles</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoicapgt.html"·title="mia-2dmyoicapgt"><link·rel="next"·href="Secmia2dmyoperiodicnonrigid.html"·title="mia-2dmyoperiodic-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyomilles</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicapgt.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoperiodicnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyomilles"></a>mia-2dmyomilles</h3></div></div></div><h4><a·name="idp5449"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyomilles</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp5458"></a>Description:</h4><p·class="description">This·program·is·use·to·run·a·modified·version·of·the·ICA·based·registration·approach·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/TMI.2008.928918"·target="_top">Milles·et·al.·'Fully·Automated·Motion·Correction·in·First-Pass·Myocardial·Perfusion·MR·Image·Sequences',·Trans.·Med.·Imaging.,·27(11),·1611-1621,·2008.</a></p><p·class="description">·Changes·include·the·extraction·of·the·quasi-periodic·movement·in·free·breathingly·acquired·data·sets·and·the·option·to·run·affine·or·rigid·registration·instead·of·the·optimization·of·translations·only.3 ········...]</p></div><h4><a·name="idp5458"></a>Description:</h4><p·class="description">This·program·is·use·to·run·a·modified·version·of·the·ICA·based·registration·approach·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/TMI.2008.928918"·target="_top">Milles·et·al.·'Fully·Automated·Motion·Correction·in·First-Pass·Myocardial·Perfusion·MR·Image·Sequences',·Trans.·Med.·Imaging.,·27(11),·1611-1621,·2008.</a></p><p·class="description">·Changes·include·the·extraction·of·the·quasi-periodic·movement·in·free·breathingly·acquired·data·sets·and·the·option·to·run·affine·or·rigid·registration·instead·of·the·optimization·of·translations·only.
4 </p><h4><a·name="idp5462"></a>Options:</h4><h4><a·name="idp5463"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=STRING</span></dt><dd><p>file·name·base·for·registered·files</p></dd><dt><span·class="term">--save-references=STRING</span></dt><dd><p>save·synthetic·reference·images·to·this·file·base</p></dd><dt><span·class="term">--save-cropped=STRING</span></dt><dd><p>save·cropped·image·set·to·this·file</p></dd><dt><span·class="term">--save-feature=STRING</span></dt><dd><p>save·the·features·images·resulting·from·the·ICA·and·some·intermediate·images·used·for·the·RV-LV·segmentation·with·the·given·file·name·base·to·PNG·files.·Also·save·the·coefficients·of·the·initial·best·and·the·final·IC·mixing·matrix.</p></dd></dl></div><h4><a·name="idp5489"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5540"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-g,·--guess</span></dt><dd><p>use·initial·guess·for·myocardial·perfusion</p></dd><dt><span·class="term">-s,·--segscale=1.4;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp5593"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5599"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-c,·--cost=ssd;·stringSTRING</span></dt><dd><p>registration·criterion</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=rigid;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-R,·--reference=-1;·int</span></dt><dd><p>Global·reference·all·image·should·be·aligned·to.·If·set·to·a·non-negative·value,·the·images·will·be·aligned·to·this·references,·and·the·cropped·output·image·date·will·be·injected·into·the·original·images.·Leave·at·-1·if·you·don't·care.·In·this·case·all·images·with·be·registered·to·a·mean·position·of·the·movement</p></dd><dt><span·class="term">-P,·--passes=2;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5627"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.4 </p><h4><a·name="idp5462"></a>Options:</h4><h4><a·name="idp5463"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=STRING</span></dt><dd><p>file·name·base·for·registered·files</p></dd><dt><span·class="term">--save-references=STRING</span></dt><dd><p>save·synthetic·reference·images·to·this·file·base</p></dd><dt><span·class="term">--save-cropped=STRING</span></dt><dd><p>save·cropped·image·set·to·this·file</p></dd><dt><span·class="term">--save-feature=STRING</span></dt><dd><p>save·the·features·images·resulting·from·the·ICA·and·some·intermediate·images·used·for·the·RV-LV·segmentation·with·the·given·file·name·base·to·PNG·files.·Also·save·the·coefficients·of·the·initial·best·and·the·final·IC·mixing·matrix.</p></dd></dl></div><h4><a·name="idp5489"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5540"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--normalize</span></dt><dd><p>normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-g,·--guess</span></dt><dd><p>use·initial·guess·for·myocardial·perfusion</p></dd><dt><span·class="term">-s,·--segscale=1.4;·float</span></dt><dd><p>segment·and·scale·the·crop·box·around·the·LV·(0=no·segmentation)</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd><dt><span·class="term">-E,·--segmethod=features;·dict</span></dt><dd><p>Segmentation·method</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">delta-feature:</td><td·align="left"·valign="top">difference·of·the·feature·images</td></tr><tr><td·align="left"·valign="top">delta-peak:</td><td·align="left"·valign="top">difference·of·the·peak·enhancement·images</td></tr><tr><td·align="left"·valign="top">features:</td><td·align="left"·valign="top">feature·images</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp5593"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5599"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-c,·--cost=ssd;·stringSTRING</span></dt><dd><p>registration·criterion</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=rigid;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-R,·--reference=-1;·int</span></dt><dd><p>Global·reference·all·image·should·be·aligned·to.·If·set·to·a·non-negative·value,·the·images·will·be·aligned·to·this·references,·and·the·cropped·output·image·date·will·be·injected·into·the·original·images.·Leave·at·-1·if·you·don't·care.·In·this·case·all·images·with·be·registered·to·a·mean·position·of·the·movement</p></dd><dt><span·class="term">-P,·--passes=2;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5627"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·automatic·ICA·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.
5 </p><pre·class="screen">mia-2dmyomilles···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5630"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicapgt.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoperiodicnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoicapgt </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoperiodic-nonrigid</td></tr></table></div></body></html>5 </p><pre·class="screen">mia-2dmyomilles···-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5630"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoicapgt.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoperiodicnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoicapgt </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoperiodic-nonrigid</td></tr></table></div></body></html>
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10 Milles_et_al._'Fully_Automated_Motion_Correction_in_First-Pass_Myocardial10 Milles_et_al._'Fully_Automated_Motion_Correction_in_First-Pass_Myocardial
11 Perfusion_MR_Image_Sequences',_Trans._Med._Imaging.,_27(11),_1611-1621,_2008.11 Perfusion_MR_Image_Sequences',_Trans._Med._Imaging.,_27(11),_1611-1621,_2008.
12 Changes·include·the·extraction·of·the·quasi-periodic·movement·in·free12 Changes·include·the·extraction·of·the·quasi-periodic·movement·in·free
13 breathingly·acquired·data·sets·and·the·option·to·run·affine·or·rigid13 breathingly·acquired·data·sets·and·the·option·to·run·affine·or·rigid
14 registration·instead·of·the·optimization·of·translations·only.14 registration·instead·of·the·optimization·of·translations·only.
15 Options:15 Options:
16 File-IO16 File-IO
17 ··-i,·--in-file=(input,·required);·string17 ··-i,·--in-file=(required,·input);·string
18 ······input·perfusion·data·set18 ······input·perfusion·data·set
19 ··-o,·--out-file=(required,·output);·string19 ··-o,·--out-file=(required,·output);·string
20 ······output·perfusion·data·set20 ······output·perfusion·data·set
21 ··-r,·--registered=STRING21 ··-r,·--registered=STRING
22 ······file·name·base·for·registered·files22 ······file·name·base·for·registered·files
23 ··--save-references=STRING23 ··--save-references=STRING
24 ······save·synthetic·reference·images·to·this·file·base24 ······save·synthetic·reference·images·to·this·file·base
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoperiodic-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyomilles.html"·title="mia-2dmyomilles"><link·rel="next"·href="Secmia2dmyopgtnonrigid.html"·title="mia-2dmyopgt-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoperiodic-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyomilles.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyopgtnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoperiodicnonrigid"></a>mia-2dmyoperiodic-nonrigid</h3></div></div></div><h4><a·name="idp5634"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoperiodic-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoperiodic-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyomilles.html"·title="mia-2dmyomilles"><link·rel="next"·href="Secmia2dmyopgtnonrigid.html"·title="mia-2dmyopgt-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoperiodic-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyomilles.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyopgtnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoperiodicnonrigid"></a>mia-2dmyoperiodic-nonrigid</h3></div></div></div><h4><a·name="idp5634"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoperiodic-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp5643"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·perfusion·image·series·preferable·acquired·letting·the·patient·breath·freely.·The·registration·algorithm·implementes·</p><p·class="citation"><a·class="ulink"·href="http://dx.doi.org/10.1109/TMI.2010.2049270"·target="_top">G.·Wollny,·M-J·Ledesma-Cabryo,·P.Kellman,·and·A.Santos,·"Exploiting·Quasiperiodicity·in·Motion·Correction·of·Free-Breathing,"·IEEE·Transactions·on·Medical·Imaging,·29(8),·2010.</a></p><h4><a·name="idp5647"></a>Options:</h4><h4><a·name="idp5648"></a>3 ········...]</p></div><h4><a·name="idp5643"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·perfusion·image·series·preferable·acquired·letting·the·patient·breath·freely.·The·registration·algorithm·implementes·</p><p·class="citation"><a·class="ulink"·href="http://dx.doi.org/10.1109/TMI.2010.2049270"·target="_top">G.·Wollny,·M-J·Ledesma-Cabryo,·P.Kellman,·and·A.Santos,·"Exploiting·Quasiperiodicity·in·Motion·Correction·of·Free-Breathing,"·IEEE·Transactions·on·Medical·Imaging,·29(8),·2010.</a></p><h4><a·name="idp5647"></a>Options:</h4><h4><a·name="idp5648"></a>
4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd><dt><span·class="term">--save-references</span></dt><dd><p>Save·synthetic·references·to·files·refXXXX.v</p></dd></dl></div><h4><a·name="idp5666"></a>4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd><dt><span·class="term">--save-references</span></dt><dd><p>Save·synthetic·references·to·files·refXXXX.v</p></dd></dl></div><h4><a·name="idp5666"></a>
5 Preconditions</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--max-candidates=20;·ulong</span></dt><dd><p>maximum·number·of·candidates·for·global·reference·image</p></dd><dt><span·class="term">-S,·--cost-series=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Const·function·to·use·for·the·analysis·of·the·series.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">--ref-idx=STRING</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-R,·--global-reference=-1;·int</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-D,·--max-subset-delta=0;·ulong</span></dt><dd><p>Maximum·delta·between·two·elements·of·the·prealigned·subset</p></dd></dl></div><h4><a·name="idp5693"></a>5 Preconditions</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--max-candidates=20;·ulong</span></dt><dd><p>maximum·number·of·candidates·for·global·reference·image</p></dd><dt><span·class="term">-S,·--cost-series=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Const·function·to·use·for·the·analysis·of·the·series.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">--ref-idx=STRING</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-R,·--global-reference=-1;·int</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-D,·--max-subset-delta=0;·ulong</span></dt><dd><p>Maximum·delta·between·two·elements·of·the·prealigned·subset</p></dd></dl></div><h4><a·name="idp5693"></a>
6 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.01;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">--refiner=</span></dt><dd><p>optimizer·used·for·additional·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mr-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline:rate=16,penalty=[divcurl:weight=0.01];·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-1,·--cost-subset=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Cost·function·for·registration·during·the·subset·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-2,·--cost-final=image:cost=ssd;·factory</span></dt><dd><p>Cost·function·for·registration·during·the·final·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd></dl></div><h4><a·name="idp5724"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5775"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5781"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'.·Skip·two·images·at·the·beginning,·usa·spline·transformation·of·a·knot·rate·16·pixels,·and·penalize·the·transformation·by·divcurl·with·weight·5.·Store·the·result·in·'registered.set'.6 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.01;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">--refiner=</span></dt><dd><p>optimizer·used·for·additional·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mr-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline:rate=16,penalty=[divcurl:weight=0.01];·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-1,·--cost-subset=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Cost·function·for·registration·during·the·subset·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd><dt><span·class="term">-2,·--cost-final=image:cost=ssd;·factory</span></dt><dd><p>Cost·function·for·registration·during·the·final·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a></p></dd></dl></div><h4><a·name="idp5724"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5775"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5781"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'.·Skip·two·images·at·the·beginning,·usa·spline·transformation·of·a·knot·rate·16·pixels,·and·penalize·the·transformation·by·divcurl·with·weight·5.·Store·the·result·in·'registered.set'.
7 </p><pre·class="screen">mia-2dmyoperiodic-nonrigid···-i·segment.set·-o·registered.set·-k·2·-d·5·-f·spline:rate=16,penalty=[divcurl:weight=5]</pre><h4><a·name="idp5784"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyomilles.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyopgtnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyomilles </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyopgt-nonrigid</td></tr></table></div></body></html>7 </p><pre·class="screen">mia-2dmyoperiodic-nonrigid···-i·segment.set·-o·registered.set·-k·2·-d·5·-f·spline:rate=16,penalty=[divcurl:weight=5]</pre><h4><a·name="idp5784"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyomilles.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyopgtnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyomilles </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyopgt-nonrigid</td></tr></table></div></body></html>
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9 preferable·acquired·letting·the·patient·breath·freely.·The·registration9 preferable·acquired·letting·the·patient·breath·freely.·The·registration
10 algorithm·implementes10 algorithm·implementes
11 G._Wollny,_M-J_Ledesma-Cabryo,_P.Kellman,_and_A.Santos,_"Exploiting11 G._Wollny,_M-J_Ledesma-Cabryo,_P.Kellman,_and_A.Santos,_"Exploiting
12 Quasiperiodicity_in_Motion_Correction_of_Free-Breathing,"_IEEE_Transactions_on12 Quasiperiodicity_in_Motion_Correction_of_Free-Breathing,"_IEEE_Transactions_on
13 Medical_Imaging,_29(8),_2010.13 Medical_Imaging,_29(8),_2010.
14 Options:14 Options:
15 ·File-IO15 ·File-IO
16 ··-i,·--in-file=(input,·required);·string16 ··-i,·--in-file=(required,·input);·string
17 ······input·perfusion·data·set17 ······input·perfusion·data·set
18 ··-o,·--out-file=(required,·output);·string18 ··-o,·--out-file=(required,·output);·string
19 ······output·perfusion·data·set19 ······output·perfusion·data·set
20 ··-r,·--registered=reg;·stringSTRING20 ··-r,·--registered=reg;·stringSTRING
21 ······file·name·base·for·registered·fiels21 ······file·name·base·for·registered·fiels
22 ··--save-references22 ··--save-references
23 ······Save·synthetic·references·to·files·refXXXX.v23 ······Save·synthetic·references·to·files·refXXXX.v
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyopgt-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoperiodicnonrigid.html"·title="mia-2dmyoperiodic-nonrigid"><link·rel="next"·href="Secmia2dmyoserialnonrigid.html"·title="mia-2dmyoserial-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyopgt-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoperiodicnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoserialnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyopgtnonrigid"></a>mia-2dmyopgt-nonrigid</h3></div></div></div><h4><a·name="idp5788"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyopgt-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyopgt-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoperiodicnonrigid.html"·title="mia-2dmyoperiodic-nonrigid"><link·rel="next"·href="Secmia2dmyoserialnonrigid.html"·title="mia-2dmyoserial-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyopgt-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoperiodicnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoserialnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyopgtnonrigid"></a>mia-2dmyopgt-nonrigid</h3></div></div></div><h4><a·name="idp5788"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyopgt-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp5797"></a>Description:</h4><p·class="description">This·program·implements·the·non-linear·registration·based·on·Pseudo·Ground·Thruth·for·motion·compensation·of·series·of·myocardial·perfusion·images·given·as·a·data·set·as·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1007/978-3-642-04268-3_21"·target="_top">Chao·Li·and·Ying·Sun,·'Nonrigid·Registration·of·Myocardial·Perfusion·MRI·Using·Pseudo·Ground·Truth'·,·In·Proc.·Medical·Image·Computing·and·Computer-Assisted·Intervention·MICCAI·2009,·165-172,·2009</a></p><p·class="description">.·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.</p><h4><a·name="idp5801"></a>Options:</h4><h4><a·name="idp5802"></a>3 ········...]</p></div><h4><a·name="idp5797"></a>Description:</h4><p·class="description">This·program·implements·the·non-linear·registration·based·on·Pseudo·Ground·Thruth·for·motion·compensation·of·series·of·myocardial·perfusion·images·given·as·a·data·set·as·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1007/978-3-642-04268-3_21"·target="_top">Chao·Li·and·Ying·Sun,·'Nonrigid·Registration·of·Myocardial·Perfusion·MRI·Using·Pseudo·Ground·Truth'·,·In·Proc.·Medical·Image·Computing·and·Computer-Assisted·Intervention·MICCAI·2009,·165-172,·2009</a></p><p·class="description">.·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.</p><h4><a·name="idp5801"></a>Options:</h4><h4><a·name="idp5802"></a>
4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set</p></dd></dl></div><h4><a·name="idp5816"></a>4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-r,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set</p></dd></dl></div><h4><a·name="idp5816"></a>
5 Pseudo·Ground·Thruth·estimation</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-A,·--alpha=1;·double</span></dt><dd><p>spacial·neighborhood·penalty·weight</p></dd><dt><span·class="term">-B,·--beta=1;·double</span></dt><dd><p>temporal·second·derivative·penalty·weight</p></dd><dt><span·class="term">-R,·--rho-thresh=0.85;·double</span></dt><dd><p>correlation·threshold·for·neighborhood·analysis</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd></dl></div><h4><a·name="idp5834"></a>5 Pseudo·Ground·Thruth·estimation</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-A,·--alpha=1;·double</span></dt><dd><p>spacial·neighborhood·penalty·weight</p></dd><dt><span·class="term">-B,·--beta=1;·double</span></dt><dd><p>temporal·second·derivative·penalty·weight</p></dd><dt><span·class="term">-R,·--rho-thresh=0.85;·double</span></dt><dd><p>correlation·threshold·for·neighborhood·analysis</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd></dl></div><h4><a·name="idp5834"></a>
6 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=32;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=20;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imageweight=1;·double</span></dt><dd><p>image·cost·weight</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=4;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5869"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5920"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5926"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·Pseudo·Ground·Truth·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyopgt-nonrigid·-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5929"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoperiodicnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoserialnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoperiodic-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoserial-nonrigid</td></tr></table></div></body></html>6 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-a,·--start-c-rate=32;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=20;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imageweight=1;·double</span></dt><dd><p>image·cost·weight</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=4;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5869"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp5920"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp5926"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·by·using·Pseudo·Ground·Truth·estimation.·Skip·two·images·at·the·beginning·and·otherwiese·use·the·default·parameters.·Store·the·result·in·'registered.set'.</p><pre·class="screen">mia-2dmyopgt-nonrigid·-i·segment.set·-o·registered.set·-k·2</pre><h4><a·name="idp5929"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoperiodicnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoserialnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoperiodic-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoserial-nonrigid</td></tr></table></div></body></html>
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11 Chao_Li_and_Ying_Sun,_'Nonrigid_Registration_of_Myocardial_Perfusion_MRI_Using11 Chao_Li_and_Ying_Sun,_'Nonrigid_Registration_of_Myocardial_Perfusion_MRI_Using
12 Pseudo_Ground_Truth'_,_In_Proc._Medical_Image_Computing_and_Computer-Assisted12 Pseudo_Ground_Truth'_,_In_Proc._Medical_Image_Computing_and_Computer-Assisted
13 Intervention_MICCAI_2009,_165-172,_200913 Intervention_MICCAI_2009,_165-172,_2009
14 .·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear14 .·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear
15 registration·step·is·usually·required.15 registration·step·is·usually·required.
16 Options:16 Options:
17 ·File-IO17 ·File-IO
18 ··-i,·--in-file=(input,·required);·string18 ··-i,·--in-file=(required,·input);·string
19 ······input·perfusion·data·set19 ······input·perfusion·data·set
20 ··-o,·--out-file=(required,·output);·string20 ··-o,·--out-file=(required,·output);·string
21 ······output·perfusion·data·set21 ······output·perfusion·data·set
22 ··-r,·--registered=reg;·stringSTRING22 ··-r,·--registered=reg;·stringSTRING
23 ······file·name·base·for·registered·files,·the·image·file·type·is·the·same·as23 ······file·name·base·for·registered·files,·the·image·file·type·is·the·same·as
24 ······given·in·the·input·data·set24 ······given·in·the·input·data·set
25 ·Pseudo·Ground·Thruth·estimation25 ·Pseudo·Ground·Thruth·estimation
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoserial-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyopgtnonrigid.html"·title="mia-2dmyopgt-nonrigid"><link·rel="next"·href="Secmia2dmyosetall2onenonrigid.html"·title="mia-2dmyoset-all2one-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoserial-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyopgtnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyosetall2onenonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoserialnonrigid"></a>mia-2dmyoserial-nonrigid</h3></div></div></div><h4><a·name="idp5933"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoserial-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoserial-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyopgtnonrigid.html"·title="mia-2dmyopgt-nonrigid"><link·rel="next"·href="Secmia2dmyosetall2onenonrigid.html"·title="mia-2dmyoset-all2one-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoserial-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyopgtnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyosetall2onenonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoserialnonrigid"></a>mia-2dmyoserial-nonrigid</h3></div></div></div><h4><a·name="idp5933"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoserial-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp5945"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·motion·compensation·registration·of·an·perfusion·image·series.·The·registration·is·run·in·a·serial·manner,·this·is,·only·images·in·temporal·succession·are·registered,·and·the·obtained·transformations·are·applied·accumulated·to·reach·full·registration.·See:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/IEMBS.2008.4649933"·target="_top">Wollny,·G.,·Ledesma-Carbayo,·M.J.,·Kellman,·P.,·Santos,·A.·"A·New·Similarity·Measure·for·Non-Rigid·Breathing·Motion·Compensation·of·Myocardial·Perfusion·MRI·".·Proc·30th·Annual·International·IEEE·EMBS·Conference,·pp.·3389-3392.·Vancouver,·Aug.·2008.</a></p><h4><a·name="idp5949"></a>Options:</h4><h4><a·name="idp5950"></a>7 ········...]</p></div><h4><a·name="idp5945"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·motion·compensation·registration·of·an·perfusion·image·series.·The·registration·is·run·in·a·serial·manner,·this·is,·only·images·in·temporal·succession·are·registered,·and·the·obtained·transformations·are·applied·accumulated·to·reach·full·registration.·See:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/IEMBS.2008.4649933"·target="_top">Wollny,·G.,·Ledesma-Carbayo,·M.J.,·Kellman,·P.,·Santos,·A.·"A·New·Similarity·Measure·for·Non-Rigid·Breathing·Motion·Compensation·of·Myocardial·Perfusion·MRI·".·Proc·30th·Annual·International·IEEE·EMBS·Conference,·pp.·3389-3392.·Vancouver,·Aug.·2008.</a></p><h4><a·name="idp5949"></a>Options:</h4><h4><a·name="idp5950"></a>
8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-R,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd></dl></div><h4><a·name="idp5964"></a>8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">-R,·--registered=reg;·stringSTRING</span></dt><dd><p>file·name·base·for·registered·fiels</p></dd></dl></div><h4><a·name="idp5964"></a>
9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline:rate=16,penalty=[divcurl:weight=0.01];·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·registration·of·these·images·at·the·beginning·of·the·series</p></dd></dl></div><h4><a·name="idp5988"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6039"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6045"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·to·reference·image·30.·Skip·two·images·at·the·beginning·and·using·mutual·information·as·cost·function,·and·penalize·the·transformation·by·divcurl·with·weight·5.·Store·the·result·in·'registered.set'.9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline:rate=16,penalty=[divcurl:weight=0.01];·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·registration·of·these·images·at·the·beginning·of·the·series</p></dd></dl></div><h4><a·name="idp5988"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6039"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6045"></a>Example:</h4><p>Register·the·perfusion·series·given·in·'segment.set'·to·reference·image·30.·Skip·two·images·at·the·beginning·and·using·mutual·information·as·cost·function,·and·penalize·the·transformation·by·divcurl·with·weight·5.·Store·the·result·in·'registered.set'.
10 </p><pre·class="screen">mia-2dmyoserial-nonrigid···-i·segment.set·-o·registered.set·-k·2··-r·30·image:cost=mi·-f·spline:rate=5,penalty=[divcurl:weight=5]</pre><h4><a·name="idp6048"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyopgtnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyosetall2onenonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyopgt-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoset-all2one-nonrigid</td></tr></table></div></body></html>10 </p><pre·class="screen">mia-2dmyoserial-nonrigid···-i·segment.set·-o·registered.set·-k·2··-r·30·image:cost=mi·-f·spline:rate=5,penalty=[divcurl:weight=5]</pre><h4><a·name="idp6048"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyopgtnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyosetall2onenonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyopgt-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoset-all2one-nonrigid</td></tr></table></div></body></html>
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12 transformations·are·applied·accumulated·to·reach·full·registration.·See:12 transformations·are·applied·accumulated·to·reach·full·registration.·See:
13 Wollny,_G.,_Ledesma-Carbayo,_M.J.,_Kellman,_P.,_Santos,_A._"A_New_Similarity13 Wollny,_G.,_Ledesma-Carbayo,_M.J.,_Kellman,_P.,_Santos,_A._"A_New_Similarity
14 Measure_for_Non-Rigid_Breathing_Motion_Compensation_of_Myocardial_Perfusion_MRI14 Measure_for_Non-Rigid_Breathing_Motion_Compensation_of_Myocardial_Perfusion_MRI
15 "._Proc_30th_Annual_International_IEEE_EMBS_Conference,_pp._3389-3392.15 "._Proc_30th_Annual_International_IEEE_EMBS_Conference,_pp._3389-3392.
16 Vancouver,_Aug._2008.16 Vancouver,_Aug._2008.
17 Options:17 Options:
18 ·File-IO18 ·File-IO
19 ··-i,·--in-file=(input,·required);·string19 ··-i,·--in-file=(required,·input);·string
20 ······input·perfusion·data·set20 ······input·perfusion·data·set
21 ··-o,·--out-file=(required,·output);·string21 ··-o,·--out-file=(required,·output);·string
22 ······output·perfusion·data·set22 ······output·perfusion·data·set
23 ··-R,·--registered=reg;·stringSTRING23 ··-R,·--registered=reg;·stringSTRING
24 ······file·name·base·for·registered·fiels24 ······file·name·base·for·registered·fiels
25 ·Registration25 ·Registration
26 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·factory26 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·factory
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoseries-compdice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyocardicaseries.html"·title="mia-2dmyocard-icaseries"><link·rel="next"·href="Secmia2dmyoseriesdice.html"·title="mia-2dmyoseries-dice"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoseries-compdice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardicaseries.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriesdice.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoseriescompdice"></a>mia-2dmyoseries-compdice</h3></div></div></div><h4><a·name="idp6734"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoseries-compdice</code>··{-1·<em·class="replaceable"><code>string</code></em>}·{-2·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoseries-compdice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyocardicaseries.html"·title="mia-2dmyocard-icaseries"><link·rel="next"·href="Secmia2dmyoseriesdice.html"·title="mia-2dmyoseries-dice"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoseries-compdice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardicaseries.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriesdice.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoseriescompdice"></a>mia-2dmyoseries-compdice</h3></div></div></div><h4><a·name="idp6734"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoseries-compdice</code>··{-1·<em·class="replaceable"><code>string</code></em>}·{-2·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp6743"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·two·image·series</p><h4><a·name="idp6745"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--first=(input,·required);·string</span></dt><dd><p>first·segmentation·set</p></dd><dt><span·class="term">-2,·--second=(input,·required);·string</span></dt><dd><p>second·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>images·to·skip·atthe·begin·of·the·series</p></dd></dl></div><h4><a·name="idp6759"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6810"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6816"></a>Example:</h4><p>Evaluate·the·per-frame·dice·index·of·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·set·reference.set·skipping·two·images·at·the·beginning.</p><pre·class="screen">mia-2dmyoseries-compdice·-i·segment.set·-r·reference.set·-k·2</pre><h4><a·name="idp6819"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardicaseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriesdice.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyocard-icaseries </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoseries-dice</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp6743"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·two·image·series</p><h4><a·name="idp6745"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--first=(required,·input);·string</span></dt><dd><p>first·segmentation·set</p></dd><dt><span·class="term">-2,·--second=(required,·input);·string</span></dt><dd><p>second·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>images·to·skip·atthe·begin·of·the·series</p></dd></dl></div><h4><a·name="idp6759"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6810"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6816"></a>Example:</h4><p>Evaluate·the·per-frame·dice·index·of·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·set·reference.set·skipping·two·images·at·the·beginning.</p><pre·class="screen">mia-2dmyoseries-compdice·-i·segment.set·-r·reference.set·-k·2</pre><h4><a·name="idp6819"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyocardicaseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dmyoseriesdice.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyocard-icaseries </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dmyoseries-dice</td></tr></table></div></body></html>
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4 mia-2dmyoseries-compdice4 mia-2dmyoseries-compdice
5 Sysnopis:5 Sysnopis:
6 mia-2dmyoseries-compdice·{-1·string}·{-2·string}·[·options·...]6 mia-2dmyoseries-compdice·{-1·string}·{-2·string}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions8 This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions
9 of·two·image·series9 of·two·image·series
10 Options:10 Options:
11 ··-1,·--first=(input,·required);·string11 ··-1,·--first=(required,·input);·string
12 ······first·segmentation·set12 ······first·segmentation·set
13 ··-2,·--second=(input,·required);·string13 ··-2,·--second=(required,·input);·string
14 ······second·segmentation·set14 ······second·segmentation·set
15 ··-k,·--skip=2;·ulong15 ··-k,·--skip=2;·ulong
16 ······images·to·skip·atthe·begin·of·the·series16 ······images·to·skip·atthe·begin·of·the·series
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
20 ······Supported·priorities·starting·at·lowest·level·are:20 ······Supported·priorities·starting·at·lowest·level·are:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoseries-dice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyoseriescompdice.html"·title="mia-2dmyoseries-compdice"><link·rel="next"·href="Secmia2dsegcompare.html"·title="mia-2dsegcompare"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoseries-dice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriescompdice.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegcompare.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoseriesdice"></a>mia-2dmyoseries-dice</h3></div></div></div><h4><a·name="idp6823"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoseries-dice</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoseries-dice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyoseriescompdice.html"·title="mia-2dmyoseries-compdice"><link·rel="next"·href="Secmia2dsegcompare.html"·title="mia-2dsegcompare"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoseries-dice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriescompdice.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegcompare.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyoseriesdice"></a>mia-2dmyoseries-dice</h3></div></div></div><h4><a·name="idp6823"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoseries-dice</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp6830"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.</p><h4><a·name="idp6832"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--input=(input,·required);·string</span></dt><dd><p>original·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=2;·int</span></dt><dd><p>images·to·skip·atthe·bgin·of·the·series</p></dd><dt><span·class="term">-r,·--reference=20;·ulong</span></dt><dd><p>reference·image</p></dd></dl></div><h4><a·name="idp6846"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6897"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6903"></a>Example:</h4><p>Evaluate·the·dice·index·of·segmentation·set·segment.set·with·reference·30·and·skipping·the·first·two·frames.</p><pre·class="screen">mia-2dmyoseries-dice·-i·segment.set·-r·30·-k·2</pre><h4><a·name="idp6906"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriescompdice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegcompare.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoseries-compdice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegcompare</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp6830"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.</p><h4><a·name="idp6832"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--input=(required,·input);·string</span></dt><dd><p>original·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=2;·int</span></dt><dd><p>images·to·skip·atthe·bgin·of·the·series</p></dd><dt><span·class="term">-r,·--reference=20;·ulong</span></dt><dd><p>reference·image</p></dd></dl></div><h4><a·name="idp6846"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6897"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6903"></a>Example:</h4><p>Evaluate·the·dice·index·of·segmentation·set·segment.set·with·reference·30·and·skipping·the·first·two·frames.</p><pre·class="screen">mia-2dmyoseries-dice·-i·segment.set·-r·30·-k·2</pre><h4><a·name="idp6906"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriescompdice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegcompare.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoseries-compdice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegcompare</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-2dmyoseries-dice·{-i·string}·[·options·...]6 mia-2dmyoseries-dice·{-i·string}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions8 This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions
9 of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same9 of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same
10 series.10 series.
11 Options:11 Options:
12 ··-i,·--input=(input,·required);·string12 ··-i,·--input=(required,·input);·string
13 ······original·segmentation·set13 ······original·segmentation·set
14 ··-k,·--skip=2;·int14 ··-k,·--skip=2;·int
15 ······images·to·skip·atthe·bgin·of·the·series15 ······images·to·skip·atthe·bgin·of·the·series
16 ··-r,·--reference=20;·ulong16 ··-r,·--reference=20;·ulong
17 ······reference·image17 ······reference·image
18 Help·&·Info18 Help·&·Info
19 ··-V,·--verbose=warning;·dict19 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoset-all2one-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoserialnonrigid.html"·title="mia-2dmyoserial-nonrigid"><link·rel="next"·href="SecToolsfortheAnalysisof2Dimageseries.html"·title="Tools·for·the·Analysis·of·2D·image·series"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoset-all2one-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoserialnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof2Dimageseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyosetall2onenonrigid"></a>mia-2dmyoset-all2one-nonrigid</h3></div></div></div><h4><a·name="idp6052"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoset-all2one-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dmyoset-all2one-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"><link·rel="prev"·href="Secmia2dmyoserialnonrigid.html"·title="mia-2dmyoserial-nonrigid"><link·rel="next"·href="SecToolsfortheAnalysisof2Dimageseries.html"·title="Tools·for·the·Analysis·of·2D·image·series"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dmyoset-all2one-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoserialnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof2Dimageseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dmyosetall2onenonrigid"></a>mia-2dmyoset-all2one-nonrigid</h3></div></div></div><h4><a·name="idp6052"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dmyoset-all2one-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefullcost.html"·title="Plugin·type:·2dimage/fullcost">Plugin·type:·2dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp6064"></a>Description:</h4><p·class="description">This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an·image·set.·All·images·are·registered·to·one·user·defined·reference·image.</p><h4><a·name="idp6066"></a>Options:</h4><h4><a·name="idp6067"></a>7 ········...]</p></div><h4><a·name="idp6064"></a>Description:</h4><p·class="description">This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an·image·set.·All·images·are·registered·to·one·user·defined·reference·image.</p><h4><a·name="idp6066"></a>Options:</h4><h4><a·name="idp6067"></a>
8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">--out-filebase=reg;·stringSTRING</span></dt><dd><p>file·name·basae·for·registered·files,·file·type·is·deducted·from·the·image·file·type·in·the·input·data·set.</p></dd></dl></div><h4><a·name="idp6081"></a>8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·perfusion·data·set</p></dd><dt><span·class="term">--out-filebase=reg;·stringSTRING</span></dt><dd><p>file·name·basae·for·registered·files,·file·type·is·deducted·from·the·image·file·type·in·the·input·data·set.</p></dd></dl></div><h4><a·name="idp6081"></a>
9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>Skip·images·at·the·beginning·of·the·series</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd></dl></div><h4><a·name="idp6104"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6155"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6161"></a>Example:</h4><p>Register·the·perfusion·series·given·in·segment.set·by·optimizing·a·spline·based·transformation·with·a·coefficient·rate·of·16·pixel·using·Mutual·Information·and·penalize·the·transformation·by·using·divcurl·with·aweight·of·2.0.</p><pre·class="screen">mia-2dmyoset-all2one-nonrigid·-i·segment.set·-o·registered.set·9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>Skip·images·at·the·beginning·of·the·series</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagetransform.html"·title="Plugin·type:·2dimage/transform">Plugin·type:·2dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd></dl></div><h4><a·name="idp6104"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6155"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6161"></a>Example:</h4><p>Register·the·perfusion·series·given·in·segment.set·by·optimizing·a·spline·based·transformation·with·a·coefficient·rate·of·16·pixel·using·Mutual·Information·and·penalize·the·transformation·by·using·divcurl·with·aweight·of·2.0.</p><pre·class="screen">mia-2dmyoset-all2one-nonrigid·-i·segment.set·-o·registered.set·
10 ····-f·spline:rate=16,penalty=[divcurl:weight=2.0]·image:cost=mi,weight=2.0</pre><h4><a·name="idp6164"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoserialnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof2Dimageseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoserial-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Tools·for·the·Analysis·of·2D·image·series</td></tr></table></div></body></html>10 ····-f·spline:rate=16,penalty=[divcurl:weight=2.0]·image:cost=mi,weight=2.0</pre><h4><a·name="idp6164"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoserialnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof2Dimageseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoserial-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Tools·for·the·Analysis·of·2D·image·series</td></tr></table></div></body></html>
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6 mia-2dmyoset-all2one-nonrigid·{-i·string}·{-o·string}·[·options·...]·[·Plugin6 mia-2dmyoset-all2one-nonrigid·{-i·string}·{-o·string}·[·options·...]·[·Plugin
7 type:_2dimage/fullcost·...]7 type:_2dimage/fullcost·...]
8 Description:8 Description:
9 This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an9 This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an
10 image·set.·All·images·are·registered·to·one·user·defined·reference·image.10 image·set.·All·images·are·registered·to·one·user·defined·reference·image.
11 Options:11 Options:
12 ·File-IO12 ·File-IO
13 ··-i,·--in-file=(input,·required);·string13 ··-i,·--in-file=(required,·input);·string
14 ······input·perfusion·data·set14 ······input·perfusion·data·set
15 ··-o,·--out-file=(required,·output);·string15 ··-o,·--out-file=(required,·output);·string
16 ······output·perfusion·data·set16 ······output·perfusion·data·set
17 ··--out-filebase=reg;·stringSTRING17 ··--out-filebase=reg;·stringSTRING
18 ······file·name·basae·for·registered·files,·file·type·is·deducted·from·the18 ······file·name·basae·for·registered·files,·file·type·is·deducted·from·the
19 ······image·file·type·in·the·input·data·set.19 ······image·file·type·in·the·input·data·set.
20 ·Registration20 ·Registration
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./usr/share/doc/mia-2.4/userref/Secmia2dsegcompare.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegcompare</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyoseriesdice.html"·title="mia-2dmyoseries-dice"><link·rel="next"·href="Secmia2dseghausdorff.html"·title="mia-2dseghausdorff"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegcompare</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriesdice.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseghausdorff.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegcompare"></a>mia-2dsegcompare</h3></div></div></div><h4><a·name="idp6910"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegcompare</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegcompare</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dmyoseriesdice.html"·title="mia-2dmyoseries-dice"><link·rel="next"·href="Secmia2dseghausdorff.html"·title="mia-2dseghausdorff"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegcompare</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriesdice.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseghausdorff.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegcompare"></a>mia-2dsegcompare</h3></div></div></div><h4><a·name="idp6910"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegcompare</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp6919"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·the·Hausdorff·distance·between·each·frame·of·a·perfusion·time·series·of·the·input·set·to·the·corresponding·frame·of·the·reference·set·and·prints·the·result·to·stdout.</p><h4><a·name="idp6921"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--ref-file=(input,·required);·string</span></dt><dd><p>reference··segmentation·set</p></dd></dl></div><h4><a·name="idp6931"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6982"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6988"></a>Example:</h4><p>Evaluate·the·per-slice·Hausdorff·distance·of·input.set·and·reference.set.</p><pre·class="screen">mia-2dsegcompare·-i·input.set·-r·reference.set</pre><h4><a·name="idp6991"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriesdice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseghausdorff.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoseries-dice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseghausdorff</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp6919"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·the·Hausdorff·distance·between·each·frame·of·a·perfusion·time·series·of·the·input·set·to·the·corresponding·frame·of·the·reference·set·and·prints·the·result·to·stdout.</p><h4><a·name="idp6921"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--ref-file=(required,·input);·string</span></dt><dd><p>reference··segmentation·set</p></dd></dl></div><h4><a·name="idp6931"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6982"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6988"></a>Example:</h4><p>Evaluate·the·per-slice·Hausdorff·distance·of·input.set·and·reference.set.</p><pre·class="screen">mia-2dsegcompare·-i·input.set·-r·reference.set</pre><h4><a·name="idp6991"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmyoseriesdice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseghausdorff.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmyoseries-dice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseghausdorff</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-2dsegcompare·{-i·string}·{-r·string}·[·options·...]6 mia-2dsegcompare·{-i·string}·{-r·string}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·evaluate·the·Hausdorff·distance·between·each·frame·of·a8 This·program·is·used·to·evaluate·the·Hausdorff·distance·between·each·frame·of·a
9 perfusion·time·series·of·the·input·set·to·the·corresponding·frame·of·the9 perfusion·time·series·of·the·input·set·to·the·corresponding·frame·of·the
10 reference·set·and·prints·the·result·to·stdout.10 reference·set·and·prints·the·result·to·stdout.
11 Options:11 Options:
12 ··-i,·--in-file=(input,·required);·string12 ··-i,·--in-file=(required,·input);·string
13 ······input·segmentation·set13 ······input·segmentation·set
14 ··-r,·--ref-file=(input,·required);·string14 ··-r,·--ref-file=(required,·input);·string
15 ······reference·segmentation·set15 ······reference·segmentation·set
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
19 ······Supported·priorities·starting·at·lowest·level·are:19 ······Supported·priorities·starting·at·lowest·level·are:
20 ······trace:···Function·call·trace20 ······trace:···Function·call·trace
21 ······debug:···Debug·output21 ······debug:···Debug·output
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseghausdorff</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegcompare.html"·title="mia-2dsegcompare"><link·rel="next"·href="Secmia2dsegmentcropbox.html"·title="mia-2dsegmentcropbox"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseghausdorff</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegcompare.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentcropbox.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseghausdorff"></a>mia-2dseghausdorff</h3></div></div></div><h4><a·name="idp6995"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseghausdorff</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>ulong</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseghausdorff</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegcompare.html"·title="mia-2dsegcompare"><link·rel="next"·href="Secmia2dsegmentcropbox.html"·title="mia-2dsegmentcropbox"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseghausdorff</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegcompare.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentcropbox.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseghausdorff"></a>mia-2dseghausdorff</h3></div></div></div><h4><a·name="idp6995"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseghausdorff</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>ulong</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7004"></a>Description:</h4><p·class="description">Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given·reference·frame·and·print·it·to·stdout.</p><h4><a·name="idp7006"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--ref-frame=(required);·ulong</span></dt><dd><p>reference·frame</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·frames·at·the·beginning</p></dd></dl></div><h4><a·name="idp7020"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7071"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7077"></a>Example:</h4><p>Evaluate·the·Hausdorff·distance·of·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·given·in·frame·20.</p><pre·class="screen">mia-2dseghausdorff··-i·segment.set·-r·20</pre><h4><a·name="idp7080"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegcompare.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentcropbox.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegcompare </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegmentcropbox</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7004"></a>Description:</h4><p·class="description">Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given·reference·frame·and·print·it·to·stdout.</p><h4><a·name="idp7006"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--ref-frame=(required);·ulong</span></dt><dd><p>reference·frame</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·frames·at·the·beginning</p></dd></dl></div><h4><a·name="idp7020"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7071"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7077"></a>Example:</h4><p>Evaluate·the·Hausdorff·distance·of·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·given·in·frame·20.</p><pre·class="screen">mia-2dseghausdorff··-i·segment.set·-r·20</pre><h4><a·name="idp7080"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegcompare.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentcropbox.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegcompare </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegmentcropbox</td></tr></table></div></body></html>
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4 mia-2dseghausdorff4 mia-2dseghausdorff
5 Sysnopis:5 Sysnopis:
6 mia-2dseghausdorff·{-i·string}·{-r·ulong}·[·options·...]6 mia-2dseghausdorff·{-i·string}·{-r·ulong}·[·options·...]
7 Description:7 Description:
8 Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given8 Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given
9 reference·frame·and·print·it·to·stdout.9 reference·frame·and·print·it·to·stdout.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·string11 ··-i,·--in-file=(required,·input);·string
12 ······input·segmentation·set12 ······input·segmentation·set
13 ··-r,·--ref-frame=(required);·ulong13 ··-r,·--ref-frame=(required);·ulong
14 ······reference·frame14 ······reference·frame
15 ··-k,·--skip=0;·int15 ··-k,·--skip=0;·int
16 ······skip·frames·at·the·beginning16 ······skip·frames·at·the·beginning
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-ahmed</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dmultiimagevar.html"·title="mia-2dmultiimagevar"><link·rel="next"·href="Secmia2dsegmentfuzzyw.html"·title="mia-2dsegment-fuzzyw"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-ahmed</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimagevar.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentfuzzyw.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentahmed"></a>mia-2dsegment-ahmed</h3></div></div></div><h4><a·name="idp2473"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-ahmed</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-ahmed</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dmultiimagevar.html"·title="mia-2dmultiimagevar"><link·rel="next"·href="Secmia2dsegmentfuzzyw.html"·title="mia-2dsegment-fuzzyw"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-ahmed</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimagevar.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentfuzzyw.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentahmed"></a>mia-2dsegment-ahmed</h3></div></div></div><h4><a·name="idp2473"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-ahmed</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2482"></a>Description:</h4><p·class="description">This·program·implements·a·variation·of·the·paper:</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/42.996338"·target="_top">Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,</a></p><p·class="description">·changes·are:·p=2,·and·exp</p><h4><a·name="idp2486"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-a,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-b,·--bias-correct</span></dt><dd><p>apply·bias·field·correction</p></dd><dt><span·class="term">-c,·--class-centres=</span></dt><dd><p>initial·class·centers</p></dd><dt><span·class="term">-s,·--spread=64;·float</span></dt><dd><p>spread·parameter·describing·the·strength·of·mattar·distinction</p></dd></dl></div><h4><a·name="idp2514"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2565"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2571"></a>Example:</h4><p>Run·a·5-class·segmentation·over·input·image·input.v·and·store·the·class·probability·images·in·cls.v.</p><pre·class="screen">mia-2dsegment-ahmed·-i·input.v·-a·5·-o·cls.v</pre><h4><a·name="idp2574"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimagevar.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentfuzzyw.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmultiimagevar </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-fuzzyw</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2482"></a>Description:</h4><p·class="description">This·program·implements·a·variation·of·the·paper:</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/42.996338"·target="_top">Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,</a></p><p·class="description">·changes·are:·p=2,·and·exp</p><h4><a·name="idp2486"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-a,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-b,·--bias-correct</span></dt><dd><p>apply·bias·field·correction</p></dd><dt><span·class="term">-c,·--class-centres=</span></dt><dd><p>initial·class·centers</p></dd><dt><span·class="term">-s,·--spread=64;·float</span></dt><dd><p>spread·parameter·describing·the·strength·of·mattar·distinction</p></dd></dl></div><h4><a·name="idp2514"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2565"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2571"></a>Example:</h4><p>Run·a·5-class·segmentation·over·input·image·input.v·and·store·the·class·probability·images·in·cls.v.</p><pre·class="screen">mia-2dsegment-ahmed·-i·input.v·-a·5·-o·cls.v</pre><h4><a·name="idp2574"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimagevar.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentfuzzyw.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmultiimagevar </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-fuzzyw</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·implements·a·variation·of·the·paper:8 This·program·implements·a·variation·of·the·paper:
9 Mohamed_N._Ahmed_et._al,_"A_Modified_Fuzzy_C-Means_Algorithm_for_Bias_Field9 Mohamed_N._Ahmed_et._al,_"A_Modified_Fuzzy_C-Means_Algorithm_for_Bias_Field
10 estimation_and_Segmentation_of_MRI_Data",_IEEE_Trans._on_Medical_Imaging,_Vol.10 estimation_and_Segmentation_of_MRI_Data",_IEEE_Trans._on_Medical_Imaging,_Vol.
11 21,_No._3,_March_2002,11 21,_No._3,_March_2002,
12 changes·are:·p=2,·and·exp12 changes·are:·p=2,·and·exp
13 Options:13 Options:
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/15 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/
16 ······io16 ······io
17 ··-o,·--out-file=(required,·output);·io17 ··-o,·--out-file=(required,·output);·io
18 ······class·probability·images,·the·image·type·must·support·multiple·images·and18 ······class·probability·images,·the·image·type·must·support·multiple·images·and
19 ······floating·point·values.·For·supported·file·types·see·Plugin_type:_2dimage/19 ······floating·point·values.·For·supported·file·types·see·Plugin_type:_2dimage/
20 ······io20 ······io
21 ··-a,·--no-of-classes=3;·int21 ··-a,·--no-of-classes=3;·int
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./usr/share/doc/mia-2.4/userref/Secmia2dsegmentcropbox.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegmentcropbox</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseghausdorff.html"·title="mia-2dseghausdorff"><link·rel="next"·href="Secmia2dsegseriesstats.html"·title="mia-2dsegseriesstats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegmentcropbox</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseghausdorff.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegseriesstats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentcropbox"></a>mia-2dsegmentcropbox</h3></div></div></div><h4><a·name="idp7084"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegmentcropbox</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegmentcropbox</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseghausdorff.html"·title="mia-2dseghausdorff"><link·rel="next"·href="Secmia2dsegseriesstats.html"·title="mia-2dsegseriesstats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegmentcropbox</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseghausdorff.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegseriesstats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentcropbox"></a>mia-2dsegmentcropbox</h3></div></div></div><h4><a·name="idp7084"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegmentcropbox</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7093"></a>Description:</h4><p·class="description">This·program·is·used·on·a·segmentation·set·and·evaluates·a·bounding·box·that·encloses·the·segmentation·in·all·slices.·This·bounding·box·is·then·used·to·crop·the·original·images,·correct·the·segmentation·and·store·a·new·segmentation·set·with·the·cropped·images.·The·cropped·images·will·be·of·the·same·type·as·the·original·images.·If·no·segmentation·is·given·in·the·set,·the·result·is·undefined.</p><h4><a·name="idp7095"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-p,·--override-imagepath</span></dt><dd><p>Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation·set,·assume·the·files·are·located·in·the·current·directory</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·segmentation·set</p></dd><dt><span·class="term">-c,·--cropped-base=crop;·stringSTRING</span></dt><dd><p>Base·name·for·the·cropped·image·files,·the·file·type·and·numbering·will·be·based·on·the·input·image·file·type·and·numbering.</p></dd><dt><span·class="term">-e,·--enlarge=5;·float</span></dt><dd><p>Enlarge·the·area·around·the·obtained·sbounding·box·by·this·number·of·pixels·in·each·direction</p></dd></dl></div><h4><a·name="idp7117"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7168"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7174"></a>Example:</h4><p>Evaluate·the·optimal·cropping·for·a·segmentation·set·segment.set·and·enlarge·it·by·3·pixels.·Store·the·resulting·set·in·the·file·cropped.set.</p><pre·class="screen">mia-2dsegmentcropbox·-i·segment.set·-o·cropped.set·-e·3</pre><h4><a·name="idp7177"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseghausdorff.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegseriesstats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseghausdorff </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegseriesstats</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7093"></a>Description:</h4><p·class="description">This·program·is·used·on·a·segmentation·set·and·evaluates·a·bounding·box·that·encloses·the·segmentation·in·all·slices.·This·bounding·box·is·then·used·to·crop·the·original·images,·correct·the·segmentation·and·store·a·new·segmentation·set·with·the·cropped·images.·The·cropped·images·will·be·of·the·same·type·as·the·original·images.·If·no·segmentation·is·given·in·the·set,·the·result·is·undefined.</p><h4><a·name="idp7095"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-p,·--override-imagepath</span></dt><dd><p>Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation·set,·assume·the·files·are·located·in·the·current·directory</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·segmentation·set</p></dd><dt><span·class="term">-c,·--cropped-base=crop;·stringSTRING</span></dt><dd><p>Base·name·for·the·cropped·image·files,·the·file·type·and·numbering·will·be·based·on·the·input·image·file·type·and·numbering.</p></dd><dt><span·class="term">-e,·--enlarge=5;·float</span></dt><dd><p>Enlarge·the·area·around·the·obtained·sbounding·box·by·this·number·of·pixels·in·each·direction</p></dd></dl></div><h4><a·name="idp7117"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7168"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7174"></a>Example:</h4><p>Evaluate·the·optimal·cropping·for·a·segmentation·set·segment.set·and·enlarge·it·by·3·pixels.·Store·the·resulting·set·in·the·file·cropped.set.</p><pre·class="screen">mia-2dsegmentcropbox·-i·segment.set·-o·cropped.set·-e·3</pre><h4><a·name="idp7177"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseghausdorff.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegseriesstats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseghausdorff </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegseriesstats</td></tr></table></div></body></html>
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8 This·program·is·used·on·a·segmentation·set·and·evaluates·a·bounding·box·that8 This·program·is·used·on·a·segmentation·set·and·evaluates·a·bounding·box·that
9 encloses·the·segmentation·in·all·slices.·This·bounding·box·is·then·used·to·crop9 encloses·the·segmentation·in·all·slices.·This·bounding·box·is·then·used·to·crop
10 the·original·images,·correct·the·segmentation·and·store·a·new·segmentation·set10 the·original·images,·correct·the·segmentation·and·store·a·new·segmentation·set
11 with·the·cropped·images.·The·cropped·images·will·be·of·the·same·type·as·the11 with·the·cropped·images.·The·cropped·images·will·be·of·the·same·type·as·the
12 original·images.·If·no·segmentation·is·given·in·the·set,·the·result·is12 original·images.·If·no·segmentation·is·given·in·the·set,·the·result·is
13 undefined.13 undefined.
14 Options:14 Options:
15 ··-i,·--in-file=(input,·required);·string15 ··-i,·--in-file=(required,·input);·string
16 ······input·segmentation·set16 ······input·segmentation·set
17 ··-p,·--override-imagepath17 ··-p,·--override-imagepath
18 ······Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation18 ······Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation
19 ······set,·assume·the·files·are·located·in·the·current·directory19 ······set,·assume·the·files·are·located·in·the·current·directory
20 ··-o,·--out-file=(required,·output);·string20 ··-o,·--out-file=(required,·output);·string
21 ······output·segmentation·set21 ······output·segmentation·set
22 ··-c,·--cropped-base=crop;·stringSTRING22 ··-c,·--cropped-base=crop;·stringSTRING
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-fuzzyw</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentahmed.html"·title="mia-2dsegment-ahmed"><link·rel="next"·href="Secmia2dsegmentlocalcmeans.html"·title="mia-2dsegment-local-cmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-fuzzyw</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentahmed.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalcmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentfuzzyw"></a>mia-2dsegment-fuzzyw</h3></div></div></div><h4><a·name="idp2578"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-fuzzyw</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-fuzzyw</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentahmed.html"·title="mia-2dsegment-ahmed"><link·rel="next"·href="Secmia2dsegmentlocalcmeans.html"·title="mia-2dsegment-local-cmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-fuzzyw</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentahmed.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalcmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentfuzzyw"></a>mia-2dsegment-fuzzyw</h3></div></div></div><h4><a·name="idp2578"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-fuzzyw</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2585"></a>Description:</h4><p·class="description">This·program·is·a··implementation·of·a·fuzzy·c-means·segmentation·algorithm</p><h4><a·name="idp2587"></a>Options:</h4><h4><a·name="idp2588"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-c,·--cls-file=(output);·io</span></dt><dd><p>class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>B-field·corrected·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-g,·--gain-log-file=(output);·io</span></dt><dd><p>Logarithmic·gain·field,·the·image·type·must·support·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2610"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2661"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2667"></a>Segmentation·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-n,·--no-of-classes=3;·uint</span></dt><dd><p>number·of·classes·to·segment</p></dd><dt><span·class="term">-C,·--class-centres=</span></dt><dd><p>initial·class·centers</p></dd><dt><span·class="term">-N,·--neighborhood=shmean:shape=8n;·factory</span></dt><dd><p>neighborhood·filter·for·B-field·correction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a></p></dd><dt><span·class="term">-a,·--alpha=0.7;·float</span></dt><dd><p>weight·of·neighborhood·filter·for·B-field·correction</p></dd><dt><span·class="term">-p,·--fuzziness=2;·float</span></dt><dd><p>·parameter·describing·the·fuzzyness·of·mattar·distinction</p></dd><dt><span·class="term">-e,·--epsilon=0.01;·float</span></dt><dd><p>Stopping·criterion·for·class·center·estimation.</p></dd></dl></div><h4><a·name="idp2694"></a>Example:</h4><p>Run·a·5-class·segmentation·over·inpt·image·input.v·and·store·the·class·probability·images·in·cls.v.</p><pre·class="screen">mia-2dsegment-fuzzyw·-i·input.v·-a·5·-o·cls.v</pre><h4><a·name="idp2697"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentahmed.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalcmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-ahmed </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-local-cmeans</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2585"></a>Description:</h4><p·class="description">This·program·is·a··implementation·of·a·fuzzy·c-means·segmentation·algorithm</p><h4><a·name="idp2587"></a>Options:</h4><h4><a·name="idp2588"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-c,·--cls-file=(output);·io</span></dt><dd><p>class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>B-field·corrected·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-g,·--gain-log-file=(output);·io</span></dt><dd><p>Logarithmic·gain·field,·the·image·type·must·support·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2610"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2661"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2667"></a>Segmentation·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-n,·--no-of-classes=3;·uint</span></dt><dd><p>number·of·classes·to·segment</p></dd><dt><span·class="term">-C,·--class-centres=</span></dt><dd><p>initial·class·centers</p></dd><dt><span·class="term">-N,·--neighborhood=shmean:shape=8n;·factory</span></dt><dd><p>neighborhood·filter·for·B-field·correction.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a></p></dd><dt><span·class="term">-a,·--alpha=0.7;·float</span></dt><dd><p>weight·of·neighborhood·filter·for·B-field·correction</p></dd><dt><span·class="term">-p,·--fuzziness=2;·float</span></dt><dd><p>·parameter·describing·the·fuzzyness·of·mattar·distinction</p></dd><dt><span·class="term">-e,·--epsilon=0.01;·float</span></dt><dd><p>Stopping·criterion·for·class·center·estimation.</p></dd></dl></div><h4><a·name="idp2694"></a>Example:</h4><p>Run·a·5-class·segmentation·over·inpt·image·input.v·and·store·the·class·probability·images·in·cls.v.</p><pre·class="screen">mia-2dsegment-fuzzyw·-i·input.v·-a·5·-o·cls.v</pre><h4><a·name="idp2697"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentahmed.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalcmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-ahmed </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-local-cmeans</td></tr></table></div></body></html>
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4 mia-2dsegment-fuzzyw4 mia-2dsegment-fuzzyw
5 Sysnopis:5 Sysnopis:
6 mia-2dsegment-fuzzyw·{-i·io}·[·options·...]6 mia-2dsegment-fuzzyw·{-i·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·a·implementation·of·a·fuzzy·c-means·segmentation·algorithm8 This·program·is·a·implementation·of·a·fuzzy·c-means·segmentation·algorithm
9 Options:9 Options:
10 File·I/O10 File·I/O
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/12 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/
13 ······io13 ······io
14 ··-c,·--cls-file=(output);·io14 ··-c,·--cls-file=(output);·io
15 ······class·probability·images,·the·image·type·must·support·multiple·images·and15 ······class·probability·images,·the·image·type·must·support·multiple·images·and
16 ······floating·point·values.·For·supported·file·types·see·Plugin_type:_2dimage/16 ······floating·point·values.·For·supported·file·types·see·Plugin_type:_2dimage/
17 ······io17 ······io
18 ··-o,·--out-file=(output);·io18 ··-o,·--out-file=(output);·io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-local-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentfuzzyw.html"·title="mia-2dsegment-fuzzyw"><link·rel="next"·href="Secmia2dsegmentlocalkmeans.html"·title="mia-2dsegment-local-kmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-local-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentfuzzyw.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalkmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentlocalcmeans"></a>mia-2dsegment-local-cmeans</h3></div></div></div><h4><a·name="idp2701"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-local-cmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-local-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentfuzzyw.html"·title="mia-2dsegment-fuzzyw"><link·rel="next"·href="Secmia2dsegmentlocalkmeans.html"·title="mia-2dsegment-local-kmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-local-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentfuzzyw.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalkmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentlocalcmeans"></a>mia-2dsegment-local-cmeans</h3></div></div></div><h4><a·name="idp2701"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-local-cmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2708"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·c-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·c-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·c-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.·This·program·implements·a·2D·prototype·of·the·algorithm·described·in:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.7717/peerj.4374"·target="_top">Dunmore·CJ,·Wollny·G,·Skinner·MM.·(2018)·MIA-Clustering:·a·novel·method·for·segmentation·of·paleontological·material.·PeerJ·6:e4374.</a></p><h4><a·name="idp2712"></a>Options:</h4><h4><a·name="idp2713"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-G,·--out-global-crisp=(output);·io</span></dt><dd><p>class·label·image·based·on·global·segmentation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-C,·--class-prob=(output);·io</span></dt><dd><p>class·probability·image·file,·filetype·must·support·floating·point·multi-frame·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2735"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2786"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-g,·--grid-spacing=15;·int·in·[3,·inf)</span></dt><dd><p>Spacing·of·the·grid·used·to·modulate·the·intensity·inhomogeneities</p></dd><dt><span·class="term">-c,·--cmeans=kmeans:nc=3;·factory</span></dt><dd><p>c-means·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd><dt><span·class="term">-e,·--c-means-epsilon=0.0001;·float·in·(0,·inf)</span></dt><dd><p>c-means·breaking·condition·for·update·tolerance</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.02;·double·in·[0,·1)</span></dt><dd><p>threshhold·to·ignore·classes·when·initializing·the·local·cmeans·from·the·global·one.</p></dd></dl></div><h4><a·name="idp2805"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2811"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-2dsegment-local-cmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp2814"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentfuzzyw.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalkmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-fuzzyw </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-local-kmeans</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2708"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·c-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·c-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·c-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.·This·program·implements·a·2D·prototype·of·the·algorithm·described·in:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.7717/peerj.4374"·target="_top">Dunmore·CJ,·Wollny·G,·Skinner·MM.·(2018)·MIA-Clustering:·a·novel·method·for·segmentation·of·paleontological·material.·PeerJ·6:e4374.</a></p><h4><a·name="idp2712"></a>Options:</h4><h4><a·name="idp2713"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-G,·--out-global-crisp=(output);·io</span></dt><dd><p>class·label·image·based·on·global·segmentation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-C,·--class-prob=(output);·io</span></dt><dd><p>class·probability·image·file,·filetype·must·support·floating·point·multi-frame·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2735"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2786"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-g,·--grid-spacing=15;·int·in·[3,·inf)</span></dt><dd><p>Spacing·of·the·grid·used·to·modulate·the·intensity·inhomogeneities</p></dd><dt><span·class="term">-c,·--cmeans=kmeans:nc=3;·factory</span></dt><dd><p>c-means·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd><dt><span·class="term">-e,·--c-means-epsilon=0.0001;·float·in·(0,·inf)</span></dt><dd><p>c-means·breaking·condition·for·update·tolerance</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.02;·double·in·[0,·1)</span></dt><dd><p>threshhold·to·ignore·classes·when·initializing·the·local·cmeans·from·the·global·one.</p></dd></dl></div><h4><a·name="idp2805"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2811"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-2dsegment-local-cmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp2814"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentfuzzyw.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentlocalkmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-fuzzyw </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-local-kmeans</td></tr></table></div></body></html>
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12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain
13 more·pixels·than·a·given·threshold.·This·program·implements·a·2D·prototype·of13 more·pixels·than·a·given·threshold.·This·program·implements·a·2D·prototype·of
14 the·algorithm·described·in:14 the·algorithm·described·in:
15 Dunmore_CJ,_Wollny_G,_Skinner_MM._(2018)_MIA-Clustering:_a_novel_method_for15 Dunmore_CJ,_Wollny_G,_Skinner_MM._(2018)_MIA-Clustering:_a_novel_method_for
16 segmentation_of_paleontological_material._PeerJ_6:e4374.16 segmentation_of_paleontological_material._PeerJ_6:e4374.
17 Options:17 Options:
18 File-IO18 File-IO
19 ··-i,·--in-file=(input,·required);·io19 ··-i,·--in-file=(required,·input);·io
20 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/20 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/
21 ······io21 ······io
22 ··-o,·--out-file=(output);·io22 ··-o,·--out-file=(output);·io
23 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types23 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types
24 ······see·Plugin_type:_2dimage/io24 ······see·Plugin_type:_2dimage/io
25 ··-G,·--out-global-crisp=(output);·io25 ··-G,·--out-global-crisp=(output);·io
26 ······class·label·image·based·on·global·segmentation.·For·supported·file·types26 ······class·label·image·based·on·global·segmentation.·For·supported·file·types
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-local-kmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentlocalcmeans.html"·title="mia-2dsegment-local-cmeans"><link·rel="next"·href="Secmia2dsegmentperpixelkmeans.html"·title="mia-2dsegment-per-pixel-kmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-local-kmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalcmeans.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentperpixelkmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentlocalkmeans"></a>mia-2dsegment-local-kmeans</h3></div></div></div><h4><a·name="idp2818"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-local-kmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-local-kmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentlocalcmeans.html"·title="mia-2dsegment-local-cmeans"><link·rel="next"·href="Secmia2dsegmentperpixelkmeans.html"·title="mia-2dsegment-per-pixel-kmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-local-kmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalcmeans.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentperpixelkmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentlocalkmeans"></a>mia-2dsegment-local-kmeans</h3></div></div></div><h4><a·name="idp2818"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-local-kmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2825"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.</p><h4><a·name="idp2827"></a>Options:</h4><h4><a·name="idp2828"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-O,·--out-file2=(output);·io</span></dt><dd><p>class·label·image·based·on·classifying·by·using·the·interpolated·class·centers·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-D,·--debug-centers=(output);·io</span></dt><dd><p>Save·the·class·center·images·to·a·debug·file·(type·is·double).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2850"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2901"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-g,·--grid-spacing=20;·int·in·[3,·inf)</span></dt><dd><p>Spacing·of·the·grid·used·to·modulate·the·intensity·inhomogeneities</p></dd><dt><span·class="term">-n,·--nclasses=3;·uint·in·[2,·127]</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.0001;·double·in·[0,·1)</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd></dl></div><h4><a·name="idp2915"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2921"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-2dsegment-local-kmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp2924"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalcmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentperpixelkmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-local-cmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-per-pixel-kmeans</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2825"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.</p><h4><a·name="idp2827"></a>Options:</h4><h4><a·name="idp2828"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-O,·--out-file2=(output);·io</span></dt><dd><p>class·label·image·based·on·classifying·by·using·the·interpolated·class·centers·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-D,·--debug-centers=(output);·io</span></dt><dd><p>Save·the·class·center·images·to·a·debug·file·(type·is·double).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2850"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp2901"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-g,·--grid-spacing=20;·int·in·[3,·inf)</span></dt><dd><p>Spacing·of·the·grid·used·to·modulate·the·intensity·inhomogeneities</p></dd><dt><span·class="term">-n,·--nclasses=3;·uint·in·[2,·127]</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.0001;·double·in·[0,·1)</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd></dl></div><h4><a·name="idp2915"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp2921"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-2dsegment-local-kmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp2924"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalcmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegmentperpixelkmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-local-cmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegment-per-pixel-kmeans</td></tr></table></div></body></html>
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9 means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.9 means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.
10 The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the10 The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the
11 image·into·overlapping·regions·where·more·k-means·iterations·are·run·only11 image·into·overlapping·regions·where·more·k-means·iterations·are·run·only
12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain
13 more·pixels·than·a·given·threshold.13 more·pixels·than·a·given·threshold.
14 Options:14 Options:
15 File-IO15 File-IO
16 ··-i,·--in-file=(input,·required);·io16 ··-i,·--in-file=(required,·input);·io
17 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/17 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/
18 ······io18 ······io
19 ··-o,·--out-file=(output);·io19 ··-o,·--out-file=(output);·io
20 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types20 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types
21 ······see·Plugin_type:_2dimage/io21 ······see·Plugin_type:_2dimage/io
22 ··-O,·--out-file2=(output);·io22 ··-O,·--out-file2=(output);·io
23 ······class·label·image·based·on·classifying·by·using·the·interpolated·class23 ······class·label·image·based·on·classifying·by·using·the·interpolated·class
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-per-pixel-kmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentlocalkmeans.html"·title="mia-2dsegment-local-kmeans"><link·rel="next"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-per-pixel-kmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalkmeans.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentperpixelkmeans"></a>mia-2dsegment-per-pixel-kmeans</h3></div></div></div><h4><a·name="idp2928"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-per-pixel-kmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegment-per-pixel-kmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"><link·rel="prev"·href="Secmia2dsegmentlocalkmeans.html"·title="mia-2dsegment-local-kmeans"><link·rel="next"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegment-per-pixel-kmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalkmeans.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegmentperpixelkmeans"></a>mia-2dsegment-per-pixel-kmeans</h3></div></div></div><h4><a·name="idp2928"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegment-per-pixel-kmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp2937"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.</p><h4><a·name="idp2939"></a>Options:</h4><h4><a·name="idp2940"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2952"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3003"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-w,·--window=20;·int·in·[3,·inf)</span></dt><dd><p>Window·size·around·the·pixel·to·be·analyzed</p></dd><dt><span·class="term">-n,·--nclasses=3;·uint·in·[2,·127]</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.0001;·double·in·[0,·1)</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd></dl></div><h4><a·name="idp3017"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3023"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-2dsegment-per-pixel-kmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp3026"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalkmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-local-kmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration,·Comparison,·and·Transformation·of·2D·images</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp2937"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.</p><h4><a·name="idp2939"></a>Options:</h4><h4><a·name="idp2940"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp2952"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3003"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-w,·--window=20;·int·in·[3,·inf)</span></dt><dd><p>Window·size·around·the·pixel·to·be·analyzed</p></dd><dt><span·class="term">-n,·--nclasses=3;·uint·in·[2,·127]</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.0001;·double·in·[0,·1)</span></dt><dd><p>Number·of·intensity·classes·to·segment</p></dd></dl></div><h4><a·name="idp3017"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3023"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-2dsegment-per-pixel-kmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp3026"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentlocalkmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegment-local-kmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration,·Comparison,·and·Transformation·of·2D·images</td></tr></table></div></body></html>
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9 means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.9 means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.
10 The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the10 The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the
11 image·into·overlapping·regions·where·more·k-means·iterations·are·run·only11 image·into·overlapping·regions·where·more·k-means·iterations·are·run·only
12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain
13 more·pixels·than·a·given·threshold.13 more·pixels·than·a·given·threshold.
14 Options:14 Options:
15 File-IO15 File-IO
16 ··-i,·--in-file=(input,·required);·io16 ··-i,·--in-file=(required,·input);·io
17 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/17 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_2dimage/
18 ······io18 ······io
19 ··-o,·--out-file=(required,·output);·io19 ··-o,·--out-file=(required,·output);·io
20 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types20 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types
21 ······see·Plugin_type:_2dimage/io21 ······see·Plugin_type:_2dimage/io
22 Help·&·Info22 Help·&·Info
23 ··-V,·--verbose=warning;·dict23 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegseriesstats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegmentcropbox.html"·title="mia-2dsegmentcropbox"><link·rel="next"·href="Secmia2dsegshift.html"·title="mia-2dsegshift"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegseriesstats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentcropbox.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshift.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegseriesstats"></a>mia-2dsegseriesstats</h3></div></div></div><h4><a·name="idp7181"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegseriesstats</code>··{-o·<em·class="replaceable"><code>string</code></em>}·{-g·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegseriesstats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegmentcropbox.html"·title="mia-2dsegmentcropbox"><link·rel="next"·href="Secmia2dsegshift.html"·title="mia-2dsegshift"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegseriesstats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentcropbox.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshift.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegseriesstats"></a>mia-2dsegseriesstats</h3></div></div></div><h4><a·name="idp7181"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegseriesstats</code>··{-o·<em·class="replaceable"><code>string</code></em>}·{-g·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7190"></a>Description:</h4><p·class="description">This·program·is·used·evaluate·various·time-intensity·curves·over·a·series·of·images·given·by·a·segmentation·set.·Specifically,·the·program·is·taylored·to·evaluate·average·intensities·and·variations·of·sections·the·left·ventricle·myocardium.·The·segmentation·set·must·contain·the·segmentations·for·all·slices·that·will·be·accessed·during·evaluation.·</p><h4><a·name="idp7192"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-o,·--original=(input,·required);·string</span></dt><dd><p>original·segmentation·set</p></dd><dt><span·class="term">-g,·--registered=(input,·required);·string</span></dt><dd><p>registered·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=2;·int</span></dt><dd><p>images·to·skip·at·the·begin·of·the·series,·if·(k·&lt;·0)·use·RV·peak·of·the·registered·set·if·set</p></dd><dt><span·class="term">-r,·--reference=-1;·int</span></dt><dd><p>reference·frame·for·automatic·curve·extraction.·Negative·values·can·be·used·to·indicate·specific·values·(if·given·in·the·segmentation·set):3 ········...]</p></div><h4><a·name="idp7190"></a>Description:</h4><p·class="description">This·program·is·used·evaluate·various·time-intensity·curves·over·a·series·of·images·given·by·a·segmentation·set.·Specifically,·the·program·is·taylored·to·evaluate·average·intensities·and·variations·of·sections·the·left·ventricle·myocardium.·The·segmentation·set·must·contain·the·segmentations·for·all·slices·that·will·be·accessed·during·evaluation.·</p><h4><a·name="idp7192"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-o,·--original=(required,·input);·string</span></dt><dd><p>original·segmentation·set</p></dd><dt><span·class="term">-g,·--registered=(required,·input);·string</span></dt><dd><p>registered·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=2;·int</span></dt><dd><p>images·to·skip·at·the·begin·of·the·series,·if·(k·&lt;·0)·use·RV·peak·of·the·registered·set·if·set</p></dd><dt><span·class="term">-r,·--reference=-1;·int</span></dt><dd><p>reference·frame·for·automatic·curve·extraction.·Negative·values·can·be·used·to·indicate·specific·values·(if·given·in·the·segmentation·set):
4 ···-3:·Middle·of·the·series4 ···-3:·Middle·of·the·series
5 ···-2:·prefererred·reference5 ···-2:·prefererred·reference
6 ···-1:·LV·peak6 ···-1:·LV·peak
7 ···if·any·of·the·above·is·not·available·or·the·value·is·&lt;·-3,·use·the·last·frame·of·the·series.</p></dd><dt><span·class="term">-c,·--curves=(output);·string</span></dt><dd><p>region·average·value·curves,·The·output·files·each·comprises·a·table·in·plain-text·format·that·contains·three·columns·for·each·section·of·the·LV·myocardium:·The·first·column·contains·the·values·obtained·by·using·the·original·segmentation·of·the·reference·on·all·images·of·the·original·series,·the·second·column·contains·the·values·obtained·by·the·registered·segmentation·of·the·reference·on·all·images·of·the·registered·series,·and·the·third·column·contains·the·values·obtained·by·using·the·segmentations·of·each·slice·on·the·original·images.</p></dd><dt><span·class="term">-v,·--varcurves=(output);·string</span></dt><dd><p>region·variation·values,·same·formt·as·described·above.·</p></dd><dt><span·class="term">-n,·--nsections=0;·ulong</span></dt><dd><p>number·of·sections·to·use,·0=use·as·segmented,·otherwise·Otherwise,·the·LV·myocardium·is·divided·into·n·sections·that·enclose·equal·angles·starting·at·the·right·ventricle·insertion·point·moving·clock-wise·using·the·LV·center·as·angular·point.</p></dd></dl></div><h4><a·name="idp7222"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7273"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7279"></a>Example:</h4><p>Evaluate·the·two·curve·typed·for·12·sections·from·segemntation·sets·orig.set·and·reg.set·skipping·the·first·2·frames.·The·output·will·be·written·to·curves.txt·and·varcurves.txt·respectively.</p><pre·class="screen">mia-2dsegseriesstats·-i·org.set·-g·reg.set·-c·curves.txt·-v·varcurves.txt·-n·12·-k·2</pre><h4><a·name="idp7282"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentcropbox.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshift.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegmentcropbox </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegshift</td></tr></table></div></body></html>7 ···if·any·of·the·above·is·not·available·or·the·value·is·&lt;·-3,·use·the·last·frame·of·the·series.</p></dd><dt><span·class="term">-c,·--curves=(output);·string</span></dt><dd><p>region·average·value·curves,·The·output·files·each·comprises·a·table·in·plain-text·format·that·contains·three·columns·for·each·section·of·the·LV·myocardium:·The·first·column·contains·the·values·obtained·by·using·the·original·segmentation·of·the·reference·on·all·images·of·the·original·series,·the·second·column·contains·the·values·obtained·by·the·registered·segmentation·of·the·reference·on·all·images·of·the·registered·series,·and·the·third·column·contains·the·values·obtained·by·using·the·segmentations·of·each·slice·on·the·original·images.</p></dd><dt><span·class="term">-v,·--varcurves=(output);·string</span></dt><dd><p>region·variation·values,·same·formt·as·described·above.·</p></dd><dt><span·class="term">-n,·--nsections=0;·ulong</span></dt><dd><p>number·of·sections·to·use,·0=use·as·segmented,·otherwise·Otherwise,·the·LV·myocardium·is·divided·into·n·sections·that·enclose·equal·angles·starting·at·the·right·ventricle·insertion·point·moving·clock-wise·using·the·LV·center·as·angular·point.</p></dd></dl></div><h4><a·name="idp7222"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7273"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7279"></a>Example:</h4><p>Evaluate·the·two·curve·typed·for·12·sections·from·segemntation·sets·orig.set·and·reg.set·skipping·the·first·2·frames.·The·output·will·be·written·to·curves.txt·and·varcurves.txt·respectively.</p><pre·class="screen">mia-2dsegseriesstats·-i·org.set·-g·reg.set·-c·curves.txt·-v·varcurves.txt·-n·12·-k·2</pre><h4><a·name="idp7282"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegmentcropbox.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshift.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegmentcropbox </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegshift</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·is·used·evaluate·various·time-intensity·curves·over·a·series·of8 This·program·is·used·evaluate·various·time-intensity·curves·over·a·series·of
9 images·given·by·a·segmentation·set.·Specifically,·the·program·is·taylored·to9 images·given·by·a·segmentation·set.·Specifically,·the·program·is·taylored·to
10 evaluate·average·intensities·and·variations·of·sections·the·left·ventricle10 evaluate·average·intensities·and·variations·of·sections·the·left·ventricle
11 myocardium.·The·segmentation·set·must·contain·the·segmentations·for·all·slices11 myocardium.·The·segmentation·set·must·contain·the·segmentations·for·all·slices
12 that·will·be·accessed·during·evaluation.12 that·will·be·accessed·during·evaluation.
13 Options:13 Options:
14 ··-o,·--original=(input,·required);·string14 ··-o,·--original=(required,·input);·string
15 ······original·segmentation·set15 ······original·segmentation·set
16 ··-g,·--registered=(input,·required);·string16 ··-g,·--registered=(required,·input);·string
17 ······registered·segmentation·set17 ······registered·segmentation·set
18 ··-k,·--skip=2;·int18 ··-k,·--skip=2;·int
19 ······images·to·skip·at·the·begin·of·the·series,·if·(k·<·0)·use·RV·peak·of·the19 ······images·to·skip·at·the·begin·of·the·series,·if·(k·<·0)·use·RV·peak·of·the
20 ······registered·set·if·set20 ······registered·set·if·set
21 ··-r,·--reference=-1;·int21 ··-r,·--reference=-1;·int
22 ······reference·frame·for·automatic·curve·extraction.·Negative·values·can·be22 ······reference·frame·for·automatic·curve·extraction.·Negative·values·can·be
23 ······used·to·indicate·specific·values·(if·given·in·the·segmentation·set):·-3:23 ······used·to·indicate·specific·values·(if·given·in·the·segmentation·set):·-3:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegshift</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegseriesstats.html"·title="mia-2dsegseriesstats"><link·rel="next"·href="Secmia2dsegshiftperslice.html"·title="mia-2dsegshiftperslice"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegshift</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegseriesstats.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshiftperslice.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegshift"></a>mia-2dsegshift</h3></div></div></div><h4><a·name="idp7286"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegshift</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegshift</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegseriesstats.html"·title="mia-2dsegseriesstats"><link·rel="next"·href="Secmia2dsegshiftperslice.html"·title="mia-2dsegshiftperslice"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegshift</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegseriesstats.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshiftperslice.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegshift"></a>mia-2dsegshift</h3></div></div></div><h4><a·name="idp7286"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegshift</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7295"></a>Description:</h4><p·class="description">This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·equal·for·all·slices.·The·program·also·may·remove·images·from·the·begin·of·the·series.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·the·images·where·cropped.</p><h4><a·name="idp7297"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·segmentation·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>input·segmentation·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-g,·--image-file=crop;·stringSTRING</span></dt><dd><p>output·image·filename·base</p></dd><dt><span·class="term">-S,·--shift=[0,0];·2dfvector</span></dt><dd><p>shift·of·segmentation</p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·frames·at·the·beginning</p></dd></dl></div><h4><a·name="idp7321"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7372"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7378"></a>Example:</h4><p>Shift·the·segmentations·of·a·set·segement.set·by·-20·pixels·in·horizontal·direction·and·-30·pixels·in·vertical·direction·(as·if·the·images·where·cropped·starting·at·(20,30)·and·store·it·in·translate.set.·The·shiftes·files·are·named·translatedXXXX.png</p><pre·class="screen">mia-2dsegshift·-i·segment.set·-o·translate.set·-g·translated·-S·"&lt;20,30&gt;"</pre><h4><a·name="idp7381"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegseriesstats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshiftperslice.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegseriesstats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegshiftperslice</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7295"></a>Description:</h4><p·class="description">This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·equal·for·all·slices.·The·program·also·may·remove·images·from·the·begin·of·the·series.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·the·images·where·cropped.</p><h4><a·name="idp7297"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·segmentation·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>input·segmentation·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-g,·--image-file=crop;·stringSTRING</span></dt><dd><p>output·image·filename·base</p></dd><dt><span·class="term">-S,·--shift=[0,0];·2dfvector</span></dt><dd><p>shift·of·segmentation</p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·frames·at·the·beginning</p></dd></dl></div><h4><a·name="idp7321"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7372"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7378"></a>Example:</h4><p>Shift·the·segmentations·of·a·set·segement.set·by·-20·pixels·in·horizontal·direction·and·-30·pixels·in·vertical·direction·(as·if·the·images·where·cropped·starting·at·(20,30)·and·store·it·in·translate.set.·The·shiftes·files·are·named·translatedXXXX.png</p><pre·class="screen">mia-2dsegshift·-i·segment.set·-o·translate.set·-g·translated·-S·"&lt;20,30&gt;"</pre><h4><a·name="idp7381"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegseriesstats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dsegshiftperslice.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegseriesstats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dsegshiftperslice</td></tr></table></div></body></html>
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6 mia-2dsegshift·{-i·io}·{-o·io}·[·options·...]6 mia-2dsegshift·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that8 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that
9 is·equal·for·all·slices.·The·program·also·may·remove·images·from·the·begin·of9 is·equal·for·all·slices.·The·program·also·may·remove·images·from·the·begin·of
10 the·series.·The·program·can·be·used·to·correct·the·segmentation·of·the·images10 the·series.·The·program·can·be·used·to·correct·the·segmentation·of·the·images
11 if·the·images·where·cropped.11 if·the·images·where·cropped.
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·segmentation·set.·For·supported·file·types·see·Plugin_type:14 ······input·segmentation·set.·For·supported·file·types·see·Plugin_type:
15 ······2dimage/io15 ······2dimage/io
16 ··-o,·--out-file=(required,·output);·io16 ··-o,·--out-file=(required,·output);·io
17 ······input·segmentation·set.·For·supported·file·types·see·Plugin_type:17 ······input·segmentation·set.·For·supported·file·types·see·Plugin_type:
18 ······2dimage/io18 ······2dimage/io
19 ··-g,·--image-file=crop;·stringSTRING19 ··-g,·--image-file=crop;·stringSTRING
20 ······output·image·filename·base20 ······output·image·filename·base
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegshiftperslice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegshift.html"·title="mia-2dsegshift"><link·rel="next"·href="Secmia2dseriesmincorr.html"·title="mia-2dseries-mincorr"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegshiftperslice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegshift.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesmincorr.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegshiftperslice"></a>mia-2dsegshiftperslice</h3></div></div></div><h4><a·name="idp7385"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegshiftperslice</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-S·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dsegshiftperslice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegshift.html"·title="mia-2dsegshift"><link·rel="next"·href="Secmia2dseriesmincorr.html"·title="mia-2dseries-mincorr"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dsegshiftperslice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegshift.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesmincorr.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dsegshiftperslice"></a>mia-2dsegshiftperslice</h3></div></div></div><h4><a·name="idp7385"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dsegshiftperslice</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-S·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7396"></a>Description:</h4><p·class="description">This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·given·on·a·per-slice·base.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·a·linear·registration·was·executed·that·only·applies·a·translation·and·does·not·correct·the·segmentation·automatically.·</p><h4><a·name="idp7398"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·segmentation·set</p></dd><dt><span·class="term">-g,·--image-file=crop;·stringSTRING</span></dt><dd><p>output·image·filename·base</p></dd><dt><span·class="term">-S,·--shift=(required);·string</span></dt><dd><p>shift·of·segmentation·-·base·name·</p></dd></dl></div><h4><a·name="idp7416"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7467"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7473"></a>Example:</h4><p>Shirt·the·segmentation·given·in·set·segment.set·by·files·shiftXXXX.txt·and·store·the·result·in·shifted.set.·Note,·the·numbering·of·the·shiftXXXX.txx·files·must·coincide.</p><pre·class="screen">mia-2dsegshiftperslice·-i·segment.set·-o·shifted.set·-g·shifted·-S·shift</pre><h4><a·name="idp7476"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegshift.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesmincorr.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegshift </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries-mincorr</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7396"></a>Description:</h4><p·class="description">This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·given·on·a·per-slice·base.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·a·linear·registration·was·executed·that·only·applies·a·translation·and·does·not·correct·the·segmentation·automatically.·</p><h4><a·name="idp7398"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·segmentation·set</p></dd><dt><span·class="term">-g,·--image-file=crop;·stringSTRING</span></dt><dd><p>output·image·filename·base</p></dd><dt><span·class="term">-S,·--shift=(required);·string</span></dt><dd><p>shift·of·segmentation·-·base·name·</p></dd></dl></div><h4><a·name="idp7416"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7467"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7473"></a>Example:</h4><p>Shirt·the·segmentation·given·in·set·segment.set·by·files·shiftXXXX.txt·and·store·the·result·in·shifted.set.·Note,·the·numbering·of·the·shiftXXXX.txx·files·must·coincide.</p><pre·class="screen">mia-2dsegshiftperslice·-i·segment.set·-o·shifted.set·-g·shifted·-S·shift</pre><h4><a·name="idp7476"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegshift.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesmincorr.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegshift </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries-mincorr</td></tr></table></div></body></html>
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6 mia-2dsegshiftperslice·{-i·string}·{-o·string}·{-S·string}·[·options·...]6 mia-2dsegshiftperslice·{-i·string}·{-o·string}·{-S·string}·[·options·...]
7 Description:7 Description:
8 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that8 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that
9 is·given·on·a·per-slice·base.·The·program·can·be·used·to·correct·the9 is·given·on·a·per-slice·base.·The·program·can·be·used·to·correct·the
10 segmentation·of·the·images·if·a·linear·registration·was·executed·that·only10 segmentation·of·the·images·if·a·linear·registration·was·executed·that·only
11 applies·a·translation·and·does·not·correct·the·segmentation·automatically.11 applies·a·translation·and·does·not·correct·the·segmentation·automatically.
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·string13 ··-i,·--in-file=(required,·input);·string
14 ······input·segmentation·set14 ······input·segmentation·set
15 ··-o,·--out-file=(required,·output);·string15 ··-o,·--out-file=(required,·output);·string
16 ······output·segmentation·set16 ······output·segmentation·set
17 ··-g,·--image-file=crop;·stringSTRING17 ··-g,·--image-file=crop;·stringSTRING
18 ······output·image·filename·base18 ······output·image·filename·base
19 ··-S,·--shift=(required);·string19 ··-S,·--shift=(required);·string
20 ······shift·of·segmentation·-·base·name20 ······shift·of·segmentation·-·base·name
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries2dordermedian</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriessegdistance.html"·title="mia-2dseries-segdistance"><link·rel="next"·href="Secmia2dseries2sets.html"·title="mia-2dseries2sets"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries2dordermedian</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriessegdistance.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2sets.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseries2dordermedian"></a>mia-2dseries2dordermedian</h3></div></div></div><h4><a·name="idp7747"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries2dordermedian</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries2dordermedian</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriessegdistance.html"·title="mia-2dseries-segdistance"><link·rel="next"·href="Secmia2dseries2sets.html"·title="mia-2dseries2sets"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries2dordermedian</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriessegdistance.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2sets.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseries2dordermedian"></a>mia-2dseries2dordermedian</h3></div></div></div><h4><a·name="idp7747"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries2dordermedian</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp7759"></a>Description:</h4><p·class="description">This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the·gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In·addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given·pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving·additional·filters·as·free·parameters·(filter/2dimage).</p><h4><a·name="idp7761"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd><dt><span·class="term">-g,·--gauss=1;·ulong</span></dt><dd><p>gauss·filter·width·for·moothing·the·gradient</p></dd><dt><span·class="term">--itc-file=STRING</span></dt><dd><p>intensity·time·curve·output·file</p></dd><dt><span·class="term">--itc-loc=[0,0];·2dbounds</span></dt><dd><p>intensity·time·curve·output·pixel·coordinates</p></dd></dl></div><h4><a·name="idp7796"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7847"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7853"></a>Example:</h4><p>Evaluate·the·median·of·the·2nd·order·derivative·of·the·series·given·in·segmentation·set·segment.set·after·filtering·with·a·Gaussian·of·width·3.·In·addition·write·the·time·intensity·curve·of·pixel·&lt;128,64&gt;·to·curve.txt.</p><pre·class="screen">mia-2dseries2dordermedian·-i·segment.set·-o·gradmedian.exr·-g·1·--itc-file·curve.txt·--itc-loc·"&lt;128,64&gt;"</pre><h4><a·name="idp7856"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriessegdistance.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2sets.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries-segdistance </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries2sets</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp7759"></a>Description:</h4><p·class="description">This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the·gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In·addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given·pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving·additional·filters·as·free·parameters·(filter/2dimage).</p><h4><a·name="idp7761"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd><dt><span·class="term">-g,·--gauss=1;·ulong</span></dt><dd><p>gauss·filter·width·for·moothing·the·gradient</p></dd><dt><span·class="term">--itc-file=STRING</span></dt><dd><p>intensity·time·curve·output·file</p></dd><dt><span·class="term">--itc-loc=[0,0];·2dbounds</span></dt><dd><p>intensity·time·curve·output·pixel·coordinates</p></dd></dl></div><h4><a·name="idp7796"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7847"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7853"></a>Example:</h4><p>Evaluate·the·median·of·the·2nd·order·derivative·of·the·series·given·in·segmentation·set·segment.set·after·filtering·with·a·Gaussian·of·width·3.·In·addition·write·the·time·intensity·curve·of·pixel·&lt;128,64&gt;·to·curve.txt.</p><pre·class="screen">mia-2dseries2dordermedian·-i·segment.set·-o·gradmedian.exr·-g·1·--itc-file·curve.txt·--itc-loc·"&lt;128,64&gt;"</pre><h4><a·name="idp7856"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriessegdistance.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2sets.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries-segdistance </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries2sets</td></tr></table></div></body></html>
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8 Description:8 Description:
9 This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the9 This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the
10 gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In10 gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In
11 addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given11 addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given
12 pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving12 pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving
13 additional·filters·as·free·parameters·(filter/2dimage).13 additional·filters·as·free·parameters·(filter/2dimage).
14 Options:14 Options:
15 ··-i,·--in-file=(input,·required);·string15 ··-i,·--in-file=(required,·input);·string
16 ······input·segmentation·set16 ······input·segmentation·set
17 ··-o,·--out-file=(required,·output);·io17 ··-o,·--out-file=(required,·output);·io
18 ······output·image·name.·For·supported·file·types·see·Plugin_type:_2dimage/io18 ······output·image·name.·For·supported·file·types·see·Plugin_type:_2dimage/io
19 ··-k,·--skip=0;·ulong19 ··-k,·--skip=0;·ulong
20 ······Skip·files·at·the·beginning20 ······Skip·files·at·the·beginning
21 ··-e,·--enlarge-boundary=5;·ulong21 ··-e,·--enlarge-boundary=5;·ulong
22 ······Enlarge·cropbox·by·number·of·pixels22 ······Enlarge·cropbox·by·number·of·pixels
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriescorr</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseries2sets.html"·title="mia-2dseries2sets"><link·rel="next"·href="Secmia2dseriesgradMAD.html"·title="mia-2dseriesgradMAD"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriescorr</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseries2sets.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradMAD.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriescorr"></a>mia-2dseriescorr</h3></div></div></div><h4><a·name="idp7946"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriescorr</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriescorr</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseries2sets.html"·title="mia-2dseries2sets"><link·rel="next"·href="Secmia2dseriesgradMAD.html"·title="mia-2dseriesgradMAD"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriescorr</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseries2sets.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradMAD.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriescorr"></a>mia-2dseriescorr</h3></div></div></div><h4><a·name="idp7946"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriescorr</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7955"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent·the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as·average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be·of·the·same·pixel·type·and·size.</p><h4><a·name="idp7957"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-base=(input,·required);·io</span></dt><dd><p>input·file·name·base.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--outname=(required,·output);·io</span></dt><dd><p>output·file·name·to·save·the·avarage·per-pixel·correlation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-z,·--horizontal=(output);·io</span></dt><dd><p>horiZontal·correlation·output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--vertical=(output);·io</span></dt><dd><p>verTical··correlation·output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-e,·--end=60;·ulong</span></dt><dd><p>last·image·in·series</p></dd></dl></div><h4><a·name="idp7987"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8038"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8044"></a>Example:</h4><p>Evaluate·the·time-intensity·correaltions·for·an·image·series·imageXXXX.png·starting·at·image·2·and·stop·at·image·30.·Store·the·results·in·horizontal.exr,·and·vertical.exr.</p><pre·class="screen">mia-2dseriescorr·-i·image0000.png·-k·2·-e·30·-z·horizontal.exr·-t·vertical.exr</pre><h4><a·name="idp8047"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseries2sets.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradMAD.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries2sets </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriesgradMAD</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7955"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent·the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as·average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be·of·the·same·pixel·type·and·size.</p><h4><a·name="idp7957"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-base=(required,·input);·io</span></dt><dd><p>input·file·name·base.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--outname=(required,·output);·io</span></dt><dd><p>output·file·name·to·save·the·avarage·per-pixel·correlation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-z,·--horizontal=(output);·io</span></dt><dd><p>horiZontal·correlation·output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--vertical=(output);·io</span></dt><dd><p>verTical··correlation·output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-e,·--end=60;·ulong</span></dt><dd><p>last·image·in·series</p></dd></dl></div><h4><a·name="idp7987"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8038"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8044"></a>Example:</h4><p>Evaluate·the·time-intensity·correaltions·for·an·image·series·imageXXXX.png·starting·at·image·2·and·stop·at·image·30.·Store·the·results·in·horizontal.exr,·and·vertical.exr.</p><pre·class="screen">mia-2dseriescorr·-i·image0000.png·-k·2·-e·30·-z·horizontal.exr·-t·vertical.exr</pre><h4><a·name="idp8047"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseries2sets.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradMAD.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries2sets </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriesgradMAD</td></tr></table></div></body></html>
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6 mia-2dseriescorr·{-i·io}·{-o·io}·[·options·...]6 mia-2dseriescorr·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent8 Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent
9 the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as9 the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as
10 average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be10 average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be
11 of·the·same·pixel·type·and·size.11 of·the·same·pixel·type·and·size.
12 Options:12 Options:
13 ··-i,·--in-base=(input,·required);·io13 ··-i,·--in-base=(required,·input);·io
14 ······input·file·name·base.·For·supported·file·types·see·Plugin_type:_2dimage/14 ······input·file·name·base.·For·supported·file·types·see·Plugin_type:_2dimage/
15 ······io15 ······io
16 ··-o,·--outname=(required,·output);·io16 ··-o,·--outname=(required,·output);·io
17 ······output·file·name·to·save·the·avarage·per-pixel·correlation.·For·supported17 ······output·file·name·to·save·the·avarage·per-pixel·correlation.·For·supported
18 ······file·types·see·Plugin_type:_2dimage/io18 ······file·types·see·Plugin_type:_2dimage/io
19 ··-z,·--horizontal=(output);·io19 ··-z,·--horizontal=(output);·io
20 ······horiZontal·correlation·output·file·name.·For·supported·file·types·see20 ······horiZontal·correlation·output·file·name.·For·supported·file·types·see
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriesgradMAD</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriescorr.html"·title="mia-2dseriescorr"><link·rel="next"·href="Secmia2dseriesgradvariation.html"·title="mia-2dseriesgradvariation"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriesgradMAD</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriescorr.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradvariation.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriesgradMAD"></a>mia-2dseriesgradMAD</h3></div></div></div><h4><a·name="idp8051"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriesgradMAD</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriesgradMAD</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriescorr.html"·title="mia-2dseriescorr"><link·rel="next"·href="Secmia2dseriesgradvariation.html"·title="mia-2dseriesgradvariation"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriesgradMAD</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriescorr.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradvariation.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriesgradMAD"></a>mia-2dseriesgradMAD</h3></div></div></div><h4><a·name="idp8051"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriesgradMAD</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp8063"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·evaluates·the·pixel-wise·temporal·gradient·and·then·its·median·average·distance·(MAD)·and·stores·the·result·in·an·image.·Spacial·pre-filtering·may·be·applied·as·given·additional·plugin(s)·(filter/2dimage).</p><h4><a·name="idp8065"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd></dl></div><h4><a·name="idp8088"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8139"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8145"></a>Example:</h4><p>Evaluate·the·MAD-image·of·the·bounding·box·surrounding·the·segmentation·from·a·series·segment.set.·No·spacial·filtering·will·be·applied.·The·bounding·box·will·be·enlarged·by·3·pixels·in·all·directions.·Store·the·image·in·OpenEXR·format.</p><pre·class="screen">mia-2dseriesgradMAD··-i·segment.set·-o·mad.exr·-c·-e·3</pre><h4><a·name="idp8148"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriescorr.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradvariation.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriescorr </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriesgradvariation</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp8063"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·evaluates·the·pixel-wise·temporal·gradient·and·then·its·median·average·distance·(MAD)·and·stores·the·result·in·an·image.·Spacial·pre-filtering·may·be·applied·as·given·additional·plugin(s)·(filter/2dimage).</p><h4><a·name="idp8065"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd></dl></div><h4><a·name="idp8088"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8139"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8145"></a>Example:</h4><p>Evaluate·the·MAD-image·of·the·bounding·box·surrounding·the·segmentation·from·a·series·segment.set.·No·spacial·filtering·will·be·applied.·The·bounding·box·will·be·enlarged·by·3·pixels·in·all·directions.·Store·the·image·in·OpenEXR·format.</p><pre·class="screen">mia-2dseriesgradMAD··-i·segment.set·-o·mad.exr·-c·-e·3</pre><h4><a·name="idp8148"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriescorr.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriesgradvariation.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriescorr </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriesgradvariation</td></tr></table></div></body></html>
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7 filter·...]7 filter·...]
8 Description:8 Description:
9 Given·a·set·of·images·of·temporal·sucession,·evaluates·the·pixel-wise·temporal9 Given·a·set·of·images·of·temporal·sucession,·evaluates·the·pixel-wise·temporal
10 gradient·and·then·its·median·average·distance·(MAD)·and·stores·the·result·in·an10 gradient·and·then·its·median·average·distance·(MAD)·and·stores·the·result·in·an
11 image.·Spacial·pre-filtering·may·be·applied·as·given·additional·plugin(s)11 image.·Spacial·pre-filtering·may·be·applied·as·given·additional·plugin(s)
12 (filter/2dimage).12 (filter/2dimage).
13 Options:13 Options:
14 ··-i,·--in-file=(input,·required);·string14 ··-i,·--in-file=(required,·input);·string
15 ······input·segmentation·set15 ······input·segmentation·set
16 ··-o,·--out-file=(required,·output);·io16 ··-o,·--out-file=(required,·output);·io
17 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io17 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io
18 ··-k,·--skip=0;·ulong18 ··-k,·--skip=0;·ulong
19 ······Skip·files·at·the·beginning19 ······Skip·files·at·the·beginning
20 ··-e,·--enlarge-boundary=5;·ulong20 ··-e,·--enlarge-boundary=5;·ulong
21 ······Enlarge·cropbox·by·number·of·pixels21 ······Enlarge·cropbox·by·number·of·pixels
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriesgradvariation</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriesgradMAD.html"·title="mia-2dseriesgradMAD"><link·rel="next"·href="Secmia2dserieshausdorff.html"·title="mia-2dserieshausdorff"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriesgradvariation</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradMAD.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dserieshausdorff.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriesgradvariation"></a>mia-2dseriesgradvariation</h3></div></div></div><h4><a·name="idp8152"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriesgradvariation</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriesgradvariation</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriesgradMAD.html"·title="mia-2dseriesgradMAD"><link·rel="next"·href="Secmia2dserieshausdorff.html"·title="mia-2dserieshausdorff"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriesgradvariation</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradMAD.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dserieshausdorff.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriesgradvariation"></a>mia-2dseriesgradvariation</h3></div></div></div><h4><a·name="idp8152"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriesgradvariation</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8161"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·gradient·variation·of·the·pixel-wise·time-intensity·curves·of·this·series.·If·the·input·image·set·provides·a·segmentation,·then·this·segmentation·can·be·used·to·create·a·bounding·box·and·restrict·evaluation·to·this·box.·</p><h4><a·name="idp8163"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd></dl></div><h4><a·name="idp8186"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8237"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8243"></a>Example:</h4><p>Evaluate·the·gradient-variation·image·of·the·bounding·box·surrounding·the·segmentation·from·a·series·'segment.set'.·The·bounding·box·will·be·enlarged·by·3·pixels·in·all·directions.·Store·the·image·in·OpenEXR·format.</p><pre·class="screen">mia-2dseriesgradvariation··-i·segment.set·-o·gradvar.exr·-c·-e·3</pre><h4><a·name="idp8246"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradMAD.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dserieshausdorff.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriesgradMAD </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dserieshausdorff</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8161"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·gradient·variation·of·the·pixel-wise·time-intensity·curves·of·this·series.·If·the·input·image·set·provides·a·segmentation,·then·this·segmentation·can·be·used·to·create·a·bounding·box·and·restrict·evaluation·to·this·box.·</p><h4><a·name="idp8163"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd></dl></div><h4><a·name="idp8186"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8237"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8243"></a>Example:</h4><p>Evaluate·the·gradient-variation·image·of·the·bounding·box·surrounding·the·segmentation·from·a·series·'segment.set'.·The·bounding·box·will·be·enlarged·by·3·pixels·in·all·directions.·Store·the·image·in·OpenEXR·format.</p><pre·class="screen">mia-2dseriesgradvariation··-i·segment.set·-o·gradvar.exr·-c·-e·3</pre><h4><a·name="idp8246"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradMAD.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dserieshausdorff.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriesgradMAD </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dserieshausdorff</td></tr></table></div></body></html>
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6 mia-2dseriesgradvariation·{-i·string}·{-o·io}·[·options·...]6 mia-2dseriesgradvariation·{-i·string}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the8 Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the
9 gradient·variation·of·the·pixel-wise·time-intensity·curves·of·this·series.·If9 gradient·variation·of·the·pixel-wise·time-intensity·curves·of·this·series.·If
10 the·input·image·set·provides·a·segmentation,·then·this·segmentation·can·be·used10 the·input·image·set·provides·a·segmentation,·then·this·segmentation·can·be·used
11 to·create·a·bounding·box·and·restrict·evaluation·to·this·box.11 to·create·a·bounding·box·and·restrict·evaluation·to·this·box.
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·string13 ··-i,·--in-file=(required,·input);·string
14 ······input·segmentation·set14 ······input·segmentation·set
15 ··-o,·--out-file=(required,·output);·io15 ··-o,·--out-file=(required,·output);·io
16 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io16 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io
17 ··-k,·--skip=0;·ulong17 ··-k,·--skip=0;·ulong
18 ······Skip·files·at·the·beginning18 ······Skip·files·at·the·beginning
19 ··-e,·--enlarge-boundary=5;·ulong19 ··-e,·--enlarge-boundary=5;·ulong
20 ······Enlarge·cropbox·by·number·of·pixels20 ······Enlarge·cropbox·by·number·of·pixels
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dserieshausdorff</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriesgradvariation.html"·title="mia-2dseriesgradvariation"><link·rel="next"·href="Secmia2dseriessmoothgradMAD.html"·title="mia-2dseriessmoothgradMAD"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dserieshausdorff</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradvariation.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessmoothgradMAD.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dserieshausdorff"></a>mia-2dserieshausdorff</h3></div></div></div><h4><a·name="idp8250"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dserieshausdorff</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dserieshausdorff</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriesgradvariation.html"·title="mia-2dseriesgradvariation"><link·rel="next"·href="Secmia2dseriessmoothgradMAD.html"·title="mia-2dseriessmoothgradMAD"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dserieshausdorff</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradvariation.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessmoothgradMAD.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dserieshausdorff"></a>mia-2dserieshausdorff</h3></div></div></div><h4><a·name="idp8250"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dserieshausdorff</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8259"></a>Description:</h4><p·class="description">Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given·reference·segmentation·set.</p><h4><a·name="idp8261"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--ref-file=(input,·required);·string</span></dt><dd><p>reference·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·images·at·the·beginning</p></dd></dl></div><h4><a·name="idp8275"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8326"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8332"></a>Example:</h4><p>Evaluate·the·per-frame·Hausdorff·distance·of·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·set·reference.set·skipping·two·images·at·the·beginning.</p><pre·class="screen">mia-2dserieshausdorff··-i·segment.set·-r·reference.set·-k·2</pre><h4><a·name="idp8335"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradvariation.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessmoothgradMAD.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriesgradvariation </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriessmoothgradMAD</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8259"></a>Description:</h4><p·class="description">Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given·reference·segmentation·set.</p><h4><a·name="idp8261"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--ref-file=(required,·input);·string</span></dt><dd><p>reference·segmentation·set</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·images·at·the·beginning</p></dd></dl></div><h4><a·name="idp8275"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8326"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8332"></a>Example:</h4><p>Evaluate·the·per-frame·Hausdorff·distance·of·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·set·reference.set·skipping·two·images·at·the·beginning.</p><pre·class="screen">mia-2dserieshausdorff··-i·segment.set·-r·reference.set·-k·2</pre><h4><a·name="idp8335"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriesgradvariation.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessmoothgradMAD.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriesgradvariation </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriessmoothgradMAD</td></tr></table></div></body></html>
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4 mia-2dserieshausdorff4 mia-2dserieshausdorff
5 Sysnopis:5 Sysnopis:
6 mia-2dserieshausdorff·{-i·string}·{-r·string}·[·options·...]6 mia-2dserieshausdorff·{-i·string}·{-r·string}·[·options·...]
7 Description:7 Description:
8 Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given8 Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given
9 reference·segmentation·set.9 reference·segmentation·set.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·string11 ··-i,·--in-file=(required,·input);·string
12 ······input·segmentation·set12 ······input·segmentation·set
13 ··-r,·--ref-file=(input,·required);·string13 ··-r,·--ref-file=(required,·input);·string
14 ······reference·segmentation·set14 ······reference·segmentation·set
15 ··-k,·--skip=0;·int15 ··-k,·--skip=0;·int
16 ······skip·images·at·the·beginning16 ······skip·images·at·the·beginning
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
20 ······Supported·priorities·starting·at·lowest·level·are:20 ······Supported·priorities·starting·at·lowest·level·are:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries-mincorr</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegshiftperslice.html"·title="mia-2dsegshiftperslice"><link·rel="next"·href="Secmia2dseriessectionmask.html"·title="mia-2dseries-sectionmask"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries-mincorr</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegshiftperslice.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessectionmask.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriesmincorr"></a>mia-2dseries-mincorr</h3></div></div></div><h4><a·name="idp7480"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries-mincorr</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries-mincorr</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dsegshiftperslice.html"·title="mia-2dsegshiftperslice"><link·rel="next"·href="Secmia2dseriessectionmask.html"·title="mia-2dseries-sectionmask"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries-mincorr</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dsegshiftperslice.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessectionmask.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriesmincorr"></a>mia-2dseries-mincorr</h3></div></div></div><h4><a·name="idp7480"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries-mincorr</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7489"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal·correlation·of·the·time-intensity·curve·between·neighboring·pixels.</p><h4><a·name="idp7491"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-set=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-set=(required,·output);·io</span></dt><dd><p>output·image·of·minimal·correlation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd></dl></div><h4><a·name="idp7506"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7557"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7563"></a>Example:</h4><p>Evaluate·the·minimal·correlation·image·of·a·series·givemn·in··segment.set·and·store·the·image·in·OpenEXR·format.·Skip·two·images·at·the·beginning·of·the·series.</p><pre·class="screen">mia-2dseries-mincorr·-i·segment.set·-o·mincorr.exr·-k·2</pre><h4><a·name="idp7566"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegshiftperslice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessectionmask.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegshiftperslice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries-sectionmask</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7489"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal·correlation·of·the·time-intensity·curve·between·neighboring·pixels.</p><h4><a·name="idp7491"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-set=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-set=(required,·output);·io</span></dt><dd><p>output·image·of·minimal·correlation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=2;·ulong</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd></dl></div><h4><a·name="idp7506"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7557"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7563"></a>Example:</h4><p>Evaluate·the·minimal·correlation·image·of·a·series·givemn·in··segment.set·and·store·the·image·in·OpenEXR·format.·Skip·two·images·at·the·beginning·of·the·series.</p><pre·class="screen">mia-2dseries-mincorr·-i·segment.set·-o·mincorr.exr·-k·2</pre><h4><a·name="idp7566"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dsegshiftperslice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessectionmask.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dsegshiftperslice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries-sectionmask</td></tr></table></div></body></html>
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4 mia-2dseries-mincorr4 mia-2dseries-mincorr
5 Sysnopis:5 Sysnopis:
6 mia-2dseries-mincorr·{-i·string}·{-o·io}·[·options·...]6 mia-2dseries-mincorr·{-i·string}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal8 Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal
9 correlation·of·the·time-intensity·curve·between·neighboring·pixels.9 correlation·of·the·time-intensity·curve·between·neighboring·pixels.
10 Options:10 Options:
11 ··-i,·--in-set=(input,·required);·string11 ··-i,·--in-set=(required,·input);·string
12 ······input·segmentation·set12 ······input·segmentation·set
13 ··-o,·--out-set=(required,·output);·io13 ··-o,·--out-set=(required,·output);·io
14 ······output·image·of·minimal·correlation.·For·supported·file·types·see·Plugin14 ······output·image·of·minimal·correlation.·For·supported·file·types·see·Plugin
15 ······type:_2dimage/io15 ······type:_2dimage/io
16 ··-k,·--skip=2;·ulong16 ··-k,·--skip=2;·ulong
17 ······skip·images·at·beginning·of·series17 ······skip·images·at·beginning·of·series
18 Help·&·Info18 Help·&·Info
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries-sectionmask</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriesmincorr.html"·title="mia-2dseries-mincorr"><link·rel="next"·href="Secmia2dseriessegdistance.html"·title="mia-2dseries-segdistance"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries-sectionmask</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriesmincorr.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessegdistance.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriessectionmask"></a>mia-2dseries-sectionmask</h3></div></div></div><h4><a·name="idp7570"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries-sectionmask</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries-sectionmask</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriesmincorr.html"·title="mia-2dseries-mincorr"><link·rel="next"·href="Secmia2dseriessegdistance.html"·title="mia-2dseries-segdistance"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries-sectionmask</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriesmincorr.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessegdistance.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriessectionmask"></a>mia-2dseries-sectionmask</h3></div></div></div><h4><a·name="idp7570"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries-sectionmask</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7579"></a>Description:</h4><p·class="description">Evaluate·the·masks·for·the·sections·of·a·segmented·frame.</p><h4><a·name="idp7581"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·containing·the·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-f,·--frame=0;·ulong</span></dt><dd><p>Frame·number·for·which·to·extract·the·mask</p></dd></dl></div><h4><a·name="idp7596"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7647"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7653"></a>Example:</h4><p>Evaluate·the·mask·image·from·the·segmentation·of·image·20·in·segment.set·and·store·it·to·mask20.png:</p><pre·class="screen">mia-2dseries-sectionmask·-i·segment.set·-f·20·-o·mask20.png</pre><h4><a·name="idp7656"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriesmincorr.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessegdistance.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries-mincorr </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries-segdistance</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7579"></a>Description:</h4><p·class="description">Evaluate·the·masks·for·the·sections·of·a·segmented·frame.</p><h4><a·name="idp7581"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·containing·the·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-f,·--frame=0;·ulong</span></dt><dd><p>Frame·number·for·which·to·extract·the·mask</p></dd></dl></div><h4><a·name="idp7596"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7647"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7653"></a>Example:</h4><p>Evaluate·the·mask·image·from·the·segmentation·of·image·20·in·segment.set·and·store·it·to·mask20.png:</p><pre·class="screen">mia-2dseries-sectionmask·-i·segment.set·-f·20·-o·mask20.png</pre><h4><a·name="idp7656"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriesmincorr.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriessegdistance.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries-mincorr </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries-segdistance</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dseries-sectionmask4 mia-2dseries-sectionmask
5 Sysnopis:5 Sysnopis:
6 mia-2dseries-sectionmask·{-i·string}·{-o·io}·[·options·...]6 mia-2dseries-sectionmask·{-i·string}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Evaluate·the·masks·for·the·sections·of·a·segmented·frame.8 Evaluate·the·masks·for·the·sections·of·a·segmented·frame.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·string10 ··-i,·--in-file=(required,·input);·string
11 ······input·segmentation·set11 ······input·segmentation·set
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·image·containing·the·mask.·For·supported·file·types·see·Plugin13 ······output·image·containing·the·mask.·For·supported·file·types·see·Plugin
14 ······type:_2dimage/io14 ······type:_2dimage/io
15 ··-f,·--frame=0;·ulong15 ··-f,·--frame=0;·ulong
16 ······Frame·number·for·which·to·extract·the·mask16 ······Frame·number·for·which·to·extract·the·mask
17 Help·&·Info17 Help·&·Info
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries-segdistance</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriessectionmask.html"·title="mia-2dseries-sectionmask"><link·rel="next"·href="Secmia2dseries2dordermedian.html"·title="mia-2dseries2dordermedian"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries-segdistance</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriessectionmask.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2dordermedian.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriessegdistance"></a>mia-2dseries-segdistance</h3></div></div></div><h4><a·name="idp7660"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries-segdistance</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseries-segdistance</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriessectionmask.html"·title="mia-2dseries-sectionmask"><link·rel="next"·href="Secmia2dseries2dordermedian.html"·title="mia-2dseries2dordermedian"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseries-segdistance</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriessectionmask.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2dordermedian.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriessegdistance"></a>mia-2dseries-segdistance</h3></div></div></div><h4><a·name="idp7660"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseries-segdistance</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp7667"></a>Description:</h4><p·class="description">Get·the·mean·distance·of·a·segmentation·boundary·to·the·reference·boundary.</p><h4><a·name="idp7669"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--reference=20;·ulong</span></dt><dd><p>reference·frame</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·images·at·the·beginning</p></dd></dl></div><h4><a·name="idp7683"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7734"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7740"></a>Example:</h4><p>Evaluate·the·mean·absolute·border·distanceof·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·given·in·frame·20.</p><pre·class="screen">mia-2dseries-segdistance··-i·segment.set·-r·20</pre><h4><a·name="idp7743"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriessectionmask.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2dordermedian.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries-sectionmask </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries2dordermedian</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp7667"></a>Description:</h4><p·class="description">Get·the·mean·distance·of·a·segmentation·boundary·to·the·reference·boundary.</p><h4><a·name="idp7669"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-r,·--reference=20;·ulong</span></dt><dd><p>reference·frame</p></dd><dt><span·class="term">-k,·--skip=0;·int</span></dt><dd><p>skip·images·at·the·beginning</p></dd></dl></div><h4><a·name="idp7683"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp7734"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp7740"></a>Example:</h4><p>Evaluate·the·mean·absolute·border·distanceof·the·segmentations·of·set·segment.set·with·respect·to·the·segmentation·given·in·frame·20.</p><pre·class="screen">mia-2dseries-segdistance··-i·segment.set·-r·20</pre><h4><a·name="idp7743"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriessectionmask.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseries2dordermedian.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseries-sectionmask </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseries2dordermedian</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dseries-segdistance4 mia-2dseries-segdistance
5 Sysnopis:5 Sysnopis:
6 mia-2dseries-segdistance·{-i·string}·[·options·...]6 mia-2dseries-segdistance·{-i·string}·[·options·...]
7 Description:7 Description:
8 Get·the·mean·distance·of·a·segmentation·boundary·to·the·reference·boundary.8 Get·the·mean·distance·of·a·segmentation·boundary·to·the·reference·boundary.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·string10 ··-i,·--in-file=(required,·input);·string
11 ······input·segmentation·set11 ······input·segmentation·set
12 ··-r,·--reference=20;·ulong12 ··-r,·--reference=20;·ulong
13 ······reference·frame13 ······reference·frame
14 ··-k,·--skip=0;·int14 ··-k,·--skip=0;·int
15 ······skip·images·at·the·beginning15 ······skip·images·at·the·beginning
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriessmoothgradMAD</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dserieshausdorff.html"·title="mia-2dserieshausdorff"><link·rel="next"·href="Secmia2dseriestovolume.html"·title="mia-2dseriestovolume"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriessmoothgradMAD</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dserieshausdorff.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriestovolume.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriessmoothgradMAD"></a>mia-2dseriessmoothgradMAD</h3></div></div></div><h4><a·name="idp8339"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriessmoothgradMAD</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriessmoothgradMAD</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dserieshausdorff.html"·title="mia-2dserieshausdorff"><link·rel="next"·href="Secmia2dseriestovolume.html"·title="mia-2dseriestovolume"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriessmoothgradMAD</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dserieshausdorff.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dseriestovolume.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriessmoothgradMAD"></a>mia-2dseriessmoothgradMAD</h3></div></div></div><h4><a·name="idp8339"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriessmoothgradMAD</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype2dimagefilter.html"·title="Plugin·type:·2dimage/filter">Plugin·type:·2dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp8351"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·evaluate·the·temporal·pixel-wise·gaussian·and·evaluate·pixel-wise·its·MAD.A·spacial·pre-filtering·may·be·applied·by·specifying·additional·plugins·(filter/2dimage)</p><h4><a·name="idp8353"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd><dt><span·class="term">-g,·--gauss=1;·ulong</span></dt><dd><p>gauss·filter·width·for·moothing·the·gradient</p></dd></dl></div><h4><a·name="idp8380"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8431"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8437"></a>Example:</h4><p>Evaluate·the·MAD-image·of·the·bounding·box·surrounding·the·segmentation·from·a·series·segment.set·after·applying·a·temporal·Gaussian·filter·of·width·5.·No·spacial·filtering·will·be·applied.·The·bounding·box·will·be·enlarged·by·3·pixels·in·all·directions.·Store·the·image·in·OpenEXR·format.</p><pre·class="screen">mia-2dseriessmoothgradMAD·-i·segment.set·-o·mad.exr·-g·2·-c·-e·3</pre><h4><a·name="idp8440"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dserieshausdorff.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriestovolume.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dserieshausdorff </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriestovolume</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp8351"></a>Description:</h4><p·class="description">Given·a·set·of·images·of·temporal·sucession,·evaluate·the·temporal·pixel-wise·gaussian·and·evaluate·pixel-wise·its·MAD.A·spacial·pre-filtering·may·be·applied·by·specifying·additional·plugins·(filter/2dimage)</p><h4><a·name="idp8353"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·ulong</span></dt><dd><p>Enlarge·cropbox·by·number·of·pixels</p></dd><dt><span·class="term">-c,·--crop</span></dt><dd><p>crop·image·before·running·statistics</p></dd><dt><span·class="term">-g,·--gauss=1;·ulong</span></dt><dd><p>gauss·filter·width·for·moothing·the·gradient</p></dd></dl></div><h4><a·name="idp8380"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8431"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8437"></a>Example:</h4><p>Evaluate·the·MAD-image·of·the·bounding·box·surrounding·the·segmentation·from·a·series·segment.set·after·applying·a·temporal·Gaussian·filter·of·width·5.·No·spacial·filtering·will·be·applied.·The·bounding·box·will·be·enlarged·by·3·pixels·in·all·directions.·Store·the·image·in·OpenEXR·format.</p><pre·class="screen">mia-2dseriessmoothgradMAD·-i·segment.set·-o·mad.exr·-g·2·-c·-e·3</pre><h4><a·name="idp8440"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dserieshausdorff.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dseriestovolume.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dserieshausdorff </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dseriestovolume</td></tr></table></div></body></html>
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6 mia-2dseriessmoothgradMAD·{-i·string}·{-o·io}·[·options·...]·[·Plugin_type:6 mia-2dseriessmoothgradMAD·{-i·string}·{-o·io}·[·options·...]·[·Plugin_type:
7 2dimage/filter·...]7 2dimage/filter·...]
8 Description:8 Description:
9 Given·a·set·of·images·of·temporal·sucession,·evaluate·the·temporal·pixel-wise9 Given·a·set·of·images·of·temporal·sucession,·evaluate·the·temporal·pixel-wise
10 gaussian·and·evaluate·pixel-wise·its·MAD.A·spacial·pre-filtering·may·be·applied10 gaussian·and·evaluate·pixel-wise·its·MAD.A·spacial·pre-filtering·may·be·applied
11 by·specifying·additional·plugins·(filter/2dimage)11 by·specifying·additional·plugins·(filter/2dimage)
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·string13 ··-i,·--in-file=(required,·input);·string
14 ······input·segmentation·set14 ······input·segmentation·set
15 ··-o,·--out-file=(required,·output);·io15 ··-o,·--out-file=(required,·output);·io
16 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io16 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io
17 ··-k,·--skip=0;·ulong17 ··-k,·--skip=0;·ulong
18 ······Skip·files·at·the·beginning18 ······Skip·files·at·the·beginning
19 ··-e,·--enlarge-boundary=5;·ulong19 ··-e,·--enlarge-boundary=5;·ulong
20 ······Enlarge·cropbox·by·number·of·pixels20 ······Enlarge·cropbox·by·number·of·pixels
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriestovolume</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriessmoothgradMAD.html"·title="mia-2dseriessmoothgradMAD"><link·rel="next"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriestovolume</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriessmoothgradMAD.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriestovolume"></a>mia-2dseriestovolume</h3></div></div></div><h4><a·name="idp8444"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriestovolume</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dseriestovolume</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"><link·rel="prev"·href="Secmia2dseriessmoothgradMAD.html"·title="mia-2dseriessmoothgradMAD"><link·rel="next"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dseriestovolume</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dseriessmoothgradMAD.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·Myocardial·Perfusion·Analysis</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dseriestovolume"></a>mia-2dseriestovolume</h3></div></div></div><h4><a·name="idp8444"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dseriestovolume</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8453"></a>Description:</h4><p·class="description">Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.</p><h4><a·name="idp8455"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·3D·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>number·of·frames·to·skip·at·the·beginning·of·the·series.</p></dd></dl></div><h4><a·name="idp8470"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8521"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8527"></a>Example:</h4><p>Create·the·volume·volume.v·from·the·series·series.set·but·skip·the·first·two·images.</p><pre·class="screen">mia-2dseriestovolume·-i·series.set·-k·2·-o·volume.v</pre><h4><a·name="idp8530"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriessmoothgradMAD.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriessmoothgradMAD </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8453"></a>Description:</h4><p·class="description">Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.</p><h4><a·name="idp8455"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·segmentation·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·3D·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>number·of·frames·to·skip·at·the·beginning·of·the·series.</p></dd></dl></div><h4><a·name="idp8470"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8521"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8527"></a>Example:</h4><p>Create·the·volume·volume.v·from·the·series·series.set·but·skip·the·first·two·images.</p><pre·class="screen">mia-2dseriestovolume·-i·series.set·-k·2·-o·volume.v</pre><h4><a·name="idp8530"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dseriessmoothgradMAD.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsforMyocardialPerfusionAnalysis.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dseriessmoothgradMAD </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dseriestovolume4 mia-2dseriestovolume
5 Sysnopis:5 Sysnopis:
6 mia-2dseriestovolume·{-i·string}·{-o·io}·[·options·...]6 mia-2dseriestovolume·{-i·string}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.8 Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·string10 ··-i,·--in-file=(required,·input);·string
11 ······input·segmentation·set11 ······input·segmentation·set
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·3D·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······output·3D·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-k,·--skip=0;·ulong14 ··-k,·--skip=0;·ulong
15 ······number·of·frames·to·skip·at·the·beginning·of·the·series.15 ······number·of·frames·to·skip·at·the·beginning·of·the·series.
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dstack-cmeans-presegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia2dimagestackcmeans.html"·title="mia-2dimagestack-cmeans"><link·rel="next"·href="Secmia2dstackfilter.html"·title="mia-2dstackfilter"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dstack-cmeans-presegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagestackcmeans.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dstackfilter.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dstackcmeanspresegment"></a>mia-2dstack-cmeans-presegment</h3></div></div></div><h4><a·name="idp8652"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dstack-cmeans-presegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-L·<em·class="replaceable"><code>int</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dstack-cmeans-presegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia2dimagestackcmeans.html"·title="mia-2dimagestack-cmeans"><link·rel="next"·href="Secmia2dstackfilter.html"·title="mia-2dstackfilter"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dstack-cmeans-presegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dimagestackcmeans.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dstackfilter.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dstackcmeanspresegment"></a>mia-2dstack-cmeans-presegment</h3></div></div></div><h4><a·name="idp8652"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dstack-cmeans-presegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-L·<em·class="replaceable"><code>int</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8663"></a>Description:</h4><p·class="description">This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram,·and·then·estimates·the·mask·for·one·(given)·class·based·on·class·probabilities.·This·program·accepts·only·images·of·eight·or·16·bit·integer·pixels.</p><h4><a·name="idp8665"></a>Options:</h4><h4><a·name="idp8666"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--out-probmap=(output);·string</span></dt><dd><p>Save·probability·map·to·this·file</p></dd><dt><span·class="term">-t,·--type=png;·stringSTRING</span></dt><dd><p>output·file·name·type</p></dd><dt><span·class="term">-o,·--out-mask=(required,·output);·string</span></dt><dd><p>output·file·name·base</p></dd></dl></div><h4><a·name="idp8685"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8736"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--histogram-thresh=5;·float·in·[0,·50]</span></dt><dd><p>Percent·of·the·extrem·parts·of·the·histogram·to·be·collapsed·into·the·respective·last·histogram·bin.</p></dd><dt><span·class="term">-C,·--classes=kmeans:nc=3;·factory</span></dt><dd><p>C-means·class·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd><dt><span·class="term">-S,·--seed-threshold=0.95;·float·in·(0,·1)</span></dt><dd><p>Probability·threshold·value·to·consider·a·pixel·as·seed·pixel.</p></dd><dt><span·class="term">-L,·--label=(required);·int·in·[0,·10]</span></dt><dd><p>Class·label·to·create·the·mask·from</p></dd></dl></div><h4><a·name="idp8755"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8761"></a>Example:</h4><p>Run·the·program·over·images·imageXXXX.png·with·the·sparse·histogram,·threshold·the·lower·30%·bins·(if·available),·run·cmeans·with·two·classes·on·the·non-zero·pixels·and·then·create·the·mask·for·class·1·as·foregroundXXXX.png.</p><pre·class="screen">mia-2dstack-cmeans-presegment·-i·imageXXXX.png·-o·foreground·-t·png·--histogram-tresh=30·--classes·2·--label·1</pre><h4><a·name="idp8764"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagestackcmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dstackfilter.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagestack-cmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dstackfilter</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8663"></a>Description:</h4><p·class="description">This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram,·and·then·estimates·the·mask·for·one·(given)·class·based·on·class·probabilities.·This·program·accepts·only·images·of·eight·or·16·bit·integer·pixels.</p><h4><a·name="idp8665"></a>Options:</h4><h4><a·name="idp8666"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-p,·--out-probmap=(output);·string</span></dt><dd><p>Save·probability·map·to·this·file</p></dd><dt><span·class="term">-t,·--type=png;·stringSTRING</span></dt><dd><p>output·file·name·type</p></dd><dt><span·class="term">-o,·--out-mask=(required,·output);·string</span></dt><dd><p>output·file·name·base</p></dd></dl></div><h4><a·name="idp8685"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8736"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--histogram-thresh=5;·float·in·[0,·50]</span></dt><dd><p>Percent·of·the·extrem·parts·of·the·histogram·to·be·collapsed·into·the·respective·last·histogram·bin.</p></dd><dt><span·class="term">-C,·--classes=kmeans:nc=3;·factory</span></dt><dd><p>C-means·class·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd><dt><span·class="term">-S,·--seed-threshold=0.95;·float·in·(0,·1)</span></dt><dd><p>Probability·threshold·value·to·consider·a·pixel·as·seed·pixel.</p></dd><dt><span·class="term">-L,·--label=(required);·int·in·[0,·10]</span></dt><dd><p>Class·label·to·create·the·mask·from</p></dd></dl></div><h4><a·name="idp8755"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8761"></a>Example:</h4><p>Run·the·program·over·images·imageXXXX.png·with·the·sparse·histogram,·threshold·the·lower·30%·bins·(if·available),·run·cmeans·with·two·classes·on·the·non-zero·pixels·and·then·create·the·mask·for·class·1·as·foregroundXXXX.png.</p><pre·class="screen">mia-2dstack-cmeans-presegment·-i·imageXXXX.png·-o·foreground·-t·png·--histogram-tresh=30·--classes·2·--label·1</pre><h4><a·name="idp8764"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dimagestackcmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dstackfilter.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dimagestack-cmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dstackfilter</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then8 This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then
9 runs·a·c-means·classification·over·the·histogram,·and·then·estimates·the·mask9 runs·a·c-means·classification·over·the·histogram,·and·then·estimates·the·mask
10 for·one·(given)·class·based·on·class·probabilities.·This·program·accepts·only10 for·one·(given)·class·based·on·class·probabilities.·This·program·accepts·only
11 images·of·eight·or·16·bit·integer·pixels.11 images·of·eight·or·16·bit·integer·pixels.
12 Options:12 Options:
13 File-IO13 File-IO
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:15 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
16 ······2dimage/io16 ······2dimage/io
17 ··-p,·--out-probmap=(output);·string17 ··-p,·--out-probmap=(output);·string
18 ······Save·probability·map·to·this·file18 ······Save·probability·map·to·this·file
19 ··-t,·--type=png;·stringSTRING19 ··-t,·--type=png;·stringSTRING
20 ······output·file·name·type20 ······output·file·name·type
21 ··-o,·--out-mask=(required,·output);·string21 ··-o,·--out-mask=(required,·output);·string
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dstackfilter</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia2dstackcmeanspresegment.html"·title="mia-2dstack-cmeans-presegment"><link·rel="next"·href="Secmia3ddistance.html"·title="mia-3ddistance"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dstackfilter</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dstackcmeanspresegment.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3ddistance.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dstackfilter"></a>mia-2dstackfilter</h3></div></div></div><h4><a·name="idp8768"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dstackfilter</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>set</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dstackfilter</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia2dstackcmeanspresegment.html"·title="mia-2dstack-cmeans-presegment"><link·rel="next"·href="Secmia3ddistance.html"·title="mia-3ddistance"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dstackfilter</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dstackcmeanspresegment.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3ddistance.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dstackfilter"></a>mia-2dstackfilter</h3></div></div></div><h4><a·name="idp8768"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dstackfilter</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>set</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype2dstackfilter.html"·title="Plugin·type:·2dstack/filter">Plugin·type:·2dstack/filter</a>5 ············<a·class="xref"·href="SecPlugintype2dstackfilter.html"·title="Plugin·type:·2dstack/filter">Plugin·type:·2dstack/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp8782"></a>Description:</h4><p·class="description">This·program·is·used·to·filter·and·convert·a·series·of·2D·gray·scale·images·in·a·3D·fashion·by·running·filters·(filter/2dimage)·as·given·on·the·command·line.</p><h4><a·name="idp8784"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name·base,·the·actual·names·is·created·by·adding·the·file·number·based·on·output·order·and·the·extension·bysed·on·the·'type'·parameter.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--type=(required);·set</span></dt><dd><p>output·file·type<td·align="left"·valign="top">·Supported·values·are:(-,·@,·BMP,·DCM,·EXR,·JPEG,·JPG,·PNG,·RAW,·TIF,·TIFF,·V,·VISTA,·bmp,·dcm,·exr,·jpeg,·jpg,·png,·raw,·tif,·tiff,·v,·vista,·)</td></p></dd></dl></div><h4><a·name="idp8801"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8852"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8858"></a>Example:</h4><p>Run·a·mean-least-varaiance·filter·on·a·series·of·images·that·follow·the·numbering·pattern·imageXXXX.exr·and·store·the·output·in·images·filteredXXXX.exr</p><pre·class="screen">mia-2dstackfilter·-i·image0000.exr·-o·filtered·-t·exr·mlv:w=2</pre><h4><a·name="idp8861"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dstackcmeanspresegment.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3ddistance.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dstack-cmeans-presegment </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3ddistance</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp8782"></a>Description:</h4><p·class="description">This·program·is·used·to·filter·and·convert·a·series·of·2D·gray·scale·images·in·a·3D·fashion·by·running·filters·(filter/2dimage)·as·given·on·the·command·line.</p><h4><a·name="idp8784"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name·base,·the·actual·names·is·created·by·adding·the·file·number·based·on·output·order·and·the·extension·bysed·on·the·'type'·parameter.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--type=(required);·set</span></dt><dd><p>output·file·type<td·align="left"·valign="top">·Supported·values·are:(-,·@,·BMP,·DCM,·EXR,·JPEG,·JPG,·PNG,·RAW,·TIF,·TIFF,·V,·VISTA,·bmp,·dcm,·exr,·jpeg,·jpg,·png,·raw,·tif,·tiff,·v,·vista,·)</td></p></dd></dl></div><h4><a·name="idp8801"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8852"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8858"></a>Example:</h4><p>Run·a·mean-least-varaiance·filter·on·a·series·of·images·that·follow·the·numbering·pattern·imageXXXX.exr·and·store·the·output·in·images·filteredXXXX.exr</p><pre·class="screen">mia-2dstackfilter·-i·image0000.exr·-o·filtered·-t·exr·mlv:w=2</pre><h4><a·name="idp8861"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dstackcmeanspresegment.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3ddistance.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dstack-cmeans-presegment </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3ddistance</td></tr></table></div></body></html>
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dto3dimage</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia2dmultiimageto3d.html"·title="mia-2dmultiimageto3d"><link·rel="next"·href="Secmia2dto3dimageb.html"·title="mia-2dto3dimageb"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dto3dimage</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageto3d.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimageb.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dto3dimage"></a>mia-2dto3dimage</h3></div></div></div><h4><a·name="idp231"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dto3dimage</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dto3dimage</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia2dmultiimageto3d.html"·title="mia-2dmultiimageto3d"><link·rel="next"·href="Secmia2dto3dimageb.html"·title="mia-2dto3dimageb"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dto3dimage</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageto3d.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimageb.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dto3dimage"></a>mia-2dto3dimage</h3></div></div></div><h4><a·name="idp231"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dto3dimage</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp240"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·a·series·of·2D·images·of·equal·size·and·type·images·following·a·certain·numbering·scheme·to·a·3D·image.</p><h4><a·name="idp242"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp254"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp305"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp311"></a>Example:</h4><p>Convert·a·series·of·images·imageXXXX.png·to·a·3D·image·3d.v</p><pre·class="screen">mia-2dto3dimage·-i·imageXXXX.png·-o·3d.v</pre><h4><a·name="idp314"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageto3d.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimageb.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmultiimageto3d </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dto3dimageb</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp240"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·a·series·of·2D·images·of·equal·size·and·type·images·following·a·certain·numbering·scheme·to·a·3D·image.</p><h4><a·name="idp242"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp254"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp305"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp311"></a>Example:</h4><p>Convert·a·series·of·images·imageXXXX.png·to·a·3D·image·3d.v</p><pre·class="screen">mia-2dto3dimage·-i·imageXXXX.png·-o·3d.v</pre><h4><a·name="idp314"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageto3d.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dto3dimageb.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmultiimageto3d </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dto3dimageb</td></tr></table></div></body></html>
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4 mia-2dto3dimage4 mia-2dto3dimage
5 Sysnopis:5 Sysnopis:
6 mia-2dto3dimage·{-i·io}·{-o·io}·[·options·...]6 mia-2dto3dimage·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·combine·a·series·of·2D·images·of·equal·size·and·type8 This·program·is·used·to·combine·a·series·of·2D·images·of·equal·size·and·type
9 images·following·a·certain·numbering·scheme·to·a·3D·image.9 images·following·a·certain·numbering·scheme·to·a·3D·image.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·image(s)·to·be·combined.·For·supported·file·types·see·Plugin_type:12 ······input·image(s)·to·be·combined.·For·supported·file·types·see·Plugin_type:
13 ······2dimage/io13 ······2dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·file·name.·For·supported·file·types·see·Plugin_type:_3dimage/io15 ······output·file·name.·For·supported·file·types·see·Plugin_type:_3dimage/io
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dtrackpixelmovement</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsfortheAnalysisof2Dimageseries.html"·title="Tools·for·the·Analysis·of·2D·image·series"><link·rel="prev"·href="Secmia2devaltransformquantity.html"·title="mia-2deval-transformquantity"><link·rel="next"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dtrackpixelmovement</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2devaltransformquantity.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·the·Analysis·of·2D·image·series</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecToolsforMyocardialPerfusionAnalysis.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dtrackpixelmovement"></a>mia-2dtrackpixelmovement</h3></div></div></div><h4><a·name="idp6288"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dtrackpixelmovement</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dtrackpixelmovement</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsfortheAnalysisof2Dimageseries.html"·title="Tools·for·the·Analysis·of·2D·image·series"><link·rel="prev"·href="Secmia2devaltransformquantity.html"·title="mia-2deval-transformquantity"><link·rel="next"·href="SecToolsforMyocardialPerfusionAnalysis.html"·title="Tools·for·Myocardial·Perfusion·Analysis"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dtrackpixelmovement</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2devaltransformquantity.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·the·Analysis·of·2D·image·series</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecToolsforMyocardialPerfusionAnalysis.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dtrackpixelmovement"></a>mia-2dtrackpixelmovement</h3></div></div></div><h4><a·name="idp6288"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dtrackpixelmovement</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp6299"></a>Description:</h4><p·class="description">Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using·image·registration.·The·pixel·data·is·given·in·CSV·format3 ········...]</p></div><h4><a·name="idp6299"></a>Description:</h4><p·class="description">Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using·image·registration.·The·pixel·data·is·given·in·CSV·format
4 ···id;time;x;y;z;reserved4 ···id;time;x;y;z;reserved
  
5 The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and·the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.</p><h4><a·name="idp6301"></a>Options:</h4><h4><a·name="idp6302"></a>5 The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and·the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.</p><h4><a·name="idp6301"></a>Options:</h4><h4><a·name="idp6302"></a>
6 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·point·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·point·set</p></dd><dt><span·class="term">-t,·--transformation=(input,·required);·io</span></dt><dd><p>transformation·describing·the·monitored·change.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp6317"></a>6 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·point·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·point·set</p></dd><dt><span·class="term">-t,·--transformation=(required,·input);·io</span></dt><dd><p>transformation·describing·the·monitored·change.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd></dl></div><h4><a·name="idp6317"></a>
7 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--time-step=1;·float</span></dt><dd><p>time·step·to·use·for·the·position·update</p></dd></dl></div><h4><a·name="idp6323"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6374"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6380"></a>Example:</h4><p>This·program·evaluated·the·changed·position·of·pixels·given·in·input.csv,·by·using··a·time·step·of·2.0·time·units·and·the·transformation·change.v2df,·and·writes·the·updated·positions·to·updated.csv.</p><pre·class="screen">mia-2dtrackpixelmovement·-i·input.csv·-o·output.cvs·--time-step·2.0·--transformation·change.v2df</pre><h4><a·name="idp6383"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2devaltransformquantity.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof2Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecToolsforMyocardialPerfusionAnalysis.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2deval-transformquantity </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Tools·for·Myocardial·Perfusion·Analysis</td></tr></table></div></body></html>7 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--time-step=1;·float</span></dt><dd><p>time·step·to·use·for·the·position·update</p></dd></dl></div><h4><a·name="idp6323"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp6374"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp6380"></a>Example:</h4><p>This·program·evaluated·the·changed·position·of·pixels·given·in·input.csv,·by·using··a·time·step·of·2.0·time·units·and·the·transformation·change.v2df,·and·writes·the·updated·positions·to·updated.csv.</p><pre·class="screen">mia-2dtrackpixelmovement·-i·input.csv·-o·output.cvs·--time-step·2.0·--transformation·change.v2df</pre><h4><a·name="idp6383"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2devaltransformquantity.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof2Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecToolsforMyocardialPerfusionAnalysis.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2deval-transformquantity </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Tools·for·Myocardial·Perfusion·Analysis</td></tr></table></div></body></html>
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7 Description:7 Description:
8 Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using8 Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using
9 image·registration.·The·pixel·data·is·given·in·CSV·format9 image·registration.·The·pixel·data·is·given·in·CSV·format
10 id;time;x;y;z;reserved·The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and10 id;time;x;y;z;reserved·The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and
11 the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.11 the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.
12 Options:12 Options:
13 ·File-IO13 ·File-IO
14 ··-i,·--in-file=(input,·required);·string14 ··-i,·--in-file=(required,·input);·string
15 ······input·point·set15 ······input·point·set
16 ··-o,·--out-file=(required,·output);·string16 ··-o,·--out-file=(required,·output);·string
17 ······output·point·set17 ······output·point·set
18 ··-t,·--transformation=(input,·required);·io18 ··-t,·--transformation=(required,·input);·io
19 ······transformation·describing·the·monitored·change.·For·supported·file·types19 ······transformation·describing·the·monitored·change.·For·supported·file·types
20 ······see·Plugin_type:_2dtransform/io20 ······see·Plugin_type:_2dtransform/io
21 ·Parameters21 ·Parameters
22 ··-T,·--time-step=1;·float22 ··-T,·--time-step=1;·float
23 ······time·step·to·use·for·the·position·update23 ······time·step·to·use·for·the·position·update
24 Help·&·Info24 Help·&·Info
25 ··-V,·--verbose=warning;·dict25 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dtransform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dmultiimageregistration.html"·title="mia-2dmultiimageregistration"><link·rel="next"·href="Secmia2dtransformationtostrain.html"·title="mia-2dtransformation-to-strain"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dtransform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageregistration.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dtransformationtostrain.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dtransform"></a>mia-2dtransform</h3></div></div></div><h4><a·name="idp3904"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dtransform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dtransform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dmultiimageregistration.html"·title="mia-2dmultiimageregistration"><link·rel="next"·href="Secmia2dtransformationtostrain.html"·title="mia-2dtransformation-to-strain"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dtransform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageregistration.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia2dtransformationtostrain.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dtransform"></a>mia-2dtransform</h3></div></div></div><h4><a·name="idp3904"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dtransform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp3915"></a>Description:</h4><p·class="description">This·program·is·used·to·deform·a·2D·image·using·a·given·transformation.</p><h4><a·name="idp3917"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output)[·...·truncated·by·diffoscope;·len:·245,·SHA:·fef5393ed1ef93721c1c225495237eb31b1e9943171c430f47d0ea38af541161·...·]);·io</span></dt><dd><p>transformation·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd><dt><span·class="term">-p,·--interpolator=STRING</span></dt><dd><p>override·the·interpolator·provided·by·the·transformation</p></dd><dt><span·class="term">-b,·--boundary=mirror;·stringSTRING</span></dt><dd><p>override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·overridden.</p></dd></dl></div><h4><a·name="idp3942"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3993"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3999"></a>Example:</h4><p>Transform·an·image·input.png·by·the·transfromation·stored·in·trans.v·by·using·linear·interpolation·and·zero·boundary·conditions·and·store·the·result·in·output.png</p><pre·class="screen">mia-2dtransform·-i·input.png·-t·trans.v··-o·output.png··-p·bspline:d=1·-b·zero</pre><h4><a·name="idp4002"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageregistration.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dtransformationtostrain.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmultiimageregistration </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dtransformation-to-strain</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp3915"></a>Description:</h4><p·class="description">This·program·is·used·to·deform·a·2D·image·using·a·given·transformation.</p><h4><a·name="idp3917"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output)[·...·truncated·by·diffoscope;·len:·245,·SHA:·be08052940d3bfd2477df57b6488daa80d45678042fdb2f297701afff4f3e807·...·]);·io</span></dt><dd><p>transformation·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd><dt><span·class="term">-p,·--interpolator=STRING</span></dt><dd><p>override·the·interpolator·provided·by·the·transformation</p></dd><dt><span·class="term">-b,·--boundary=mirror;·stringSTRING</span></dt><dd><p>override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·overridden.</p></dd></dl></div><h4><a·name="idp3942"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp3993"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp3999"></a>Example:</h4><p>Transform·an·image·input.png·by·the·transfromation·stored·in·trans.v·by·using·linear·interpolation·and·zero·boundary·conditions·and·store·the·result·in·output.png</p><pre·class="screen">mia-2dtransform·-i·input.png·-t·trans.v··-o·output.png··-p·bspline:d=1·-b·zero</pre><h4><a·name="idp4002"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dmultiimageregistration.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia2dtransformationtostrain.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dmultiimageregistration </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-2dtransformation-to-strain</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-2dtransform4 mia-2dtransform
5 Sysnopis:5 Sysnopis:
6 mia-2dtransform·{-i·io}·{-o·io}·{-t·io}·[·options·...]6 mia-2dtransform·{-i·io}·{-o·io}·{-t·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·deform·a·2D·image·using·a·given·transformation.8 This·program·is·used·to·deform·a·2D·image·using·a·given·transformation.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io11 ······input·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·image.·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······output·image.·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-t,·--transformation=(input,·required);·io14 ··-t,·--transformation=(required,·input);·io
15 ······transformation·file·name.·For·supported·file·types·see·Plugin_type:15 ······transformation·file·name.·For·supported·file·types·see·Plugin_type:
16 ······2dtransform/io16 ······2dtransform/io
17 ··-p,·--interpolator=STRING17 ··-p,·--interpolator=STRING
18 ······override·the·interpolator·provided·by·the·transformation18 ······override·the·interpolator·provided·by·the·transformation
19 ··-b,·--boundary=mirror;·stringSTRING19 ··-b,·--boundary=mirror;·stringSTRING
20 ······override·the·boundary·conditions·provided·by·the·transformation.·This·is20 ······override·the·boundary·conditions·provided·by·the·transformation.·This·is
21 ······only·used·if·the·interpolator·is·overridden.21 ······only·used·if·the·interpolator·is·overridden.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dtransformation-to-strain</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dtransform.html"·title="mia-2dtransform"><link·rel="next"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dtransformation-to-strain</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dtransform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof2Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dtransformationtostrain"></a>mia-2dtransformation-to-strain</h3></div></div></div><h4><a·name="idp4006"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dtransformation-to-strain</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-2dtransformation-to-strain</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof2Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·2D·images"><link·rel="prev"·href="Secmia2dtransform.html"·title="mia-2dtransform"><link·rel="next"·href="SecRegistrationofseriesof2Dimages.html"·title="Registration·of·series·of·2D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-2dtransformation-to-strain</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dtransform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·2D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof2Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia2dtransformationtostrain"></a>mia-2dtransformation-to-strain</h3></div></div></div><h4><a·name="idp4006"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-2dtransformation-to-strain</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp4015"></a>Description:</h4><p·class="description">Evaluate·the·Green·strain·tensor·corresponding·to·a·given·2D·transformation·for·each·grid·point.</p><h4><a·name="idp4017"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·Green's·strain·tensor</p></dd></dl></div><h4><a·name="idp4028"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4079"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4085"></a>Example:</h4><p>Evaluate·the·Green·strain·tensor·from·the·transformation·stored·in·trans.v·and·save·it·to·output.v</p><pre·class="screen">mia-2dtransformation-to-strain·-i··trans.v··-o·output.mt</pre><h4><a·name="idp4088"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dtransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof2Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dtransform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration·of·series·of·2D·images</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp4015"></a>Description:</h4><p·class="description">Evaluate·the·Green·strain·tensor·corresponding·to·a·given·2D·transformation·for·each·grid·point.</p><h4><a·name="idp4017"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dtransformio.html"·title="Plugin·type:·2dtransform/io">Plugin·type:·2dtransform/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·Green's·strain·tensor</p></dd></dl></div><h4><a·name="idp4028"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp4079"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp4085"></a>Example:</h4><p>Evaluate·the·Green·strain·tensor·from·the·transformation·stored·in·trans.v·and·save·it·to·output.v</p><pre·class="screen">mia-2dtransformation-to-strain·-i··trans.v··-o·output.mt</pre><h4><a·name="idp4088"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dtransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof2Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof2Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dtransform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration·of·series·of·2D·images</td></tr></table></div></body></html>
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4 mia-2dtransformation-to-strain4 mia-2dtransformation-to-strain
5 Sysnopis:5 Sysnopis:
6 mia-2dtransformation-to-strain·{-i·io}·{-o·string}·[·options·...]6 mia-2dtransformation-to-strain·{-i·io}·{-o·string}·[·options·...]
7 Description:7 Description:
8 Evaluate·the·Green·strain·tensor·corresponding·to·a·given·2D·transformation·for8 Evaluate·the·Green·strain·tensor·corresponding·to·a·given·2D·transformation·for
9 each·grid·point.9 each·grid·point.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·transformation.·For·supported·file·types·see·Plugin_type:12 ······input·transformation.·For·supported·file·types·see·Plugin_type:
13 ······2dtransform/io13 ······2dtransform/io
14 ··-o,·--out-file=(required,·output);·string14 ··-o,·--out-file=(required,·output);·string
15 ······output·Green's·strain·tensor15 ······output·Green's·strain·tensor
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dbinarycombine</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="next"·href="Secmia3dbrainextractT1.html"·title="mia-3dbrainextractT1"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dbinarycombine</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dbrainextractT1.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dbinarycombine"></a>mia-3dbinarycombine</h3></div></div></div><h4><a·name="idp9131"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dbinarycombine</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dbinarycombine</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="next"·href="Secmia3dbrainextractT1.html"·title="mia-3dbrainextractT1"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dbinarycombine</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dbrainextractT1.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dbinarycombine"></a>mia-3dbinarycombine</h3></div></div></div><h4><a·name="idp9131"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dbinarycombine</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp9142"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.</p><h4><a·name="idp9144"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--file1=(input,·required);·io</span></dt><dd><p>input·mask·image·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-2,·--file2=(input,·requir[·...·truncated·by·diffoscope;·len:·2,·SHA:·9c1623f0d38e28e9594f2ef31a7ec909291c4fdb05a777dccd2e936a7f406011·...·]);·io</span></dt><dd><p>input·mask·image·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-p,·--operation=nor;·dict</span></dt><dd><p>Operation·to·be·applied</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">or:</td><td·align="left"·valign="top">logocal·or</td></tr><tr><td·align="left"·valign="top">nor:</td><td·align="left"·valign="top">logocal·nor</td></tr><tr><td·align="left"·valign="top">and:</td><td·align="left"·valign="top">logocal·and</td></tr><tr><td·align="left"·valign="top">nand:</td><td·align="left"·valign="top">logocal·nand</td></tr><tr><td·align="left"·valign="top">xor:</td><td·align="left"·valign="top">logocal·xor</td></tr><tr><td·align="left"·valign="top">nxor:</td><td·align="left"·valign="top">logocal·nxor</td></tr></tbody></table></div></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mask·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9188"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9239"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9245"></a>Example:</h4><p>Combine·the·binary·images·b1.png·and·b2.png·by·using·the·'nor'·operation·and·store·the·result·in·b1nor2.png.</p><pre·class="screen">mia-3dbinarycombine·-1·b1.png·-2·b2.png·-p·nor·-o·b1nor2.png</pre><h4><a·name="idp9248"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dbrainextractT1.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Analysis,·filtering,·combining,·and·segmentation·of·3D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dbrainextractT1</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp9142"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.</p><h4><a·name="idp9144"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--file1=(required,·input);·io</span></dt><dd><p>input·mask·image·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-2,·--file2=(required,·inp[·...·truncated·by·diffoscope;·len:·2,·SHA:·469cc643a19fb75901e5d331b8dc14befa8b98810b246c2fb22fff0c382dc39e·...·]);·io</span></dt><dd><p>input·mask·image·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-p,·--operation=nor;·dict</span></dt><dd><p>Operation·to·be·applied</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">or:</td><td·align="left"·valign="top">logocal·or</td></tr><tr><td·align="left"·valign="top">nor:</td><td·align="left"·valign="top">logocal·nor</td></tr><tr><td·align="left"·valign="top">and:</td><td·align="left"·valign="top">logocal·and</td></tr><tr><td·align="left"·valign="top">nand:</td><td·align="left"·valign="top">logocal·nand</td></tr><tr><td·align="left"·valign="top">xor:</td><td·align="left"·valign="top">logocal·xor</td></tr><tr><td·align="left"·valign="top">nxor:</td><td·align="left"·valign="top">logocal·nxor</td></tr></tbody></table></div></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mask·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9188"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9239"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9245"></a>Example:</h4><p>Combine·the·binary·images·b1.png·and·b2.png·by·using·the·'nor'·operation·and·store·the·result·in·b1nor2.png.</p><pre·class="screen">mia-3dbinarycombine·-1·b1.png·-2·b2.png·-p·nor·-o·b1nor2.png</pre><h4><a·name="idp9248"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dbrainextractT1.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Analysis,·filtering,·combining,·and·segmentation·of·3D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dbrainextractT1</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dbinarycombine4 mia-3dbinarycombine
5 Sysnopis:5 Sysnopis:
6 mia-3dbinarycombine·{-1·io}·{-2·io}·{-o·io}·[·options·...]6 mia-3dbinarycombine·{-1·io}·{-2·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.8 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.
9 Options:9 Options:
10 ··-1,·--file1=(input,·required);·io10 ··-1,·--file1=(required,·input);·io
11 ······input·mask·image·1.·For·supported·file·types·see·Plugin_type:_3dimage/io11 ······input·mask·image·1.·For·supported·file·types·see·Plugin_type:_3dimage/io
12 ··-2,·--file2=(input,·required);·io12 ··-2,·--file2=(required,·input);·io
13 ······input·mask·image·2.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······input·mask·image·2.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-p,·--operation=nor;·dict14 ··-p,·--operation=nor;·dict
15 ······Operation·to·be·applied15 ······Operation·to·be·applied
16 ······or:···logocal·or16 ······or:···logocal·or
17 ······nor:··logocal·nor17 ······nor:··logocal·nor
18 ······and:··logocal·and18 ······and:··logocal·and
19 ······nand:·logocal·nand19 ······nand:·logocal·nand
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dbrainextractT1</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dbinarycombine.html"·title="mia-3dbinarycombine"><link·rel="next"·href="Secmia3dcombineimageseries.html"·title="mia-3dcombine-imageseries"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dbrainextractT1</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dbinarycombine.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dcombineimageseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dbrainextractT1"></a>mia-3dbrainextractT1</h3></div></div></div><h4><a·name="idp9252"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dbrainextractT1</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dbrainextractT1</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dbinarycombine.html"·title="mia-3dbinarycombine"><link·rel="next"·href="Secmia3dcombineimageseries.html"·title="mia-3dcombine-imageseries"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dbrainextractT1</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dbinarycombine.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dcombineimageseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dbrainextractT1"></a>mia-3dbrainextractT1</h3></div></div></div><h4><a·name="idp9252"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dbrainextractT1</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp9261"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter·segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to·obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the·brain·from·the·B0·field·corrected·images.</p><h4><a·name="idp9263"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>brain·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-w,·--wm-class=2;·int</span></dt><dd><p>index·of·white·matter</p></dd><dt><span·class="term">-p,·--wm-prob=0.7;·float</span></dt><dd><p>white·matter·class·probability·for·initial·mask·creation</p></dd><dt><span·class="term">-t,·--grow-threshold=20;·int</span></dt><dd><p>intensity·threshold·for·region·growing</p></dd><dt><span·class="term">--grow-shape=18n;·stringSTRING</span></dt><dd><p>neighbourhood·mask·region·growing</p></dd></dl></div><h4><a·name="idp9295"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9346"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9352"></a>Example:</h4><p>Create·a·mask·from·the·input·image·by·running·a·5-class·segmentation·over·inpt·image·input.v·and·use·class·4·as·white·matter·class·and·store·the·masked·image·in·masked.v·and·the·B0-field·corrected·image·in·b0.v</p><pre·class="screen">mia-3dbrainextractT1·-i·input.v·-n·5·-w·4·-o·masked.v</pre><h4><a·name="idp9355"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dbinarycombine.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dcombineimageseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dbinarycombine </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dcombine-imageseries</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp9261"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter·segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to·obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the·brain·from·the·B0·field·corrected·images.</p><h4><a·name="idp9263"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>brain·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-w,·--wm-class=2;·int</span></dt><dd><p>index·of·white·matter</p></dd><dt><span·class="term">-p,·--wm-prob=0.7;·float</span></dt><dd><p>white·matter·class·probability·for·initial·mask·creation</p></dd><dt><span·class="term">-t,·--grow-threshold=20;·int</span></dt><dd><p>intensity·threshold·for·region·growing</p></dd><dt><span·class="term">--grow-shape=18n;·stringSTRING</span></dt><dd><p>neighbourhood·mask·region·growing</p></dd></dl></div><h4><a·name="idp9295"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9346"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9352"></a>Example:</h4><p>Create·a·mask·from·the·input·image·by·running·a·5-class·segmentation·over·inpt·image·input.v·and·use·class·4·as·white·matter·class·and·store·the·masked·image·in·masked.v·and·the·B0-field·corrected·image·in·b0.v</p><pre·class="screen">mia-3dbrainextractT1·-i·input.v·-n·5·-w·4·-o·masked.v</pre><h4><a·name="idp9355"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dbinarycombine.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dcombineimageseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dbinarycombine </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dcombine-imageseries</td></tr></table></div></body></html>
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8 This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a8 This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a
9 combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D9 combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D
10 segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter10 segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter
11 segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to11 segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to
12 obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the12 obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the
13 brain·from·the·B0·field·corrected·images.13 brain·from·the·B0·field·corrected·images.
14 Options:14 Options:
15 ··-i,·--in-file=(input,·required);·io15 ··-i,·--in-file=(required,·input);·io
16 ······input·image(s)·to·be·segmented.·For·supported·file·types·see·Plugin_type:16 ······input·image(s)·to·be·segmented.·For·supported·file·types·see·Plugin_type:
17 ······3dimage/io17 ······3dimage/io
18 ··-o,·--out-file=(required,·output);·io18 ··-o,·--out-file=(required,·output);·io
19 ······brain·mask.·For·supported·file·types·see·Plugin_type:_3dimage/io19 ······brain·mask.·For·supported·file·types·see·Plugin_type:_3dimage/io
20 ··-n,·--no-of-classes=3;·int20 ··-n,·--no-of-classes=3;·int
21 ······number·of·classes21 ······number·of·classes
22 ··-w,·--wm-class=2;·int22 ··-w,·--wm-class=2;·int
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dcombine-mr-segmentations</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dcombineimageseries.html"·title="mia-3dcombine-imageseries"><link·rel="next"·href="Secmia3dcrispsegment.html"·title="mia-3dcrispsegment"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dcombine-mr-segmentations</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcombineimageseries.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dcrispsegment.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dcombinemrsegmentations"></a>mia-3dcombine-mr-segmentations</h3></div></div></div><h4><a·name="idp9505"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dcombine-mr-segmentations</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dcombine-mr-segmentations</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dcombineimageseries.html"·title="mia-3dcombine-imageseries"><link·rel="next"·href="Secmia3dcrispsegment.html"·title="mia-3dcrispsegment"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dcombine-mr-segmentations</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcombineimageseries.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dcrispsegment.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dcombinemrsegmentations"></a>mia-3dcombine-mr-segmentations</h3></div></div></div><h4><a·name="idp9505"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dcombine-mr-segmentations</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a>5 ············<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp9517"></a>Description:</h4><p·class="description">This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue·probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are·translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel·is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.</p><h4><a·name="idp9519"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·probability·images.·The·number·of·mask·images·must·correspond·to·the·number·of·probability·images·given·here..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·that·contains·the·labeling..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9531"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9582"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9588"></a>Example:</h4><p>7 ········...]</p></div><h4><a·name="idp9517"></a>Description:</h4><p·class="description">This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue·probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are·translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel·is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.</p><h4><a·name="idp9519"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·probability·images.·The·number·of·mask·images·must·correspond·to·the·number·of·probability·images·given·here..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·that·contains·the·labeling..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9531"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9582"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9588"></a>Example:</h4><p>
8 ····</p><pre·class="screen">mia-3dcombine-mr-segmentations·</pre><h4><a·name="idp9591"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcombineimageseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dcrispsegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcombine-imageseries </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dcrispsegment</td></tr></table></div></body></html>8 ····</p><pre·class="screen">mia-3dcombine-mr-segmentations·</pre><h4><a·name="idp9591"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcombineimageseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dcrispsegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcombine-imageseries </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dcrispsegment</td></tr></table></div></body></html>
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7 3dimage/io·...]7 3dimage/io·...]
8 Description:8 Description:
9 This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue9 This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue
10 probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are10 probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are
11 translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel11 translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel
12 is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.12 is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.
13 Options:13 Options:
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······input·probability·images.·The·number·of·mask·images·must·correspond·to15 ······input·probability·images.·The·number·of·mask·images·must·correspond·to
16 ······the·number·of·probability·images·given·here..·For·supported·file·types16 ······the·number·of·probability·images·given·here..·For·supported·file·types
17 ······see·Plugin_type:_3dimage/io17 ······see·Plugin_type:_3dimage/io
18 ··-o,·--out-file=(required,·output);·io18 ··-o,·--out-file=(required,·output);·io
19 ······output·image·that·contains·the·labeling..·For·supported·file·types·see19 ······output·image·that·contains·the·labeling..·For·supported·file·types·see
20 ······Plugin_type:_3dimage/io20 ······Plugin_type:_3dimage/io
21 Help·&·Info21 Help·&·Info
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dcost-translatedgrad</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dcost.html"·title="mia-3dcost"><link·rel="next"·href="Secmia3ddeform.html"·title="mia-3ddeform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dcost-translatedgrad</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcost.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3ddeform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dcosttranslatedgrad"></a>mia-3dcost-translatedgrad</h3></div></div></div><h4><a·name="idp11354"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dcost-translatedgrad</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dcost-translatedgrad</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dcost.html"·title="mia-3dcost"><link·rel="next"·href="Secmia3ddeform.html"·title="mia-3ddeform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dcost-translatedgrad</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcost.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3ddeform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dcosttranslatedgrad"></a>mia-3dcost-translatedgrad</h3></div></div></div><h4><a·name="idp11354"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dcost-translatedgrad</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11365"></a>Description:</h4><p·class="description">Evaluate·the·cost·gradient·between·two·images·and·evaluate·the·transformation·related·gradient·for·it·based·on·the·given·transformation·model.</p><h4><a·name="idp11367"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-file=(input,·required);·io</span></dt><dd><p>reference·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-g,·--gradimg-file=(output);·io</span></dt><dd><p>norm·image·of·the·spline·transformed·gradient.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-C,·--cost-gradimg-file=(output);·io</span></dt><dd><p>norm·image·of·the·cost·gradient.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-f,·--transForm=spline:rate=5;·factory</span></dt><dd><p>Transformation·the·gradient·relates·to.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>cost·function·to·use.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd></dl></div><h4><a·name="idp11404"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11455"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11461"></a>Example:</h4><p>Evaluate·the·SSD·cost·between·src.v·and·ref.v·and·store·the·gradient·gradient·corresponding·to·a·spline·transformation·in·grad.v3dt.</p><pre·class="screen">mia-3dcost-translatedgrad·-i·src.v·-o·grad.v3dt·-f·spline:rate=8·-c·ssd</pre><h4><a·name="idp11464"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcost.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3ddeform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcost </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3ddeform</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11365"></a>Description:</h4><p·class="description">Evaluate·the·cost·gradient·between·two·images·and·evaluate·the·transformation·related·gradient·for·it·based·on·the·given·transformation·model.</p><h4><a·name="idp11367"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-file=(required,·input);·io</span></dt><dd><p>reference·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-g,·--gradimg-file=(output);·io</span></dt><dd><p>norm·image·of·the·spline·transformed·gradient.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-C,·--cost-gradimg-file=(output);·io</span></dt><dd><p>norm·image·of·the·cost·gradient.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-f,·--transForm=spline:rate=5;·factory</span></dt><dd><p>Transformation·the·gradient·relates·to.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>cost·function·to·use.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd></dl></div><h4><a·name="idp11404"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11455"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11461"></a>Example:</h4><p>Evaluate·the·SSD·cost·between·src.v·and·ref.v·and·store·the·gradient·gradient·corresponding·to·a·spline·transformation·in·grad.v3dt.</p><pre·class="screen">mia-3dcost-translatedgrad·-i·src.v·-o·grad.v3dt·-f·spline:rate=8·-c·ssd</pre><h4><a·name="idp11464"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcost.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3ddeform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcost </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3ddeform</td></tr></table></div></body></html>
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4 mia-3dcost-translatedgrad4 mia-3dcost-translatedgrad
5 Sysnopis:5 Sysnopis:
6 mia-3dcost-translatedgrad·{-i·io}·{-r·io}·{-o·io}·[·options·...]6 mia-3dcost-translatedgrad·{-i·io}·{-r·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Evaluate·the·cost·gradient·between·two·images·and·evaluate·the·transformation8 Evaluate·the·cost·gradient·between·two·images·and·evaluate·the·transformation
9 related·gradient·for·it·based·on·the·given·transformation·model.9 related·gradient·for·it·based·on·the·given·transformation·model.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io12 ······input·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io
13 ··-r,·--ref-file=(input,·required);·io13 ··-r,·--ref-file=(required,·input);·io
14 ······reference·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io14 ······reference·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io
15 ··-o,·--out-file=(required,·output);·io15 ··-o,·--out-file=(required,·output);·io
16 ······output·vector·field·.·For·supported·file·types·see·Plugin_type:16 ······output·vector·field·.·For·supported·file·types·see·Plugin_type:
17 ······3dtransform/io17 ······3dtransform/io
18 ··-g,·--gradimg-file=(output);·io18 ··-g,·--gradimg-file=(output);·io
19 ······norm·image·of·the·spline·transformed·gradient.·For·supported·file·types19 ······norm·image·of·the·spline·transformed·gradient.·For·supported·file·types
20 ······see·Plugin_type:_3dimage/io20 ······see·Plugin_type:_3dimage/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dcrispsegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dcombinemrsegmentations.html"·title="mia-3dcombine-mr-segmentations"><link·rel="next"·href="Secmia3ddistancestats.html"·title="mia-3ddistance-stats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dcrispsegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcombinemrsegmentations.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3ddistancestats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dcrispsegment"></a>mia-3dcrispsegment</h3></div></div></div><h4><a·name="idp9595"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dcrispsegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dcrispsegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dcombinemrsegmentations.html"·title="mia-3dcombine-mr-segmentations"><link·rel="next"·href="Secmia3ddistancestats.html"·title="mia-3ddistance-stats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dcrispsegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcombinemrsegmentations.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3ddistancestats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dcrispsegment"></a>mia-3dcrispsegment</h3></div></div></div><h4><a·name="idp9595"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dcrispsegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp9604"></a>Description:</h4><p·class="description">This·program·creates·a·label·image·from·a·fuzzy·segmentation.·or·each·pixel·the·label·is·set·to·the·class·with·the·higest·probability·plus·a·given·offset</p><h4><a·name="idp9606"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·class·file,·should·contain·multiple·images·with·tissue·class·probabilities.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·class·label·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-l,·--label-offset=1;·uint</span></dt><dd><p>label·offset</p></dd></dl></div><h4><a·name="idp9622"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9673"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9679"></a>Example:</h4><p>Set·the·labels·based·on·the·input·class·probability·file·cls.v·adding·the·offset·2·to·each·label·and·save·the·result·to·labeled.v.</p><pre·class="screen">mia-3dcrispsegment·-i·cls.v·-o·labeled.v·-l·2</pre><h4><a·name="idp9682"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcombinemrsegmentations.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3ddistancestats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcombine-mr-segmentations </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3ddistance-stats</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp9604"></a>Description:</h4><p·class="description">This·program·creates·a·label·image·from·a·fuzzy·segmentation.·or·each·pixel·the·label·is·set·to·the·class·with·the·higest·probability·plus·a·given·offset</p><h4><a·name="idp9606"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·class·file,·should·contain·multiple·images·with·tissue·class·probabilities.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·class·label·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-l,·--label-offset=1;·uint</span></dt><dd><p>label·offset</p></dd></dl></div><h4><a·name="idp9622"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9673"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9679"></a>Example:</h4><p>Set·the·labels·based·on·the·input·class·probability·file·cls.v·adding·the·offset·2·to·each·label·and·save·the·result·to·labeled.v.</p><pre·class="screen">mia-3dcrispsegment·-i·cls.v·-o·labeled.v·-l·2</pre><h4><a·name="idp9682"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcombinemrsegmentations.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3ddistancestats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcombine-mr-segmentations </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3ddistance-stats</td></tr></table></div></body></html>
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4 mia-3dcrispsegment4 mia-3dcrispsegment
5 Sysnopis:5 Sysnopis:
6 mia-3dcrispsegment·{-i·io}·{-o·io}·[·options·...]6 mia-3dcrispsegment·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·creates·a·label·image·from·a·fuzzy·segmentation.·or·each·pixel·the8 This·program·creates·a·label·image·from·a·fuzzy·segmentation.·or·each·pixel·the
9 label·is·set·to·the·class·with·the·higest·probability·plus·a·given·offset9 label·is·set·to·the·class·with·the·higest·probability·plus·a·given·offset
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·class·file,·should·contain·multiple·images·with·tissue·class12 ······input·class·file,·should·contain·multiple·images·with·tissue·class
13 ······probabilities.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······probabilities.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·class·label·image.·For·supported·file·types·see·Plugin_type:15 ······output·class·label·image.·For·supported·file·types·see·Plugin_type:
16 ······3dimage/io16 ······3dimage/io
17 ··-l,·--label-offset=1;·uint17 ··-l,·--label-offset=1;·uint
18 ······label·offset18 ······label·offset
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3ddeform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dcosttranslatedgrad.html"·title="mia-3dcost-translatedgrad"><link·rel="next"·href="Secmia3dfluid.html"·title="mia-3dfluid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3ddeform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcosttranslatedgrad.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dfluid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3ddeform"></a>mia-3ddeform</h3></div></div></div><h4><a·name="idp11468"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3ddeform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3ddeform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dcosttranslatedgrad.html"·title="mia-3dcost-translatedgrad"><link·rel="next"·href="Secmia3dfluid.html"·title="mia-3dfluid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3ddeform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dcosttranslatedgrad.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dfluid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3ddeform"></a>mia-3ddeform</h3></div></div></div><h4><a·name="idp11468"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3ddeform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11479"></a>Description:</h4><p·class="description">Transform·a·3D·image·by·applying·a·given·3D·transformation·that·is·defined·by·a·3D·vector·field·v·according·to·x:=x-v(x)</p><h4><a·name="idp11481"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output[·...·truncated·by·diffoscope;·len:·251,·SHA:·4daed5dcb2044200b1091131afe76a56e6049ef935f45cb86f3bd5eee163f0ff·...·]);·io</span></dt><dd><p>transformation·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd></dl></div><h4><a·name="idp11503"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11554"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11560"></a>Example:</h4><p>Transform·an·image·input.v·by·the·transformation·defined·by·the·vector·field·field.v·by·using·bspline·interpolation·of·degree·4·and·store·the·result·in·output.v</p><pre·class="screen">mia-3ddeform·-i·input.v·-t·field.v··-o·output.v··-p·bspline:d=4</pre><h4><a·name="idp11563"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcosttranslatedgrad.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dfluid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcost-translatedgrad </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dfluid</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11479"></a>Description:</h4><p·class="description">Transform·a·3D·image·by·applying·a·given·3D·transformation·that·is·defined·by·a·3D·vector·field·v·according·to·x:=x-v(x)</p><h4><a·name="idp11481"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output[·...·truncated·by·diffoscope;·len:·251,·SHA:·01ebc35361945dcaa428134ec8837688085867c175af1ba3bb4eca75e9f0dfb2·...·]);·io</span></dt><dd><p>transformation·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd></dl></div><h4><a·name="idp11503"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11554"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11560"></a>Example:</h4><p>Transform·an·image·input.v·by·the·transformation·defined·by·the·vector·field·field.v·by·using·bspline·interpolation·of·degree·4·and·store·the·result·in·output.v</p><pre·class="screen">mia-3ddeform·-i·input.v·-t·field.v··-o·output.v··-p·bspline:d=4</pre><h4><a·name="idp11563"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcosttranslatedgrad.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dfluid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcost-translatedgrad </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dfluid</td></tr></table></div></body></html>
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4 mia-3ddeform4 mia-3ddeform
5 Sysnopis:5 Sysnopis:
6 mia-3ddeform·{-i·io}·{-o·io}·{-t·io}·[·options·...]6 mia-3ddeform·{-i·io}·{-o·io}·{-t·io}·[·options·...]
7 Description:7 Description:
8 Transform·a·3D·image·by·applying·a·given·3D·transformation·that·is·defined·by·a8 Transform·a·3D·image·by·applying·a·given·3D·transformation·that·is·defined·by·a
9 3D·vector·field·v·according·to·x:=x-v(x)9 3D·vector·field·v·according·to·x:=x-v(x)
10 Options:10 Options:
11 ··-i,·--in-image=(input,·required);·io11 ··-i,·--in-image=(required,·input);·io
12 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io12 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
13 ··-o,·--out-image=(required,·output);·io13 ··-o,·--out-image=(required,·output);·io
14 ······transformed·image.·For·supported·file·types·see·Plugin_type:_3dimage/io14 ······transformed·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
15 ··-t,·--transformation=(input,·required);·io15 ··-t,·--transformation=(required,·input);·io
16 ······transformation·vector·field.·For·supported·file·types·see·Plugin_type:16 ······transformation·vector·field.·For·supported·file·types·see·Plugin_type:
17 ······3dvf/io17 ······3dvf/io
18 ··-p,·--interpolator=bspline:d=3;·factory18 ··-p,·--interpolator=bspline:d=3;·factory
19 ······image·interpolator·kernel.·For·supported·plug-ins·see·Plugin_type:_1d/19 ······image·interpolator·kernel.·For·supported·plug-ins·see·Plugin_type:_1d/
20 ······splinekernel20 ······splinekernel
21 Help·&·Info21 Help·&·Info
22 ··-V,·--verbose=warning;·dict22 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3ddistance</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia2dstackfilter.html"·title="mia-2dstackfilter"><link·rel="next"·href="Secmiamultihist.html"·title="mia-multihist"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3ddistance</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dstackfilter.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiamultihist.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3ddistance"></a>mia-3ddistance</h3></div></div></div><h4><a·name="idp8865"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3ddistance</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3ddistance</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia2dstackfilter.html"·title="mia-2dstackfilter"><link·rel="next"·href="Secmiamultihist.html"·title="mia-multihist"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3ddistance</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dstackfilter.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiamultihist.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3ddistance"></a>mia-3ddistance</h3></div></div></div><h4><a·name="idp8865"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3ddistance</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-r·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8876"></a>Description:</h4><p·class="description">This·program·takes·two·binary·masks·as·input·and·evaluates·the·distance·of·one·mask·with·respect·to·the·other·in·voxel·space.·The·output·is·given·as·text·file·with·the·coordinates·of·the·source·voxels·and·their·distance·to·the·reference·mask.·Correction·for·voxel·size·must·be·done·after·processing.</p><h4><a·name="idp8878"></a>Options:</h4><h4><a·name="idp8879"></a>File·IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·image(s)·that·contain·the·source·pixel·mask</p></dd><dt><span·class="term">-r,·--ref-file=(input,·required);·string</span></dt><dd><p>reference·mask·to·evaluate·the·distance·from</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name</p></dd></dl></div><h4><a·name="idp8893"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8944"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8950"></a>Test</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--self-test</span></dt><dd><p>run·a·self·test</p></dd></dl></div><h4><a·name="idp8956"></a>Example:</h4><p>Evaluate·the·distance·of·the·mask·given·in·the·images·srcXXXX.png·to·the·mask·given·in·refXXXX.png·and·save·the·result·to·distances.txt</p><pre·class="screen">mia-3ddistance·-i·srcXXXX.png·-r·refXXXX.png·-o·distances.txt</pre><h4><a·name="idp8959"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dstackfilter.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiamultihist.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dstackfilter </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-multihist</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8876"></a>Description:</h4><p·class="description">This·program·takes·two·binary·masks·as·input·and·evaluates·the·distance·of·one·mask·with·respect·to·the·other·in·voxel·space.·The·output·is·given·as·text·file·with·the·coordinates·of·the·source·voxels·and·their·distance·to·the·reference·mask.·Correction·for·voxel·size·must·be·done·after·processing.</p><h4><a·name="idp8878"></a>Options:</h4><h4><a·name="idp8879"></a>File·IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·image(s)·that·contain·the·source·pixel·mask</p></dd><dt><span·class="term">-r,·--ref-file=(required,·input);·string</span></dt><dd><p>reference·mask·to·evaluate·the·distance·from</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name</p></dd></dl></div><h4><a·name="idp8893"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp8944"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp8950"></a>Test</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--self-test</span></dt><dd><p>run·a·self·test</p></dd></dl></div><h4><a·name="idp8956"></a>Example:</h4><p>Evaluate·the·distance·of·the·mask·given·in·the·images·srcXXXX.png·to·the·mask·given·in·refXXXX.png·and·save·the·result·to·distances.txt</p><pre·class="screen">mia-3ddistance·-i·srcXXXX.png·-r·refXXXX.png·-o·distances.txt</pre><h4><a·name="idp8959"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dstackfilter.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiamultihist.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dstackfilter </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-multihist</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·takes·two·binary·masks·as·input·and·evaluates·the·distance·of·one8 This·program·takes·two·binary·masks·as·input·and·evaluates·the·distance·of·one
9 mask·with·respect·to·the·other·in·voxel·space.·The·output·is·given·as·text·file9 mask·with·respect·to·the·other·in·voxel·space.·The·output·is·given·as·text·file
10 with·the·coordinates·of·the·source·voxels·and·their·distance·to·the·reference10 with·the·coordinates·of·the·source·voxels·and·their·distance·to·the·reference
11 mask.·Correction·for·voxel·size·must·be·done·after·processing.11 mask.·Correction·for·voxel·size·must·be·done·after·processing.
12 Options:12 Options:
13 File·IO13 File·IO
14 ··-i,·--in-file=(input,·required);·string14 ··-i,·--in-file=(required,·input);·string
15 ······input·image(s)·that·contain·the·source·pixel·mask15 ······input·image(s)·that·contain·the·source·pixel·mask
16 ··-r,·--ref-file=(input,·required);·string16 ··-r,·--ref-file=(required,·input);·string
17 ······reference·mask·to·evaluate·the·distance·from17 ······reference·mask·to·evaluate·the·distance·from
18 ··-o,·--out-file=(required,·output);·string18 ··-o,·--out-file=(required,·output);·string
19 ······output·file·name19 ······output·file·name
20 Help·&·Info20 Help·&·Info
21 ··-V,·--verbose=warning;·dict21 ··-V,·--verbose=warning;·dict
22 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.22 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
23 ······Supported·priorities·starting·at·lowest·level·are:23 ······Supported·priorities·starting·at·lowest·level·are:
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14 ········end_range·&lt;-·2·+·as.numeric(line[2])14 ········end_range·&lt;-·2·+·as.numeric(line[2])
15 ········s·&lt;-·as.numeric(line[3:end_range])15 ········s·&lt;-·as.numeric(line[3:end_range])
16 ········result·&lt;-·sprintf("%d·%8.4f·%8.4f·%8.4f·%8.4f\n"16 ········result·&lt;-·sprintf("%d·%8.4f·%8.4f·%8.4f·%8.4f\n"
17 ············label,·mean(s),·sqrt(var(s)),··median(s),·max(s))17 ············label,·mean(s),·sqrt(var(s)),··median(s),·max(s))
18 ········cat(result)18 ········cat(result)
19 ····}19 ····}
  
20 </p><h4><a·name="idp9699"></a>Options:</h4><h4><a·name="idp9700"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-labels=(input,·required);·io</span></dt><dd><p>input·label·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-labels=(input,·re[·...·truncated·by·diffoscope;·len:·6,·SHA:·87df40f17a1a9bf62235e31d92fb864cc9aecba19fc5d0acc818e56948799f0a·...·]);·io</span></dt><dd><p>reference·label·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-l,·--label-map=(input);·string</span></dt><dd><p>optional·mapping·of·label·numbers</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.</p></dd></dl></div><h4><a·name="idp9720"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9771"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9777"></a>Example:</h4><p>Evaluate·the·distances·for·each·label·available·in·image.v·to·the·corresponding·labels·in·the·image·reference.v·ans·store·the·result·a·coma·separated·list·of·values,·i.e.·distances.csv.</p><pre·class="screen">mia-3ddistance-stats·-i·image.v·-r·reference.v·-o·distances.csv</pre><h4><a·name="idp9780"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcrispsegment.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dfuzzysegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcrispsegment </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dfuzzysegment</td></tr></table></div></body></html>20 </p><h4><a·name="idp9699"></a>Options:</h4><h4><a·name="idp9700"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-labels=(required,·input);·io</span></dt><dd><p>input·label·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-labels=(required,[·...·truncated·by·diffoscope;·len:·6,·SHA:·0a165eaf8b9d2e6200b543810c0dce22a8bd8807f513611ea20728c744ca5fc3·...·]);·io</span></dt><dd><p>reference·label·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-l,·--label-map=(input);·string</span></dt><dd><p>optional·mapping·of·label·numbers</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.</p></dd></dl></div><h4><a·name="idp9720"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9771"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9777"></a>Example:</h4><p>Evaluate·the·distances·for·each·label·available·in·image.v·to·the·corresponding·labels·in·the·image·reference.v·ans·store·the·result·a·coma·separated·list·of·values,·i.e.·distances.csv.</p><pre·class="screen">mia-3ddistance-stats·-i·image.v·-r·reference.v·-o·distances.csv</pre><h4><a·name="idp9780"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dcrispsegment.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dfuzzysegment.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dcrispsegment </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dfuzzysegment</td></tr></table></div></body></html>
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12 statistics·from·this·data·would·look·like·args·<-·commandArgs(TRUE)·data·<-12 statistics·from·this·data·would·look·like·args·<-·commandArgs(TRUE)·data·<-
13 read.csv(args[1],·header=FALSE)·for·(·i·in·1:dim(data)[1]·)·{·line·<-·data[i,]13 read.csv(args[1],·header=FALSE)·for·(·i·in·1:dim(data)[1]·)·{·line·<-·data[i,]
14 label·<-·as.integer(line[1])·end_range·<-·2·+·as.numeric(line[2])·s·<-14 label·<-·as.integer(line[1])·end_range·<-·2·+·as.numeric(line[2])·s·<-
15 as.numeric(line[3:end_range])·result·<-·sprintf("%d·%8.4f·%8.4f·%8.4f·%8.4f\n"15 as.numeric(line[3:end_range])·result·<-·sprintf("%d·%8.4f·%8.4f·%8.4f·%8.4f\n"
16 label,·mean(s),·sqrt(var(s)),·median(s),·max(s))·cat(result)·}16 label,·mean(s),·sqrt(var(s)),·median(s),·max(s))·cat(result)·}
17 Options:17 Options:
18 File-IO18 File-IO
19 ··-i,·--in-labels=(input,·required);·io19 ··-i,·--in-labels=(required,·input);·io
20 ······input·label·image.·For·supported·file·types·see·Plugin_type:_3dimage/io20 ······input·label·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
21 ··-r,·--ref-labels=(input,·required);·io21 ··-r,·--ref-labels=(required,·input);·io
22 ······reference·label·image.·For·supported·file·types·see·Plugin_type:_3dimage/22 ······reference·label·image.·For·supported·file·types·see·Plugin_type:_3dimage/
23 ······io23 ······io
24 ··-l,·--label-map=(input);·string24 ··-l,·--label-map=(input);·string
25 ······optional·mapping·of·label·numbers25 ······optional·mapping·of·label·numbers
26 ··-o,·--out-file=(required,·output);·string26 ··-o,·--out-file=(required,·output);·string
27 ······output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv27 ······output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv
28 ······file,·containing·distances·listed·for·each·label.28 ······file,·containing·distances·listed·for·each·label.
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14 ··style=sparse···#storage·style·(sparse|grid)·14 ··style=sparse···#storage·style·(sparse|grid)·
15 ··repn=float32···#representation·of·values·15 ··repn=float32···#representation·of·values·
16 ··size=1000·1000·200·#grid·size·of·the·transformation16 ··size=1000·1000·200·#grid·size·of·the·transformation
17 ··endian=low·····#endianess·of·binary·data·(low|big)·17 ··endian=low·····#endianess·of·binary·data·(low|big)·
18 }18 }
  
19 This·example·header·has·to·be·interpreted·like·follows:·three-dimensional·data,·each·entry·consists·of·13·values·the·values·etry·consists·of·a·3D·vector,·a·scalar,·and·a·3x3·matrix·(saved·in·row-major·format).The·data·records·represent·strain·tensors,·and·only·a·sparse·set·of·points·is·given.·The·values·are·given·as·single·floating·point·(32·bit).·The·original·transformation·field·corresponds·to·images·of·1000x1000x200·voxels·and·the·binary·data·is·stored·in·low·endian·format.</p><h4><a·name="idp13441"></a>Options:</h4><h4><a·name="idp13442"></a>19 This·example·header·has·to·be·interpreted·like·follows:·three-dimensional·data,·each·entry·consists·of·13·values·the·values·etry·consists·of·a·3D·vector,·a·scalar,·and·a·3x3·matrix·(saved·in·row-major·format).The·data·records·represent·strain·tensors,·and·only·a·sparse·set·of·points·is·given.·The·values·are·given·as·single·floating·point·(32·bit).·The·original·transformation·field·corresponds·to·images·of·1000x1000x200·voxels·and·the·binary·data·is·stored·in·low·endian·format.</p><h4><a·name="idp13441"></a>Options:</h4><h4><a·name="idp13442"></a>
20 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input);·string</span></dt><dd><p>input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·strains·file,·for·a·format·description·see·above.</p></dd><dt><span·class="term">-t,·--transformation=(input,·required);·io</span></dt><dd><p>transformation·of·which·the·quantity·will·be·evaluated..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp13457"></a>20 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input);·string</span></dt><dd><p>input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·strains·file,·for·a·format·description·see·above.</p></dd><dt><span·class="term">-t,·--transformation=(required,·input);·io</span></dt><dd><p>transformation·of·which·the·quantity·will·be·evaluated..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp13457"></a>
21 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-q,·--quantity=strain;·dict</span></dt><dd><p>Specify·the·quantity·to·be·evaluated·at·the·given·points</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">derivative:</td><td·align="left"·valign="top">Evaluate·the·transformation·derivative·at·the·given·points</td></tr><tr><td·align="left"·valign="top">strain:</td><td·align="left"·valign="top">Evaluate·the·strain·tensor·at·the·given·points</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp13474"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13525"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13531"></a>Example:</h4><p>Derivative·of·the·transformation·change.v3df·for·each··point·given·in·input.csv·are·evaluated·and·written·to·output.s.</p><pre·class="screen">mia-3deval-transformquantity·-i·input.csv·-o·output.s·--transformation·change.v3df</pre><h4><a·name="idp13534"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecToolsfortheAnalysisof3Dimageseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof3Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dseriestrackintensity.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Tools·for·the·Analysis·of·3D·image·series </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dseries-track-intensity</td></tr></table></div></body></html>21 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-q,·--quantity=strain;·dict</span></dt><dd><p>Specify·the·quantity·to·be·evaluated·at·the·given·points</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">derivative:</td><td·align="left"·valign="top">Evaluate·the·transformation·derivative·at·the·given·points</td></tr><tr><td·align="left"·valign="top">strain:</td><td·align="left"·valign="top">Evaluate·the·strain·tensor·at·the·given·points</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp13474"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13525"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13531"></a>Example:</h4><p>Derivative·of·the·transformation·change.v3df·for·each··point·given·in·input.csv·are·evaluated·and·written·to·output.s.</p><pre·class="screen">mia-3deval-transformquantity·-i·input.csv·-o·output.s·--transformation·change.v3df</pre><h4><a·name="idp13534"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecToolsfortheAnalysisof3Dimageseries.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof3Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dseriestrackintensity.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Tools·for·the·Analysis·of·3D·image·series </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dseries-track-intensity</td></tr></table></div></body></html>
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26 ·File-IO26 ·File-IO
27 ··-i,·--in-file=(input);·string27 ··-i,·--in-file=(input);·string
28 ······input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the28 ······input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the
29 ······quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid29 ······quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid
30 ······point·of·the·transformation·range.30 ······point·of·the·transformation·range.
31 ··-o,·--out-file=(required,·output);·string31 ··-o,·--out-file=(required,·output);·string
32 ······output·strains·file,·for·a·format·description·see·above.32 ······output·strains·file,·for·a·format·description·see·above.
33 ··-t,·--transformation=(input,·required);·io33 ··-t,·--transformation=(required,·input);·io
34 ······transformation·of·which·the·quantity·will·be·evaluated..·For·supported34 ······transformation·of·which·the·quantity·will·be·evaluated..·For·supported
35 ······file·types·see·Plugin_type:_3dtransform/io35 ······file·types·see·Plugin_type:_3dtransform/io
36 ·Parameters36 ·Parameters
37 ··-q,·--quantity=strain;·dict37 ··-q,·--quantity=strain;·dict
38 ······Specify·the·quantity·to·be·evaluated·at·the·given·points38 ······Specify·the·quantity·to·be·evaluated·at·the·given·points
39 ······derivative:·Evaluate·the·transformation·derivative·at·the·given·points39 ······derivative:·Evaluate·the·transformation·derivative·at·the·given·points
40 ······strain:·····Evaluate·the·strain·tensor·at·the·given·points40 ······strain:·····Evaluate·the·strain·tensor·at·the·given·points
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./usr/share/doc/mia-2.4/userref/Secmia3dfield2norm.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfield2norm</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="next"·href="Secmia3dimageaddattributes.html"·title="mia-3dimageaddattributes"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfield2norm</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecMiscellaneousprograms.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimageaddattributes.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfield2norm"></a>mia-3dfield2norm</h3></div></div></div><h4><a·name="idp13753"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfield2norm</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfield2norm</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="next"·href="Secmia3dimageaddattributes.html"·title="mia-3dimageaddattributes"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfield2norm</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecMiscellaneousprograms.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimageaddattributes.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfield2norm"></a>mia-3dfield2norm</h3></div></div></div><h4><a·name="idp13753"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfield2norm</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp13762"></a>Description:</h4><p·class="description">This·program·converts·a·3d·vector·field·to·an·image·of·its·voxel-wise·norm.</p><h4><a·name="idp13764"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-vectorfield=(input,·required);·io</span></dt><dd><p>input·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output);·io</span></dt><dd><p>output·image·comprising·the·per·voxel·norm·of·each·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp13776"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13827"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13833"></a>Example:</h4><p>Evaluate·the·norm·image·norm.v·from·a·vector·field·field.v.</p><pre·class="screen">mia-3dfield2norm·-i·field.v·-o·norm.v</pre><h4><a·name="idp13836"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecMiscellaneousprograms.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimageaddattributes.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Miscellaneous·programs </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimageaddattributes</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp13762"></a>Description:</h4><p·class="description">This·program·converts·a·3d·vector·field·to·an·image·of·its·voxel-wise·norm.</p><h4><a·name="idp13764"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-vectorfield=(required,·input);·io</span></dt><dd><p>input·vector·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output);·io</span></dt><dd><p>output·image·comprising·the·per·voxel·norm·of·each·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp13776"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13827"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13833"></a>Example:</h4><p>Evaluate·the·norm·image·norm.v·from·a·vector·field·field.v.</p><pre·class="screen">mia-3dfield2norm·-i·field.v·-o·norm.v</pre><h4><a·name="idp13836"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecMiscellaneousprograms.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimageaddattributes.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Miscellaneous·programs </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimageaddattributes</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dfield2norm4 mia-3dfield2norm
5 Sysnopis:5 Sysnopis:
6 mia-3dfield2norm·{-i·io}·{-o·io}·[·options·...]6 mia-3dfield2norm·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·converts·a·3d·vector·field·to·an·image·of·its·voxel-wise·norm.8 This·program·converts·a·3d·vector·field·to·an·image·of·its·voxel-wise·norm.
9 Options:9 Options:
10 ··-i,·--in-vectorfield=(input,·required);·io10 ··-i,·--in-vectorfield=(required,·input);·io
11 ······input·vector·field.·For·supported·file·types·see·Plugin_type:_3dvf/io11 ······input·vector·field.·For·supported·file·types·see·Plugin_type:_3dvf/io
12 ··-o,·--out-image=(required,·output);·io12 ··-o,·--out-image=(required,·output);·io
13 ······output·image·comprising·the·per·voxel·norm·of·each·image.·For·supported13 ······output·image·comprising·the·per·voxel·norm·of·each·image.·For·supported
14 ······file·types·see·Plugin_type:_3dimage/io14 ······file·types·see·Plugin_type:_3dimage/io
15 Help·&·Info15 Help·&·Info
16 ··-V,·--verbose=warning;·dict16 ··-V,·--verbose=warning;·dict
17 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.17 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfluid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3ddeform.html"·title="mia-3ddeform"><link·rel="next"·href="Secmia3dfluidsynregistration.html"·title="mia-3dfluid-syn-registration"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfluid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3ddeform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dfluidsynregistration.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfluid"></a>mia-3dfluid</h3></div></div></div><h4><a·name="idp11567"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfluid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfluid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3ddeform.html"·title="mia-3ddeform"><link·rel="next"·href="Secmia3dfluidsynregistration.html"·title="mia-3dfluid-syn-registration"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfluid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3ddeform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dfluidsynregistration.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfluid"></a>mia-3dfluid</h3></div></div></div><h4><a·name="idp11567"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfluid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11578"></a>Description:</h4><p·class="description">This·program·is·used·for·non-rigid·registration·based·on·fluid·dynamics·as·described·in:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/TMI.2002.803113"·target="_top">Wollny,·G.·and·Kruggel,·F.,·'Computational·cost·of·non-rigid·registration·algorithms··based·on·fluid·dynamics',·IEEE·Transactions·on·Medical·Imaging,·11(8),·pp.·946-952,·2002.</a></p><p·class="description">·It·uses·SSD·as·the·sole·registration·criterion.</p><h4><a·name="idp11582"></a>Options:</h4><h4><a·name="idp11583"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(input,·required);·io</span></dt><dd><p>reference·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-transformation=(required,·output);·io</span></dt><dd><p>output·transformation·comprising·the·registering·transformation·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-d,·--out-image=(output);·io</span></dt><dd><p>save·deformed·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp11605"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11656"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11662"></a>Registration·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--disable-multigrid</span></dt><dd><p>disable·multi-grid·processing</p></dd><dt><span·class="term">--disable-fullres</span></dt><dd><p>disable·processing·on·the·full·resolution·image</p></dd><dt><span·class="term">--lambda=1;·float</span></dt><dd><p>elasticy·constant</p></dd><dt><span·class="term">--mu=1;·float</span></dt><dd><p>elasticy·constant</p></dd><dt><span·class="term">-s,·--start-size=16;·int</span></dt><dd><p>initial·multigrided·size</p></dd><dt><span·class="term">-m,·--method=sora;·dict</span></dt><dd><p>method·for·solving·PDE</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">sor:</td><td·align="left"·valign="top">successive·overrelaxation</td></tr><tr><td·align="left"·valign="top">sora:</td><td·align="left"·valign="top">Gauss·Southwell·relexation</td></tr></tbody></table></div></dd><dt><span·class="term">--step=0.8;·float</span></dt><dd><p>Initial·stepsize</p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">--relax=1;·float</span></dt><dd><p>overrelaxation·factor·vor·method·sor</p></dd><dt><span·class="term">--maxiter=10;·int</span></dt><dd><p>maximum·iterations</p></dd><dt><span·class="term">--epsilon=0.01;·float</span></dt><dd><p>truncation·condition</p></dd><dt><span·class="term">--matter=4;·float</span></dt><dd><p>intensity·above·which·real·matter·is·assumed·(experimental)</p></dd></dl></div><h4><a·name="idp11724"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·and·write·the·deformation·vector·field·regfield.v.·Start·registration·at·the·smallest·size·above·16·pixel.</p><pre·class="screen">mia-3dfluid·-i·test.v·-r·ref.v·-o·regfield.v·-s·16</pre><h4><a·name="idp11727"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3ddeform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dfluidsynregistration.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3ddeform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dfluid-syn-registration</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11578"></a>Description:</h4><p·class="description">This·program·is·used·for·non-rigid·registration·based·on·fluid·dynamics·as·described·in:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/TMI.2002.803113"·target="_top">Wollny,·G.·and·Kruggel,·F.,·'Computational·cost·of·non-rigid·registration·algorithms··based·on·fluid·dynamics',·IEEE·Transactions·on·Medical·Imaging,·11(8),·pp.·946-952,·2002.</a></p><p·class="description">·It·uses·SSD·as·the·sole·registration·criterion.</p><h4><a·name="idp11582"></a>Options:</h4><h4><a·name="idp11583"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(required,·input);·io</span></dt><dd><p>reference·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-transformation=(required,·output);·io</span></dt><dd><p>output·transformation·comprising·the·registering·transformation·field.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-d,·--out-image=(output);·io</span></dt><dd><p>save·deformed·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp11605"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11656"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11662"></a>Registration·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--disable-multigrid</span></dt><dd><p>disable·multi-grid·processing</p></dd><dt><span·class="term">--disable-fullres</span></dt><dd><p>disable·processing·on·the·full·resolution·image</p></dd><dt><span·class="term">--lambda=1;·float</span></dt><dd><p>elasticy·constant</p></dd><dt><span·class="term">--mu=1;·float</span></dt><dd><p>elasticy·constant</p></dd><dt><span·class="term">-s,·--start-size=16;·int</span></dt><dd><p>initial·multigrided·size</p></dd><dt><span·class="term">-m,·--method=sora;·dict</span></dt><dd><p>method·for·solving·PDE</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">sor:</td><td·align="left"·valign="top">successive·overrelaxation</td></tr><tr><td·align="left"·valign="top">sora:</td><td·align="left"·valign="top">Gauss·Southwell·relexation</td></tr></tbody></table></div></dd><dt><span·class="term">--step=0.8;·float</span></dt><dd><p>Initial·stepsize</p></dd><dt><span·class="term">-p,·--interpolator=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">--relax=1;·float</span></dt><dd><p>overrelaxation·factor·vor·method·sor</p></dd><dt><span·class="term">--maxiter=10;·int</span></dt><dd><p>maximum·iterations</p></dd><dt><span·class="term">--epsilon=0.01;·float</span></dt><dd><p>truncation·condition</p></dd><dt><span·class="term">--matter=4;·float</span></dt><dd><p>intensity·above·which·real·matter·is·assumed·(experimental)</p></dd></dl></div><h4><a·name="idp11724"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·and·write·the·deformation·vector·field·regfield.v.·Start·registration·at·the·smallest·size·above·16·pixel.</p><pre·class="screen">mia-3dfluid·-i·test.v·-r·ref.v·-o·regfield.v·-s·16</pre><h4><a·name="idp11727"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3ddeform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dfluidsynregistration.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3ddeform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dfluid-syn-registration</td></tr></table></div></body></html>
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9 described·in:9 described·in:
10 Wollny,_G._and_Kruggel,_F.,_'Computational_cost_of_non-rigid_registration10 Wollny,_G._and_Kruggel,_F.,_'Computational_cost_of_non-rigid_registration
11 algorithms_based_on_fluid_dynamics',_IEEE_Transactions_on_Medical_Imaging,_1111 algorithms_based_on_fluid_dynamics',_IEEE_Transactions_on_Medical_Imaging,_11
12 (8),_pp._946-952,_2002.12 (8),_pp._946-952,_2002.
13 It·uses·SSD·as·the·sole·registration·criterion.13 It·uses·SSD·as·the·sole·registration·criterion.
14 Options:14 Options:
15 File-IO15 File-IO
16 ··-i,·--in-image=(input,·required);·io16 ··-i,·--in-image=(required,·input);·io
17 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io17 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
18 ··-r,·--ref-image=(input,·required);·io18 ··-r,·--ref-image=(required,·input);·io
19 ······reference·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io19 ······reference·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io
20 ··-o,·--out-transformation=(required,·output);·io20 ··-o,·--out-transformation=(required,·output);·io
21 ······output·transformation·comprising·the·registering·transformation·field.21 ······output·transformation·comprising·the·registering·transformation·field.
22 ······For·supported·file·types·see·Plugin_type:_3dtransform/io22 ······For·supported·file·types·see·Plugin_type:_3dtransform/io
23 ··-d,·--out-image=(output);·io23 ··-d,·--out-image=(output);·io
24 ······save·deformed·image.·For·supported·file·types·see·Plugin_type:_3dimage/io24 ······save·deformed·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
25 Help·&·Info25 Help·&·Info
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfluid-syn-registration</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dfluid.html"·title="mia-3dfluid"><link·rel="next"·href="Secmia3dforce.html"·title="mia-3dforce"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfluid-syn-registration</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfluid.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dforce.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfluidsynregistration"></a>mia-3dfluid-syn-registration</h3></div></div></div><h4><a·name="idp11731"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfluid-syn-registration</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-O·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfluid-syn-registration</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dfluid.html"·title="mia-3dfluid"><link·rel="next"·href="Secmia3dforce.html"·title="mia-3dforce"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfluid-syn-registration</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfluid.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dforce.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfluidsynregistration"></a>mia-3dfluid-syn-registration</h3></div></div></div><h4><a·name="idp11731"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfluid-syn-registration</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-O·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11744"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·3D·images.·The·transformation·applied·is·a·symmeric·diffeomorpic·fluid·dynamic·registration.·To·work·most·efficiently,·this·program·makes·a·few·assumptions·about·the·imput·data,·i.e.·the·image·must·be·of·the·same·size,·have·the·same·voxel·spacing,·and·any·intensity·range·normalization·or·equalization·should·also·be·done·before·calling·this·program.</p><h4><a·name="idp11746"></a>Options:</h4><h4><a·name="idp11747"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11798"></a>IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(input,·required);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--transform=(required,·output);·io</span></dt><dd><p>output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-O,·--inverse-transform=(required,·output);·io</span></dt><dd><p>inverse·output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp11820"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11826"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--mg-levels=3;·uint</span></dt><dd><p>Number·of·multi-resolution·levels·to·run·the·registration·on.·Not·that·some·registration·parameters·can·be·given·as·a·coma·seperated·list·to·indicate·per·level·values.·In·these·cases··if·the·number·of·given·values·is·smaller·than·the·number·of·multi-resolution·levels·(this·parameter),·the·the·last·given·value·is·used·for·all·subsequest·multi-resolution·levels.</p></dd><dt><span·class="term">-S,·--step=0.25;·float·in·(0,·0.5]</span></dt><dd><p>Initial·step·size·for·all·levels</p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>Image·similarity·function·to·be·minimized.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd><dt><span·class="term">-R,·--regularizer=sor:kernel=fluid,maxiter=50;·factory</span></dt><dd><p>Regularization·for·the·force·to·transformation·update.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dvfregularizer.html"·title="Plugin·type:·3dvf/regularizer">Plugin·type:·3dvf/regularizer</a></p></dd><dt><span·class="term">-T,·--conv-test-interval=·in·[4,·40]</span></dt><dd><p>Convergence·test·interations·intervall:·In·order·to·measure·convergence·the·cost·function·value·is·averaged·over·this·amount·of·iterations,·and·the·decline·rate·is·evaluated·based·on·the·linare·regression·of·the·cost·function·values·in·this·intervall.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-D,·--stop-decline-rate=·in·[0,·inf)</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·decline·rate.·If·the·rate·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-C,·--stop-cost=</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·value.·If·the·cost·drops·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-I,·--iter=·in·[4,·inf)</span></dt><dd><p>Naximum·number·if·iterations·done·on·each·multi-resolution·level.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd></dl></div><h4><a·name="idp11862"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·saving·the·transformation·to·transform.v·and·the·inverse·transform·to·inverse-transform.v.·Use·three·multiresolution·levels,·ssd·as·image·cost·function.</p><pre·class="screen">mia-3dfluid-syn-registration·-i·test.v·-r·ref.v·-t·transform.v·-T·inverse-transform.v··-l·3·ssd</pre><h4><a·name="idp11865"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfluid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dforce.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfluid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dforce</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11744"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·3D·images.·The·transformation·applied·is·a·symmeric·diffeomorpic·fluid·dynamic·registration.·To·work·most·efficiently,·this·program·makes·a·few·assumptions·about·the·imput·data,·i.e.·the·image·must·be·of·the·same·size,·have·the·same·voxel·spacing,·and·any·intensity·range·normalization·or·equalization·should·also·be·done·before·calling·this·program.</p><h4><a·name="idp11746"></a>Options:</h4><h4><a·name="idp11747"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11798"></a>IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(required,·input);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--transform=(required,·output);·io</span></dt><dd><p>output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-O,·--inverse-transform=(required,·output);·io</span></dt><dd><p>inverse·output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp11820"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11826"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--mg-levels=3;·uint</span></dt><dd><p>Number·of·multi-resolution·levels·to·run·the·registration·on.·Not·that·some·registration·parameters·can·be·given·as·a·coma·seperated·list·to·indicate·per·level·values.·In·these·cases··if·the·number·of·given·values·is·smaller·than·the·number·of·multi-resolution·levels·(this·parameter),·the·the·last·given·value·is·used·for·all·subsequest·multi-resolution·levels.</p></dd><dt><span·class="term">-S,·--step=0.25;·float·in·(0,·0.5]</span></dt><dd><p>Initial·step·size·for·all·levels</p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>Image·similarity·function·to·be·minimized.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd><dt><span·class="term">-R,·--regularizer=sor:kernel=fluid,maxiter=50;·factory</span></dt><dd><p>Regularization·for·the·force·to·transformation·update.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dvfregularizer.html"·title="Plugin·type:·3dvf/regularizer">Plugin·type:·3dvf/regularizer</a></p></dd><dt><span·class="term">-T,·--conv-test-interval=·in·[4,·40]</span></dt><dd><p>Convergence·test·interations·intervall:·In·order·to·measure·convergence·the·cost·function·value·is·averaged·over·this·amount·of·iterations,·and·the·decline·rate·is·evaluated·based·on·the·linare·regression·of·the·cost·function·values·in·this·intervall.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-D,·--stop-decline-rate=·in·[0,·inf)</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·decline·rate.·If·the·rate·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-C,·--stop-cost=</span></dt><dd><p>Stopping·criterium·for·registration·based·on·the·cost·value.·If·the·cost·drops·below·this·value,·the·iteration·is·stopped.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd><dt><span·class="term">-I,·--iter=·in·[4,·inf)</span></dt><dd><p>Naximum·number·if·iterations·done·on·each·multi-resolution·level.·This·parameter·can·be·given·as·a·coma-seperated·list·with·values·corresponding·to·the·multi-resolution·levels,·see·option·--mg-levels·for·more·information.</p></dd></dl></div><h4><a·name="idp11862"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·saving·the·transformation·to·transform.v·and·the·inverse·transform·to·inverse-transform.v.·Use·three·multiresolution·levels,·ssd·as·image·cost·function.</p><pre·class="screen">mia-3dfluid-syn-registration·-i·test.v·-r·ref.v·-t·transform.v·-T·inverse-transform.v··-l·3·ssd</pre><h4><a·name="idp11865"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfluid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dforce.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfluid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dforce</td></tr></table></div></body></html>
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29 ··-h,·--help=();·bool29 ··-h,·--help=();·bool
30 ······print·this·help30 ······print·this·help
31 ··-?,·--usage=();·bool31 ··-?,·--usage=();·bool
32 ······print·a·short·help32 ······print·a·short·help
33 ··--version=();·bool33 ··--version=();·bool
34 ······print·the·version·number·and·exit34 ······print·the·version·number·and·exit
35 IO35 IO
36 ··-i,·--in-image=(input,·required);·io36 ··-i,·--in-image=(required,·input);·io
37 ······test·image.·For·supported·file·types·see·Plugin_type:_3dimage/io37 ······test·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
38 ··-r,·--ref-image=(input,·required);·io38 ··-r,·--ref-image=(required,·input);·io
39 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io39 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
40 ··-o,·--transform=(required,·output);·io40 ··-o,·--transform=(required,·output);·io
41 ······output·transformation.·For·supported·file·types·see·Plugin_type:41 ······output·transformation.·For·supported·file·types·see·Plugin_type:
42 ······3dtransform/io42 ······3dtransform/io
43 ··-O,·--inverse-transform=(required,·output);·io43 ··-O,·--inverse-transform=(required,·output);·io
44 ······inverse·output·transformation.·For·supported·file·types·see·Plugin_type:44 ······inverse·output·transformation.·For·supported·file·types·see·Plugin_type:
45 ······3dtransform/io45 ······3dtransform/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dforce</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dfluidsynregistration.html"·title="mia-3dfluid-syn-registration"><link·rel="next"·href="Secmia3dlandmarksdistances.html"·title="mia-3dlandmarks-distances"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dforce</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfluidsynregistration.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarksdistances.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dforce"></a>mia-3dforce</h3></div></div></div><h4><a·name="idp11869"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dforce</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dforce</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dfluidsynregistration.html"·title="mia-3dfluid-syn-registration"><link·rel="next"·href="Secmia3dlandmarksdistances.html"·title="mia-3dlandmarks-distances"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dforce</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfluidsynregistration.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarksdistances.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dforce"></a>mia-3dforce</h3></div></div></div><h4><a·name="idp11869"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dforce</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11880"></a>Description:</h4><p·class="description">This·program·is·used·to·create·an·image·comprising·the·pixel-wise·norm·of·the·ggradient·of·a·given·cost·function.</p><h4><a·name="idp11882"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--src-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-file=(input,·required);·io</span></dt><dd><p>output·force·norm·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>cost·function·to·use.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd></dl></div><h4><a·name="idp11904"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11955"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11961"></a>Example:</h4><p>Evaluate·the·weigtes·sum·of·SSD·between·src.v·and·ref.v·and·store·the·result·in·forcenorm.v.</p><pre·class="screen">mia-3dforce·-i·src.v·-r·ref.v·-c·ssd·-o·forcenorm.v</pre><h4><a·name="idp11964"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfluidsynregistration.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarksdistances.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfluid-syn-registration </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dlandmarks-distances</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11880"></a>Description:</h4><p·class="description">This·program·is·used·to·create·an·image·comprising·the·pixel-wise·norm·of·the·ggradient·of·a·given·cost·function.</p><h4><a·name="idp11882"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--src-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-file=(required,·input);·io</span></dt><dd><p>output·force·norm·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>cost·function·to·use.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd></dl></div><h4><a·name="idp11904"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11955"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11961"></a>Example:</h4><p>Evaluate·the·weigtes·sum·of·SSD·between·src.v·and·ref.v·and·store·the·result·in·forcenorm.v.</p><pre·class="screen">mia-3dforce·-i·src.v·-r·ref.v·-c·ssd·-o·forcenorm.v</pre><h4><a·name="idp11964"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfluidsynregistration.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarksdistances.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfluid-syn-registration </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dlandmarks-distances</td></tr></table></div></body></html>
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4 mia-3dforce4 mia-3dforce
5 Sysnopis:5 Sysnopis:
6 mia-3dforce·{-i·io}·{-r·io}·{-o·io}·[·options·...]6 mia-3dforce·{-i·io}·{-r·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·create·an·image·comprising·the·pixel-wise·norm·of·the8 This·program·is·used·to·create·an·image·comprising·the·pixel-wise·norm·of·the
9 ggradient·of·a·given·cost·function.9 ggradient·of·a·given·cost·function.
10 Options:10 Options:
11 ··-i,·--src-file=(input,·required);·io11 ··-i,·--src-file=(required,·input);·io
12 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io12 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
13 ··-r,·--ref-file=(input,·required);·io13 ··-r,·--ref-file=(required,·input);·io
14 ······output·force·norm·image.·For·supported·file·types·see·Plugin_type:14 ······output·force·norm·image.·For·supported·file·types·see·Plugin_type:
15 ······3dimage/io15 ······3dimage/io
16 ··-o,·--out-file=(required,·output);·io16 ··-o,·--out-file=(required,·output);·io
17 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io17 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
18 ··-c,·--cost=ssd;·factory18 ··-c,·--cost=ssd;·factory
19 ······cost·function·to·use.·For·supported·plug-ins·see·Plugin_type:_3dimage/19 ······cost·function·to·use.·For·supported·plug-ins·see·Plugin_type:_3dimage/
20 ······cost20 ······cost
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfuzzysegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3ddistancestats.html"·title="mia-3ddistance-stats"><link·rel="next"·href="Secmia3dgetsize.html"·title="mia-3dgetsize"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfuzzysegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3ddistancestats.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dgetsize.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfuzzysegment"></a>mia-3dfuzzysegment</h3></div></div></div><h4><a·name="idp9784"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfuzzysegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dfuzzysegment</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3ddistancestats.html"·title="mia-3ddistance-stats"><link·rel="next"·href="Secmia3dgetsize.html"·title="mia-3dgetsize"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dfuzzysegment</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3ddistancestats.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dgetsize.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dfuzzysegment"></a>mia-3dfuzzysegment</h3></div></div></div><h4><a·name="idp9784"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dfuzzysegment</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp9791"></a>Description:</h4><p·class="description">This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image</p><h4><a·name="idp9793"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·segmenetd.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--cls-file=(output);·io</span></dt><dd><p>output·class·probability·images.·Note,·the·used·file·format·must·support·multible·images·(best·is·to·use·vista).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--b0-file=(output);·io</span></dt><dd><p>image·corrected·for·intensity·non-uniformity.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-r,·--residuum=0.1;·float</span></dt><dd><p>relative·residuum</p></dd></dl></div><h4><a·name="idp9818"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9869"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9875"></a>Example:</h4><p>Run·a·5-class·segmentation·over·inpt·image·input.v·and·store·the·class·probability·images·in·cls.v·and·the·B0-field·corrected·image·in·b0.v.</p><pre·class="screen">mia-3dfuzzysegment·-i·input.v·-c·5·-o·b0.v·-c·cls.v</pre><h4><a·name="idp9878"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3ddistancestats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dgetsize.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3ddistance-stats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dgetsize</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp9791"></a>Description:</h4><p·class="description">This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image</p><h4><a·name="idp9793"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·segmenetd.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--cls-file=(output);·io</span></dt><dd><p>output·class·probability·images.·Note,·the·used·file·format·must·support·multible·images·(best·is·to·use·vista).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--b0-file=(output);·io</span></dt><dd><p>image·corrected·for·intensity·non-uniformity.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-r,·--residuum=0.1;·float</span></dt><dd><p>relative·residuum</p></dd></dl></div><h4><a·name="idp9818"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9869"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9875"></a>Example:</h4><p>Run·a·5-class·segmentation·over·inpt·image·input.v·and·store·the·class·probability·images·in·cls.v·and·the·B0-field·corrected·image·in·b0.v.</p><pre·class="screen">mia-3dfuzzysegment·-i·input.v·-c·5·-o·b0.v·-c·cls.v</pre><h4><a·name="idp9878"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3ddistancestats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dgetsize.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3ddistance-stats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dgetsize</td></tr></table></div></body></html>
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4 mia-3dfuzzysegment4 mia-3dfuzzysegment
5 Sysnopis:5 Sysnopis:
6 mia-3dfuzzysegment·{-i·io}·[·options·...]6 mia-3dfuzzysegment·{-i·io}·[·options·...]
7 Description:7 Description:
8 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to8 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to
9 facilitate·a·3D·segmentation·of·3D·image9 facilitate·a·3D·segmentation·of·3D·image
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·image(s)·to·be·segmenetd.·For·supported·file·types·see·Plugin_type:12 ······input·image(s)·to·be·segmenetd.·For·supported·file·types·see·Plugin_type:
13 ······3dimage/io13 ······3dimage/io
14 ··-c,·--cls-file=(output);·io14 ··-c,·--cls-file=(output);·io
15 ······output·class·probability·images.·Note,·the·used·file·format·must·support15 ······output·class·probability·images.·Note,·the·used·file·format·must·support
16 ······multible·images·(best·is·to·use·vista).·For·supported·file·types·see16 ······multible·images·(best·is·to·use·vista).·For·supported·file·types·see
17 ······Plugin_type:_3dimage/io17 ······Plugin_type:_3dimage/io
18 ··-o,·--b0-file=(output);·io18 ··-o,·--b0-file=(output);·io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dgetsize</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dfuzzysegment.html"·title="mia-3dfuzzysegment"><link·rel="next"·href="Secmia3dimagecombine.html"·title="mia-3dimagecombine"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dgetsize</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfuzzysegment.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecombine.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dgetsize"></a>mia-3dgetsize</h3></div></div></div><h4><a·name="idp9882"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dgetsize</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dgetsize</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dfuzzysegment.html"·title="mia-3dfuzzysegment"><link·rel="next"·href="Secmia3dimagecombine.html"·title="mia-3dimagecombine"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dgetsize</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfuzzysegment.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecombine.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dgetsize"></a>mia-3dgetsize</h3></div></div></div><h4><a·name="idp9882"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dgetsize</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp9889"></a>Description:</h4><p·class="description">Write·the·dimensions·of·the·input·3D·image·to·stdout.</p><h4><a·name="idp9891"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9898"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9949"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9955"></a>Example:</h4><p>Print·out·the·size·of·image.v.</p><pre·class="screen">mia-3dgetsize·-i·image.v</pre><h4><a·name="idp9958"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfuzzysegment.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecombine.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfuzzysegment </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagecombine</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp9889"></a>Description:</h4><p·class="description">Write·the·dimensions·of·the·input·3D·image·to·stdout.</p><h4><a·name="idp9891"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9898"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9949"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9955"></a>Example:</h4><p>Print·out·the·size·of·image.v.</p><pre·class="screen">mia-3dgetsize·-i·image.v</pre><h4><a·name="idp9958"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfuzzysegment.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecombine.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfuzzysegment </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagecombine</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dgetsize4 mia-3dgetsize
5 Sysnopis:5 Sysnopis:
6 mia-3dgetsize·{-i·io}·[·options·...]6 mia-3dgetsize·{-i·io}·[·options·...]
7 Description:7 Description:
8 Write·the·dimensions·of·the·input·3D·image·to·stdout.8 Write·the·dimensions·of·the·input·3D·image·to·stdout.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:11 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
12 ······3dimage/io12 ······3dimage/io
13 Help·&·Info13 Help·&·Info
14 ··-V,·--verbose=warning;·dict14 ··-V,·--verbose=warning;·dict
15 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.15 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
16 ······Supported·priorities·starting·at·lowest·level·are:16 ······Supported·priorities·starting·at·lowest·level·are:
17 ······trace:···Function·call·trace17 ······trace:···Function·call·trace
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./usr/share/doc/mia-2.4/userref/Secmia3dgetslice.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dgetslice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia2dto3dimageb.html"·title="mia-2dto3dimageb"><link·rel="next"·href="Secmia3dimageselect.html"·title="mia-3dimageselect"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dgetslice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dto3dimageb.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimageselect.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dgetslice"></a>mia-3dgetslice</h3></div></div></div><h4><a·name="idp401"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dgetslice</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dgetslice</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia2dto3dimageb.html"·title="mia-2dto3dimageb"><link·rel="next"·href="Secmia3dimageselect.html"·title="mia-3dimageselect"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dgetslice</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia2dto3dimageb.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimageselect.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dgetslice"></a>mia-3dgetslice</h3></div></div></div><h4><a·name="idp401"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dgetslice</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp410"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·2D·slices·from·a·3D·data·set·and·store·them·in·separate·files.·Output·files·will·be·numbered·according·to·their·slice·index.</p><h4><a·name="idp412"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s).·If·number·!=·1·than·this·is·used·as·a·base·name·and·should·be·given·without·extension·since·this·will·be·based·on·the·'--type'·option.·If·number=1·then·this·exact·file·name·will·be·used..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--type=png;·set</span></dt><dd><p>output·file·type·for·number·!=·1<td·align="left"·valign="top">·Supported·values·are:(bmp,·datapool,·dicom,·exr,·jpg,·png,·raw,·tif,·vista,·)</td></p></dd><dt><span·class="term">-s,·--start=0;·ulong</span></dt><dd><p>start·slice·number</p></dd><dt><span·class="term">-n,·--number=1;·ulong</span></dt><dd><p>number·of·slices·(all=0)</p></dd><dt><span·class="term">--ndigits=4;·int</span></dt><dd><p>minimum·number·of·digits·of·the·file·name·numbers·(if·n·!=·1)</p></dd><dt><span·class="term">-d,·--dir=xy;·dict</span></dt><dd><p>slice·direction·(xy=axial,·xz=coronal,·yz=saggital)</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">xy:</td><td·align="left"·valign="top">get·xy·(axial)·slice</td></tr><tr><td·align="left"·valign="top">xz:</td><td·align="left"·valign="top">get·xz·(coronal)·slice</td></tr><tr><td·align="left"·valign="top">yz:</td><td·align="left"·valign="top">get·yz·(saggital)·slice</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp459"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp510"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp516"></a>Example:</h4><p>Store·5·coronal·slices·starting·at·slice·120·coronalXXXX.png·from··image.v.</p><pre·class="screen">mia-3dgetslice·-i·image.v·-o·coronal·-t·png·-n·5·-s·120</pre><h4><a·name="idp519"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dto3dimageb.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimageselect.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dto3dimageb </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimageselect</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp410"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·2D·slices·from·a·3D·data·set·and·store·them·in·separate·files.·Output·files·will·be·numbered·according·to·their·slice·index.</p><h4><a·name="idp412"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s).·If·number·!=·1·than·this·is·used·as·a·base·name·and·should·be·given·without·extension·since·this·will·be·based·on·the·'--type'·option.·If·number=1·then·this·exact·file·name·will·be·used..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-t,·--type=png;·set</span></dt><dd><p>output·file·type·for·number·!=·1<td·align="left"·valign="top">·Supported·values·are:(bmp,·datapool,·dicom,·exr,·jpg,·png,·raw,·tif,·vista,·)</td></p></dd><dt><span·class="term">-s,·--start=0;·ulong</span></dt><dd><p>start·slice·number</p></dd><dt><span·class="term">-n,·--number=1;·ulong</span></dt><dd><p>number·of·slices·(all=0)</p></dd><dt><span·class="term">--ndigits=4;·int</span></dt><dd><p>minimum·number·of·digits·of·the·file·name·numbers·(if·n·!=·1)</p></dd><dt><span·class="term">-d,·--dir=xy;·dict</span></dt><dd><p>slice·direction·(xy=axial,·xz=coronal,·yz=saggital)</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">xy:</td><td·align="left"·valign="top">get·xy·(axial)·slice</td></tr><tr><td·align="left"·valign="top">xz:</td><td·align="left"·valign="top">get·xz·(coronal)·slice</td></tr><tr><td·align="left"·valign="top">yz:</td><td·align="left"·valign="top">get·yz·(saggital)·slice</td></tr></tbody></table></div></dd></dl></div><h4><a·name="idp459"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp510"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp516"></a>Example:</h4><p>Store·5·coronal·slices·starting·at·slice·120·coronalXXXX.png·from··image.v.</p><pre·class="screen">mia-3dgetslice·-i·image.v·-o·coronal·-t·png·-n·5·-s·120</pre><h4><a·name="idp519"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia2dto3dimageb.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimageselect.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-2dto3dimageb </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimageselect</td></tr></table></div></body></html>
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10.7 KB
./usr/share/doc/mia-2.4/userref/Secmia3dimageaddattributes.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimageaddattributes</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmia3dfield2norm.html"·title="mia-3dfield2norm"><link·rel="next"·href="Secmia3dvectorfieldcreate.html"·title="mia-3dvectorfieldcreate"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimageaddattributes</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfield2norm.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dvectorfieldcreate.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimageaddattributes"></a>mia-3dimageaddattributes</h3></div></div></div><h4><a·name="idp13840"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimageaddattributes</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-a·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimageaddattributes</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmia3dfield2norm.html"·title="mia-3dfield2norm"><link·rel="next"·href="Secmia3dvectorfieldcreate.html"·title="mia-3dvectorfieldcreate"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimageaddattributes</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dfield2norm.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dvectorfieldcreate.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimageaddattributes"></a>mia-3dimageaddattributes</h3></div></div></div><h4><a·name="idp13840"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimageaddattributes</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-a·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp13851"></a>Description:</h4><p·class="description">This·program·appends·all·the·meta-data·attributes·found·in·a·2D·input·image·to·a·3D·image·(if·the·output·format·supports·such·attributes).·Attributes·that·are·already·present·in·the·3D·image·are·not·overwritten.</p><h4><a·name="idp13853"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=[·...·truncated·by·diffoscope;·len:·282,·SHA:·91c65d11fd1216717b458bd00eddf29bed4561702a49c13327f8e882b0e47988·...·]);·io</span></dt><dd><p>2D·image·providing·the·attributes.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp13870"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13921"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13927"></a>Example:</h4><p>Append·the·attributes·found·in·2d.v·to·3d.v·and·store·the·result·in·attr3d.v</p><pre·class="screen">mia-3dimageaddattributes··-i·3d.v·-o·attr3d.v·-a·2d.v</pre><h4><a·name="idp13930"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfield2norm.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dvectorfieldcreate.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfield2norm </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dvectorfieldcreate</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp13851"></a>Description:</h4><p·class="description">This·program·appends·all·the·meta-data·attributes·found·in·a·2D·input·image·to·a·3D·image·(if·the·output·format·supports·such·attributes).·Attributes·that·are·already·present·in·the·3D·image·are·not·overwritten.</p><h4><a·name="idp13853"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=[·...·truncated·by·diffoscope;·len:·282,·SHA:·4895104dc3377ae902cced4025f35d8e27079d8b071146a8c5bed68fa8a3e7d6·...·]);·io</span></dt><dd><p>2D·image·providing·the·attributes.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd></dl></div><h4><a·name="idp13870"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13921"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13927"></a>Example:</h4><p>Append·the·attributes·found·in·2d.v·to·3d.v·and·store·the·result·in·attr3d.v</p><pre·class="screen">mia-3dimageaddattributes··-i·3d.v·-o·attr3d.v·-a·2d.v</pre><h4><a·name="idp13930"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dfield2norm.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dvectorfieldcreate.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dfield2norm </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dvectorfieldcreate</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-3dimageaddattributes·{-i·io}·{-o·io}·{-a·io}·[·options·...]6 mia-3dimageaddattributes·{-i·io}·{-o·io}·{-a·io}·[·options·...]
7 Description:7 Description:
8 This·program·appends·all·the·meta-data·attributes·found·in·a·2D·input·image·to8 This·program·appends·all·the·meta-data·attributes·found·in·a·2D·input·image·to
9 a·3D·image·(if·the·output·format·supports·such·attributes).·Attributes·that·are9 a·3D·image·(if·the·output·format·supports·such·attributes).·Attributes·that·are
10 already·present·in·the·3D·image·are·not·overwritten.10 already·present·in·the·3D·image·are·not·overwritten.
11 Options:11 Options:
12 ··-i,·--in-file=(input,·required);·io12 ··-i,·--in-file=(required,·input);·io
13 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:13 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
14 ······3dimage/io14 ······3dimage/io
15 ··-o,·--out-file=(required,·output);·io15 ··-o,·--out-file=(required,·output);·io
16 ······output·image(s)·with·the·added·attributes.·For·supported·file·types·see16 ······output·image(s)·with·the·added·attributes.·For·supported·file·types·see
17 ······Plugin_type:_3dimage/io17 ······Plugin_type:_3dimage/io
18 ··-a,·--attr=(input,·required);·io18 ··-a,·--attr=(required,·input);·io
19 ······2D·image·providing·the·attributes.·For·supported·file·types·see·Plugin19 ······2D·image·providing·the·attributes.·For·supported·file·types·see·Plugin
20 ······type:_2dimage/io20 ······type:_2dimage/io
21 Help·&·Info21 Help·&·Info
22 ··-V,·--verbose=warning;·dict22 ··-V,·--verbose=warning;·dict
23 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.23 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
24 ······Supported·priorities·starting·at·lowest·level·are:24 ······Supported·priorities·starting·at·lowest·level·are:
25 ······trace:···Function·call·trace25 ······trace:···Function·call·trace
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagecombine</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dgetsize.html"·title="mia-3dgetsize"><link·rel="next"·href="Secmia3dimagecreator.html"·title="mia-3dimagecreator"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagecombine</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dgetsize.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecreator.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagecombine"></a>mia-3dimagecombine</h3></div></div></div><h4><a·name="idp9962"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagecombine</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-c·<em·class="replaceable"><code>factory</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagecombine</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dgetsize.html"·title="mia-3dgetsize"><link·rel="next"·href="Secmia3dimagecreator.html"·title="mia-3dimagecreator"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagecombine</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dgetsize.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecreator.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagecombine"></a>mia-3dimagecombine</h3></div></div></div><h4><a·name="idp9962"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagecombine</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-c·<em·class="replaceable"><code>factory</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp9975"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·two·images·using·a·given·image·combiner.</p><h4><a·name="idp9977"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--image1=(input,·required);·io</span></dt><dd><p>input·image··1·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-2,·--image2=(i[·...·truncated·by·diffoscope;·len:·14,·SHA:·fd1c382e5785db8308b9a0fb4436e9d7d56afc11f73c341f8a2314bc8a4dea35·...·]);·io</span></dt><dd><p>input·image··2·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--combiner=(required);·factory</span></dt><dd><p>combiner·operation.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecombiner.html"·title="Plugin·type:·3dimage/combiner">Plugin·type:·3dimage/combiner</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·file.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9999"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10050"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10056"></a>Example:</h4><p>Take·two·images·l1.v·and·l2.v·and·evaluate·the·per-voxel·sum.</p><pre·class="screen">mia-3dimagecombine·-1·l1.v·-2·l2.v·-c·sum.v·-c·add</pre><h4><a·name="idp10059"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dgetsize.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecreator.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dgetsize </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagecreator</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp9975"></a>Description:</h4><p·class="description">This·program·is·used·to·combine·two·images·using·a·given·image·combiner.</p><h4><a·name="idp9977"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--image1=(required,·input);·io</span></dt><dd><p>input·image··1·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-2,·--image2=(r[·...·truncated·by·diffoscope;·len:·14,·SHA:·365c1f095074386171b0ecd726b0add6ea233e93bba9bacac6f34fe091f83d4a·...·]);·io</span></dt><dd><p>input·image··2·to·be·combined.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--combiner=(required);·factory</span></dt><dd><p>combiner·operation.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecombiner.html"·title="Plugin·type:·3dimage/combiner">Plugin·type:·3dimage/combiner</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·file.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp9999"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10050"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10056"></a>Example:</h4><p>Take·two·images·l1.v·and·l2.v·and·evaluate·the·per-voxel·sum.</p><pre·class="screen">mia-3dimagecombine·-1·l1.v·-2·l2.v·-c·sum.v·-c·add</pre><h4><a·name="idp10059"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dgetsize.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagecreator.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dgetsize </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagecreator</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dimagecombine4 mia-3dimagecombine
5 Sysnopis:5 Sysnopis:
6 mia-3dimagecombine·{-1·io}·{-2·io}·{-c·factory}·{-o·io}·[·options·...]6 mia-3dimagecombine·{-1·io}·{-2·io}·{-c·factory}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·combine·two·images·using·a·given·image·combiner.8 This·program·is·used·to·combine·two·images·using·a·given·image·combiner.
9 Options:9 Options:
10 ··-1,·--image1=(input,·required);·io10 ··-1,·--image1=(required,·input);·io
11 ······input·image·1·to·be·combined.·For·supported·file·types·see·Plugin_type:11 ······input·image·1·to·be·combined.·For·supported·file·types·see·Plugin_type:
12 ······3dimage/io12 ······3dimage/io
13 ··-2,·--image2=(input,·required);·io13 ··-2,·--image2=(required,·input);·io
14 ······input·image·2·to·be·combined.·For·supported·file·types·see·Plugin_type:14 ······input·image·2·to·be·combined.·For·supported·file·types·see·Plugin_type:
15 ······3dimage/io15 ······3dimage/io
16 ··-c,·--combiner=(required);·factory16 ··-c,·--combiner=(required);·factory
17 ······combiner·operation.·For·supported·plug-ins·see·Plugin_type:_3dimage/17 ······combiner·operation.·For·supported·plug-ins·see·Plugin_type:_3dimage/
18 ······combiner18 ······combiner
19 ··-o,·--out-file=(required,·output);·io19 ··-o,·--out-file=(required,·output);·io
20 ······output·image·file.·For·supported·file·types·see·Plugin_type:_3dimage/io20 ······output·image·file.·For·supported·file·types·see·Plugin_type:_3dimage/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagefilter</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagecreator.html"·title="mia-3dimagecreator"><link·rel="next"·href="Secmia3dimagefilterstack.html"·title="mia-3dimagefilterstack"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagefilter</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagecreator.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagefilterstack.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagefilter"></a>mia-3dimagefilter</h3></div></div></div><h4><a·name="idp10197"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagefilter</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagefilter</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagecreator.html"·title="mia-3dimagecreator"><link·rel="next"·href="Secmia3dimagefilterstack.html"·title="mia-3dimagefilterstack"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagefilter</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagecreator.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagefilterstack.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagefilter"></a>mia-3dimagefilter</h3></div></div></div><h4><a·name="idp10197"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagefilter</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp10209"></a>Description:</h4><p·class="description">This·program·is·used·to·filter·and·convert·gray·scale·3D·images.</p><h4><a·name="idp10211"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp10223"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10274"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10280"></a>Example:</h4><p>Run·a·mean-least-varaiance·filter·on·input.v,·then·run·a·5-class·k-means·classification·and·binarize·by·selecting·the·4th·class.</p><pre·class="screen">mia-3dimagefilter·-i·image.v·-o·filtered.v·mlv:w=2·kmeans:c=5·binarize:min=4,max=4</pre><h4><a·name="idp10283"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagecreator.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagefilterstack.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagecreator </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagefilterstack</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp10209"></a>Description:</h4><p·class="description">This·program·is·used·to·filter·and·convert·gray·scale·3D·images.</p><h4><a·name="idp10211"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp10223"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10274"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10280"></a>Example:</h4><p>Run·a·mean-least-varaiance·filter·on·input.v,·then·run·a·5-class·k-means·classification·and·binarize·by·selecting·the·4th·class.</p><pre·class="screen">mia-3dimagefilter·-i·image.v·-o·filtered.v·mlv:w=2·kmeans:c=5·binarize:min=4,max=4</pre><h4><a·name="idp10283"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagecreator.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagefilterstack.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagecreator </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagefilterstack</td></tr></table></div></body></html>
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4 mia-3dimagefilter4 mia-3dimagefilter
5 Sysnopis:5 Sysnopis:
6 mia-3dimagefilter·{-i·io}·{-o·io}·[·options·...]·[·Plugin_type:_3dimage/filter6 mia-3dimagefilter·{-i·io}·{-o·io}·[·options·...]·[·Plugin_type:_3dimage/filter
7 ...]7 ...]
8 Description:8 Description:
9 This·program·is·used·to·filter·and·convert·gray·scale·3D·images.9 This·program·is·used·to·filter·and·convert·gray·scale·3D·images.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:12 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
13 ······3dimage/io13 ······3dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see15 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see
16 ······Plugin_type:_3dimage/io16 ······Plugin_type:_3dimage/io
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagefilterstack</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagefilter.html"·title="mia-3dimagefilter"><link·rel="next"·href="Secmia3dimagestatisticsinmask.html"·title="mia-3dimagestatistics-in-mask"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagefilterstack</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilter.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestatisticsinmask.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagefilterstack"></a>mia-3dimagefilterstack</h3></div></div></div><h4><a·name="idp10287"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagefilterstack</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>set</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagefilterstack</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagefilter.html"·title="mia-3dimagefilter"><link·rel="next"·href="Secmia3dimagestatisticsinmask.html"·title="mia-3dimagestatistics-in-mask"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagefilterstack</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilter.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestatisticsinmask.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagefilterstack"></a>mia-3dimagefilterstack</h3></div></div></div><h4><a·name="idp10287"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagefilterstack</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>set</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a>5 ············<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp10301"></a>Description:</h4><p·class="description">This·program·is·used·to·filter·and·convert·a·consecutive·numbered·series·gray·of·scale·images.·File·names·must·follow·the·pattern·'dataXXXX.v'·(X·being·digits),·i.e.·the·numbering·comes·right·before·the·dot.·</p><h4><a·name="idp10303"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name·base,·numbers·are·added·accorfing·to·the·input·file·pattern,·and·the·file··extension·is·added·according·to·the·'type'·option..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--type=(required);·set</span></dt><dd><p>output·file·type<td·align="left"·valign="top">·Supported·values·are:(analyze,·datapool,·dicom,·hdf5,·inria,·mhd,·nifti,·vff,·vista,·vti,·vtk,·)</td></p></dd></dl></div><h4><a·name="idp10320"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10371"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10377"></a>Example:</h4><p>Run·a·mean-least-varaiance·filter·on·a·series·of·images·that·follow·the·numbering·pattern·imageXXXX.hdr·and·store·the·output·in·images·filteredXXXX.hdr</p><pre·class="screen">mia-3dimagefilterstack·-i·image0000.hdr·-o·filtered·-t·hdr·mlv:w=2</pre><h4><a·name="idp10380"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilter.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestatisticsinmask.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagefilter </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagestatistics-in-mask</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp10301"></a>Description:</h4><p·class="description">This·program·is·used·to·filter·and·convert·a·consecutive·numbered·series·gray·of·scale·images.·File·names·must·follow·the·pattern·'dataXXXX.v'·(X·being·digits),·i.e.·the·numbering·comes·right·before·the·dot.·</p><h4><a·name="idp10303"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name·base,·numbers·are·added·accorfing·to·the·input·file·pattern,·and·the·file··extension·is·added·according·to·the·'type'·option..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--type=(required);·set</span></dt><dd><p>output·file·type<td·align="left"·valign="top">·Supported·values·are:(analyze,·datapool,·dicom,·hdf5,·inria,·mhd,·nifti,·vff,·vista,·vti,·vtk,·)</td></p></dd></dl></div><h4><a·name="idp10320"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10371"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10377"></a>Example:</h4><p>Run·a·mean-least-varaiance·filter·on·a·series·of·images·that·follow·the·numbering·pattern·imageXXXX.hdr·and·store·the·output·in·images·filteredXXXX.hdr</p><pre·class="screen">mia-3dimagefilterstack·-i·image0000.hdr·-o·filtered·-t·hdr·mlv:w=2</pre><h4><a·name="idp10380"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilter.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestatisticsinmask.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagefilter </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagestatistics-in-mask</td></tr></table></div></body></html>
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimageselect</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia3dgetslice.html"·title="mia-3dgetslice"><link·rel="next"·href="Secmiaraw2image.html"·title="mia-raw2image"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimageselect</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dgetslice.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiaraw2image.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimageselect"></a>mia-3dimageselect</h3></div></div></div><h4><a·name="idp523"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimageselect</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimageselect</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia3dgetslice.html"·title="mia-3dgetslice"><link·rel="next"·href="Secmiaraw2image.html"·title="mia-raw2image"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimageselect</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dgetslice.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiaraw2image.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimageselect"></a>mia-3dimageselect</h3></div></div></div><h4><a·name="idp523"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimageselect</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp532"></a>Description:</h4><p·class="description">This·program·is·used·to·select·one·3D·images·from·a·multi-image·file.</p><h4><a·name="idp534"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-n,·--number=0;·ulong</span></dt><dd><p>image·number·to·be·selected</p></dd></dl></div><h4><a·name="idp550"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp601"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp607"></a>Example:</h4><p>Store·the·third·image·in·multiimage.v·to·image.v·(note:·counting·starts·with·zero).</p><pre·class="screen">mia-3dimageselect·-i·multiimage.v·-o·image.v·-n·2</pre><h4><a·name="idp610"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dgetslice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiaraw2image.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dgetslice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-raw2image</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp532"></a>Description:</h4><p·class="description">This·program·is·used·to·select·one·3D·images·from·a·multi-image·file.</p><h4><a·name="idp534"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-n,·--number=0;·ulong</span></dt><dd><p>image·number·to·be·selected</p></dd></dl></div><h4><a·name="idp550"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp601"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp607"></a>Example:</h4><p>Store·the·third·image·in·multiimage.v·to·image.v·(note:·counting·starts·with·zero).</p><pre·class="screen">mia-3dimageselect·-i·multiimage.v·-o·image.v·-n·2</pre><h4><a·name="idp610"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dgetslice.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiaraw2image.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dgetslice </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-raw2image</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dimageselect4 mia-3dimageselect
5 Sysnopis:5 Sysnopis:
6 mia-3dimageselect·{-i·io}·{-o·io}·[·options·...]6 mia-3dimageselect·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·select·one·3D·images·from·a·multi-image·file.8 This·program·is·used·to·select·one·3D·images·from·a·multi-image·file.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·images.·For·supported·file·types·see·Plugin_type:_3dimage/io11 ······input·images.·For·supported·file·types·see·Plugin_type:_3dimage/io
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·image.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······output·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-n,·--number=0;·ulong14 ··-n,·--number=0;·ulong
15 ······image·number·to·be·selected15 ······image·number·to·be·selected
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagestatistics-in-mask</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagefilterstack.html"·title="mia-3dimagefilterstack"><link·rel="next"·href="Secmia3dimagestats.html"·title="mia-3dimagestats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagestatistics-in-mask</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilterstack.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagestatisticsinmask"></a>mia-3dimagestatistics-in-mask</h3></div></div></div><h4><a·name="idp10384"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagestatistics-in-mask</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-m·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagestatistics-in-mask</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagefilterstack.html"·title="mia-3dimagefilterstack"><link·rel="next"·href="Secmia3dimagestats.html"·title="mia-3dimagestats"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagestatistics-in-mask</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilterstack.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestats.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagestatisticsinmask"></a>mia-3dimagestatistics-in-mask</h3></div></div></div><h4><a·name="idp10384"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagestatistics-in-mask</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-m·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp10393"></a>Description:</h4><p·class="description">This·program·evaluates·the·statistics·of·an·image·within·a·masked·region·of·the·image.·Possible·outputs·are·a·summary·statistics·and·a·histogram·of·the·values.</p><h4><a·name="idp10395"></a>Options:</h4><h4><a·name="idp10396"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--image=(input,·required);·io</span></dt><dd><p>input·image·to·be·analyzed.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-m,·--mask=(input,[·...·truncated·by·diffoscope;·len:·9,·SHA:·1307c284df7b37d5fd5aed9015946ed2bd37b6cfdba17ff3de48b9c1bcfbdecd·...·]);·io</span></dt><dd><p>mask·image·to·use·to·restrict·the·analysis.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-s,·--summary=(output);·string</span></dt><dd><p>File·to·write·the·summary·statistics·to·as·plain·text.</p></dd><dt><span·class="term">-H,·--histogram=(output);·string</span></dt><dd><p>File·to·write·the·histogram·to</p></dd></dl></div><h4><a·name="idp10416"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10467"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--struct-name=undefined;·stringSTRING</span></dt><dd><p>Name·of·the·structure·the·statistics·are·evaluated·for</p></dd><dt><span·class="term">-l,·--limit=20;·uint·in·[20,·inf)</span></dt><dd><p>Number·of·pixels·the·mask·should·at·least·contain.</p></dd><dt><span·class="term">-b,·--bins=8;·ulong·in·[4,·inf)</span></dt><dd><p>number·of·histogram·bins·to·be·used</p></dd><dt><span·class="term">--hmin=0;·float</span></dt><dd><p>lower·bound·for·the·histogram·mapping.·All·values·below·this·value·will·be·mapped·into·the·lowest·bin.·If·this·parameter·is·equal·or·larger·than·hmax,·the·histogram·range·is·evaluated·automatically.</p></dd><dt><span·class="term">--hmax=0;·float</span></dt><dd><p>hpper·bound·for·the·histogram·mapping.·All·values·above·this·valuewill·be·mapped·into·the·highest·bin.·If·this·parameter·is·equal·or·smaller·than·hmin,·the·histogram·range·is·evaluated·automatically.</p></dd></dl></div><h4><a·name="idp10489"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10495"></a>Example:</h4><p>evaluate·the·summary·statistics·on·the·input·and·a·histogram·with·10·bins·and·automtically·evaluated·boundaries.·Save·summary·in·summary.txt·and·the·histogram·in·hist.txt</p><pre·class="screen">mia-3dimagestatistics-in-mask·--image·image.v.gz·--mask·mask.v.gz·--summary·summary.txt·--histogram·hist.txt</pre><h4><a·name="idp10498"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilterstack.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagefilterstack </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagestats</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp10393"></a>Description:</h4><p·class="description">This·program·evaluates·the·statistics·of·an·image·within·a·masked·region·of·the·image.·Possible·outputs·are·a·summary·statistics·and·a·histogram·of·the·values.</p><h4><a·name="idp10395"></a>Options:</h4><h4><a·name="idp10396"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--image=(required,·input);·io</span></dt><dd><p>input·image·to·be·analyzed.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-m,·--mask=(requir[·...·truncated·by·diffoscope;·len:·9,·SHA:·96c1c0c8734e3474ffde546006e5c8311c12d951db167287b6d52b7878707a6c·...·]);·io</span></dt><dd><p>mask·image·to·use·to·restrict·the·analysis.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-s,·--summary=(output);·string</span></dt><dd><p>File·to·write·the·summary·statistics·to·as·plain·text.</p></dd><dt><span·class="term">-H,·--histogram=(output);·string</span></dt><dd><p>File·to·write·the·histogram·to</p></dd></dl></div><h4><a·name="idp10416"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10467"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--struct-name=undefined;·stringSTRING</span></dt><dd><p>Name·of·the·structure·the·statistics·are·evaluated·for</p></dd><dt><span·class="term">-l,·--limit=20;·uint·in·[20,·inf)</span></dt><dd><p>Number·of·pixels·the·mask·should·at·least·contain.</p></dd><dt><span·class="term">-b,·--bins=8;·ulong·in·[4,·inf)</span></dt><dd><p>number·of·histogram·bins·to·be·used</p></dd><dt><span·class="term">--hmin=0;·float</span></dt><dd><p>lower·bound·for·the·histogram·mapping.·All·values·below·this·value·will·be·mapped·into·the·lowest·bin.·If·this·parameter·is·equal·or·larger·than·hmax,·the·histogram·range·is·evaluated·automatically.</p></dd><dt><span·class="term">--hmax=0;·float</span></dt><dd><p>hpper·bound·for·the·histogram·mapping.·All·values·above·this·valuewill·be·mapped·into·the·highest·bin.·If·this·parameter·is·equal·or·smaller·than·hmin,·the·histogram·range·is·evaluated·automatically.</p></dd></dl></div><h4><a·name="idp10489"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10495"></a>Example:</h4><p>evaluate·the·summary·statistics·on·the·input·and·a·histogram·with·10·bins·and·automtically·evaluated·boundaries.·Save·summary·in·summary.txt·and·the·histogram·in·hist.txt</p><pre·class="screen">mia-3dimagestatistics-in-mask·--image·image.v.gz·--mask·mask.v.gz·--summary·summary.txt·--histogram·hist.txt</pre><h4><a·name="idp10498"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagefilterstack.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dimagestats.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagefilterstack </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dimagestats</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-3dimagestatistics-in-mask·{-i·io}·{-m·io}·[·options·...]6 mia-3dimagestatistics-in-mask·{-i·io}·{-m·io}·[·options·...]
7 Description:7 Description:
8 This·program·evaluates·the·statistics·of·an·image·within·a·masked·region·of·the8 This·program·evaluates·the·statistics·of·an·image·within·a·masked·region·of·the
9 image.·Possible·outputs·are·a·summary·statistics·and·a·histogram·of·the·values.9 image.·Possible·outputs·are·a·summary·statistics·and·a·histogram·of·the·values.
10 Options:10 Options:
11 File-IO11 File-IO
12 ··-i,·--image=(input,·required);·io12 ··-i,·--image=(required,·input);·io
13 ······input·image·to·be·analyzed.·For·supported·file·types·see·Plugin_type:13 ······input·image·to·be·analyzed.·For·supported·file·types·see·Plugin_type:
14 ······3dimage/io14 ······3dimage/io
15 ··-m,·--mask=(input,·required);·io15 ··-m,·--mask=(required,·input);·io
16 ······mask·image·to·use·to·restrict·the·analysis.·For·supported·file·types·see16 ······mask·image·to·use·to·restrict·the·analysis.·For·supported·file·types·see
17 ······Plugin_type:_3dimage/io17 ······Plugin_type:_3dimage/io
18 ··-s,·--summary=(output);·string18 ··-s,·--summary=(output);·string
19 ······File·to·write·the·summary·statistics·to·as·plain·text.19 ······File·to·write·the·summary·statistics·to·as·plain·text.
20 ··-H,·--histogram=(output);·string20 ··-H,·--histogram=(output);·string
21 ······File·to·write·the·histogram·to21 ······File·to·write·the·histogram·to
22 Help·&·Info22 Help·&·Info
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagestats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagestatisticsinmask.html"·title="mia-3dimagestatistics-in-mask"><link·rel="next"·href="Secmia3disosurfacefromstack.html"·title="mia-3disosurface-from-stack"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagestats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagestatisticsinmask.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3disosurfacefromstack.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagestats"></a>mia-3dimagestats</h3></div></div></div><h4><a·name="idp10502"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagestats</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dimagestats</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagestatisticsinmask.html"·title="mia-3dimagestatistics-in-mask"><link·rel="next"·href="Secmia3disosurfacefromstack.html"·title="mia-3disosurface-from-stack"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dimagestats</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagestatisticsinmask.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3disosurfacefromstack.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dimagestats"></a>mia-3dimagestats</h3></div></div></div><h4><a·name="idp10502"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dimagestats</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp10509"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·certain·image·statistics·and·print·them·out·on·the·console.</p><h4><a·name="idp10511"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--thresh=10;·float</span></dt><dd><p>intensity·thresh·to·ignore</p></dd></dl></div><h4><a·name="idp10522"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10573"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10579"></a>Example:</h4><p>Evaluate·the·statistics·of·image·input.v·and·ignore·all·voxels·with·an·intensity·below·5.</p><pre·class="screen">mia-3dimagestats·-i·input.v·-t·5</pre><h4><a·name="idp10582"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagestatisticsinmask.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3disosurfacefromstack.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagestatistics-in-mask </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3disosurface-from-stack</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp10509"></a>Description:</h4><p·class="description">This·program·is·used·to·evaluate·certain·image·statistics·and·print·them·out·on·the·console.</p><h4><a·name="idp10511"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--thresh=10;·float</span></dt><dd><p>intensity·thresh·to·ignore</p></dd></dl></div><h4><a·name="idp10522"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10573"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10579"></a>Example:</h4><p>Evaluate·the·statistics·of·image·input.v·and·ignore·all·voxels·with·an·intensity·below·5.</p><pre·class="screen">mia-3dimagestats·-i·input.v·-t·5</pre><h4><a·name="idp10582"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagestatisticsinmask.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3disosurfacefromstack.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagestatistics-in-mask </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3disosurface-from-stack</td></tr></table></div></body></html>
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4 mia-3dimagestats4 mia-3dimagestats
5 Sysnopis:5 Sysnopis:
6 mia-3dimagestats·{-i·io}·[·options·...]6 mia-3dimagestats·{-i·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·evaluate·certain·image·statistics·and·print·them·out·on8 This·program·is·used·to·evaluate·certain·image·statistics·and·print·them·out·on
9 the·console.9 the·console.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:12 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
13 ······3dimage/io13 ······3dimage/io
14 ··-t,·--thresh=10;·float14 ··-t,·--thresh=10;·float
15 ······intensity·thresh·to·ignore15 ······intensity·thresh·to·ignore
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3disosurface-from-stack</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagestats.html"·title="mia-3dimagestats"><link·rel="next"·href="Secmia3dlerp.html"·title="mia-3dlerp"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3disosurface-from-stack</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagestats.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dlerp.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3disosurfacefromstack"></a>mia-3disosurface-from-stack</h3></div></div></div><h4><a·name="idp10586"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3disosurface-from-stack</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3disosurface-from-stack</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dimagestats.html"·title="mia-3dimagestats"><link·rel="next"·href="Secmia3dlerp.html"·title="mia-3dlerp"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3disosurface-from-stack</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimagestats.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dlerp.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3disosurfacefromstack"></a>mia-3disosurface-from-stack</h3></div></div></div><h4><a·name="idp10586"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3disosurface-from-stack</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp10595"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·given·as·slices.</p><h4><a·name="idp10597"></a>Options:</h4><h4><a·name="idp10598"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·string</span></dt><dd><p>input·image·filename·pattern</p></dd><dt><span·class="term">-o,·--out-mesh=(required,·output);·string</span></dt><dd><p>output·mesh</p></dd></dl></div><h4><a·name="idp10608"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10659"></a>Image·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--iso-value=128;·float</span></dt><dd><p>iso-value·of·iso·surface·to·be·extracted</p></dd></dl></div><h4><a·name="idp10665"></a>Mesh·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-f,·--max-faces=-1;·int</span></dt><dd><p>maximum·number·of·Faces,</p></dd><dt><span·class="term">-e,·--max-edges=-1;·int</span></dt><dd><p>maximum·number·of·Edges</p></dd><dt><span·class="term">-c,·--max-cost=0.1;·float</span></dt><dd><p>maximum·cost·for·edge·collaps</p></dd><dt><span·class="term">-r,·--ratio=4;·float</span></dt><dd><p>ratio·of·faces(edges)·to·target·number,·at·which··the·optimization·changes·from·edge-length·to·volume-optimized</p></dd><dt><span·class="term">-w,·--reverse-winding</span></dt><dd><p>reverse·the·winding·of·the·triangles·in·order·to·make·normals·point·away·from·the·high·intensity·area</p></dd></dl></div><h4><a·name="idp10687"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10693"></a>Example:</h4><p>Extract·the·surface·from·an·image·set·with·numbers·imageXXXX.png·that·corresponds·to··the·value·30·and·stop·optimizing·when·the·mesh·consists·of·less·than·100000·triangles.</p><pre·class="screen">mia-3disosurface-from-stack·-i·image0000.png·-o·mesh.vmesh·-s·30·-f·100000</pre><h4><a·name="idp10696"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagestats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dlerp.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagestats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dlerp</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp10595"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·given·as·slices.</p><h4><a·name="idp10597"></a>Options:</h4><h4><a·name="idp10598"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·string</span></dt><dd><p>input·image·filename·pattern</p></dd><dt><span·class="term">-o,·--out-mesh=(required,·output);·string</span></dt><dd><p>output·mesh</p></dd></dl></div><h4><a·name="idp10608"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10659"></a>Image·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--iso-value=128;·float</span></dt><dd><p>iso-value·of·iso·surface·to·be·extracted</p></dd></dl></div><h4><a·name="idp10665"></a>Mesh·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-f,·--max-faces=-1;·int</span></dt><dd><p>maximum·number·of·Faces,</p></dd><dt><span·class="term">-e,·--max-edges=-1;·int</span></dt><dd><p>maximum·number·of·Edges</p></dd><dt><span·class="term">-c,·--max-cost=0.1;·float</span></dt><dd><p>maximum·cost·for·edge·collaps</p></dd><dt><span·class="term">-r,·--ratio=4;·float</span></dt><dd><p>ratio·of·faces(edges)·to·target·number,·at·which··the·optimization·changes·from·edge-length·to·volume-optimized</p></dd><dt><span·class="term">-w,·--reverse-winding</span></dt><dd><p>reverse·the·winding·of·the·triangles·in·order·to·make·normals·point·away·from·the·high·intensity·area</p></dd></dl></div><h4><a·name="idp10687"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10693"></a>Example:</h4><p>Extract·the·surface·from·an·image·set·with·numbers·imageXXXX.png·that·corresponds·to··the·value·30·and·stop·optimizing·when·the·mesh·consists·of·less·than·100000·triangles.</p><pre·class="screen">mia-3disosurface-from-stack·-i·image0000.png·-o·mesh.vmesh·-s·30·-f·100000</pre><h4><a·name="idp10696"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimagestats.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dlerp.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimagestats </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dlerp</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-3disosurface-from-stack·{-i·string}·{-o·string}·[·options·...]6 mia-3disosurface-from-stack·{-i·string}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image8 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image
9 given·as·slices.9 given·as·slices.
10 Options:10 Options:
11 File-IO11 File-IO
12 ··-i,·--in-image=(input,·required);·string12 ··-i,·--in-image=(required,·input);·string
13 ······input·image·filename·pattern13 ······input·image·filename·pattern
14 ··-o,·--out-mesh=(required,·output);·string14 ··-o,·--out-mesh=(required,·output);·string
15 ······output·mesh15 ······output·mesh
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
19 ······Supported·priorities·starting·at·lowest·level·are:19 ······Supported·priorities·starting·at·lowest·level·are:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3disosurface-from-volume</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="next"·href="Secmiameshdeformablemodel.html"·title="mia-mesh-deformable-model"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3disosurface-from-volume</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshdeformablemodel.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3disosurfacefromvolume"></a>mia-3disosurface-from-volume</h3></div></div></div><h4><a·name="idp14529"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3disosurface-from-volume</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3disosurface-from-volume</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="next"·href="Secmiameshdeformablemodel.html"·title="mia-mesh-deformable-model"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3disosurface-from-volume</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshdeformablemodel.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3disosurfacefromvolume"></a>mia-3disosurface-from-volume</h3></div></div></div><h4><a·name="idp14529"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3disosurface-from-volume</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14538"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·by·using·marching·thetrahedra.</p><h4><a·name="idp14540"></a>Options:</h4><h4><a·name="idp14541"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mesh.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd></dl></div><h4><a·name="idp14553"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14604"></a>Image·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--iso-value=128;·float</span></dt><dd><p>iso-value·of·iso·surface·to·be·extracted</p></dd><dt><span·class="term">-b,·--bordered</span></dt><dd><p>put·an·empty·border·around·the·image·to·ensure·a·closed·surface</p></dd></dl></div><h4><a·name="idp14614"></a>Mesh·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-f,·--max-faces=-1;·int</span></dt><dd><p>maximum·number·of·Faces,</p></dd><dt><span·class="term">-e,·--max-edges=-1;·int</span></dt><dd><p>maximum·number·of·Edges</p></dd><dt><span·class="term">-c,·--max-cost=0.1;·float</span></dt><dd><p>maximum·cost·for·edge·collaps</p></dd><dt><span·class="term">-r,·--ratio=4;·float</span></dt><dd><p>ratio·of·faces(edges)·to·target·number,·at·which··the·optimization·changes·from·edge-length·to·volume-optimized</p></dd><dt><span·class="term">-w,·--reverse-winding</span></dt><dd><p>reverse·the·winding·of·the·triangles·in·order·to·make·normals·point·away·from·the·high·intensity·area</p></dd></dl></div><h4><a·name="idp14636"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14642"></a>Example:</h4><p>Extract·the·surface·corresponding·to·the·value·30·and·stop·optimizing·when·the·mesh·consists·of·less·than·100000·triangles.</p><pre·class="screen">mia-3disosurface-from-volume·-i·image.v·-o·mesh.vmesh·-s·30·-f·100000</pre><h4><a·name="idp14645"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshdeformablemodel.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Creation,·analysis,·and·filtering·of·triangular·3D·meshes </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-mesh-deformable-model</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp14538"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·by·using·marching·thetrahedra.</p><h4><a·name="idp14540"></a>Options:</h4><h4><a·name="idp14541"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mesh.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd></dl></div><h4><a·name="idp14553"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14604"></a>Image·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-s,·--iso-value=128;·float</span></dt><dd><p>iso-value·of·iso·surface·to·be·extracted</p></dd><dt><span·class="term">-b,·--bordered</span></dt><dd><p>put·an·empty·border·around·the·image·to·ensure·a·closed·surface</p></dd></dl></div><h4><a·name="idp14614"></a>Mesh·options</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-f,·--max-faces=-1;·int</span></dt><dd><p>maximum·number·of·Faces,</p></dd><dt><span·class="term">-e,·--max-edges=-1;·int</span></dt><dd><p>maximum·number·of·Edges</p></dd><dt><span·class="term">-c,·--max-cost=0.1;·float</span></dt><dd><p>maximum·cost·for·edge·collaps</p></dd><dt><span·class="term">-r,·--ratio=4;·float</span></dt><dd><p>ratio·of·faces(edges)·to·target·number,·at·which··the·optimization·changes·from·edge-length·to·volume-optimized</p></dd><dt><span·class="term">-w,·--reverse-winding</span></dt><dd><p>reverse·the·winding·of·the·triangles·in·order·to·make·normals·point·away·from·the·high·intensity·area</p></dd></dl></div><h4><a·name="idp14636"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14642"></a>Example:</h4><p>Extract·the·surface·corresponding·to·the·value·30·and·stop·optimizing·when·the·mesh·consists·of·less·than·100000·triangles.</p><pre·class="screen">mia-3disosurface-from-volume·-i·image.v·-o·mesh.vmesh·-s·30·-f·100000</pre><h4><a·name="idp14645"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshdeformablemodel.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Creation,·analysis,·and·filtering·of·triangular·3D·meshes </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-mesh-deformable-model</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-3disosurface-from-volume·{-i·io}·{-o·io}·[·options·...]6 mia-3disosurface-from-volume·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image8 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image
9 by·using·marching·thetrahedra.9 by·using·marching·thetrahedra.
10 Options:10 Options:
11 File-IO11 File-IO
12 ··-i,·--in-file=(input,·required);·io12 ··-i,·--in-file=(required,·input);·io
13 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·mesh.·For·supported·file·types·see·Plugin_type:_mesh/io15 ······output·mesh.·For·supported·file·types·see·Plugin_type:_mesh/io
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
19 ······Supported·priorities·starting·at·lowest·level·are:19 ······Supported·priorities·starting·at·lowest·level·are:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dlandmarks-distances</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dforce.html"·title="mia-3dforce"><link·rel="next"·href="Secmia3dlandmarkstransform.html"·title="mia-3dlandmarks-transform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dlandmarks-distances</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dforce.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarkstransform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dlandmarksdistances"></a>mia-3dlandmarks-distances</h3></div></div></div><h4><a·name="idp11968"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dlandmarks-distances</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dlandmarks-distances</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dforce.html"·title="mia-3dforce"><link·rel="next"·href="Secmia3dlandmarkstransform.html"·title="mia-3dlandmarks-transform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dlandmarks-distances</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dforce.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarkstransform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dlandmarksdistances"></a>mia-3dlandmarks-distances</h3></div></div></div><h4><a·name="idp11968"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dlandmarks-distances</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11977"></a>Description:</h4><p·class="description">Evaluate·Euclidian·distances·between·the·corresponding·landmarks·in·two·landmark·sets.·The·programs·prints·out·only·values·for·landmarks·that·are·available·and·have·location·values·in·both·sets·</p><h4><a·name="idp11979"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file-1=(input,·required);·io</span></dt><dd><p>input·landmark·set·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dlandmarklistio.html"·title="Plugin·type:·3dlandmarklist/io">Plugin·type:·3dlandmarklist/io</a></p></dd><dt><span·class="term">-o,[·...·truncated·by·diffoscope;·len:·29,·SHA:·9e0b7cfc4be7227f4cf27479f95dcf8526cd20d4a8464d67cb95588a1c37e4de·...·]);·io</span></dt><dd><p>input·landmark·set·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dlandmarklistio.html"·title="Plugin·type:·3dlandmarklist/io">Plugin·type:·3dlandmarklist/io</a></p></dd></dl></div><h4><a·name="idp11991"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12042"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12048"></a>Example:</h4><p>Evaluate·the·distance·between·the·landmarks·in·set·input1.lmx·and·input2.lmx·and·write·the·result·to·stdout</p><pre·class="screen">mia-3dlandmarks-distances·-1·input1.lmx·-2·input2.v</pre><h4><a·name="idp12051"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dforce.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarkstransform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dforce </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dlandmarks-transform</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11977"></a>Description:</h4><p·class="description">Evaluate·Euclidian·distances·between·the·corresponding·landmarks·in·two·landmark·sets.·The·programs·prints·out·only·values·for·landmarks·that·are·available·and·have·location·values·in·both·sets·</p><h4><a·name="idp11979"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file-1=(required,·input);·io</span></dt><dd><p>input·landmark·set·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dlandmarklistio.html"·title="Plugin·type:·3dlandmarklist/io">Plugin·type:·3dlandmarklist/io</a></p></dd><dt><span·class="term">-o,[·...·truncated·by·diffoscope;·len:·29,·SHA:·729ef51b64991090f79e0cac0ab3d967dc4ceb646bb45c40e9f441ddfe42ea65·...·]);·io</span></dt><dd><p>input·landmark·set·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dlandmarklistio.html"·title="Plugin·type:·3dlandmarklist/io">Plugin·type:·3dlandmarklist/io</a></p></dd></dl></div><h4><a·name="idp11991"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12042"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12048"></a>Example:</h4><p>Evaluate·the·distance·between·the·landmarks·in·set·input1.lmx·and·input2.lmx·and·write·the·result·to·stdout</p><pre·class="screen">mia-3dlandmarks-distances·-1·input1.lmx·-2·input2.v</pre><h4><a·name="idp12051"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dforce.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dlandmarkstransform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dforce </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dlandmarks-transform</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-3dlandmarks-distances·{-i·io}·{-o·io}·[·options·...]6 mia-3dlandmarks-distances·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Evaluate·Euclidian·distances·between·the·corresponding·landmarks·in·two8 Evaluate·Euclidian·distances·between·the·corresponding·landmarks·in·two
9 landmark·sets.·The·programs·prints·out·only·values·for·landmarks·that·are9 landmark·sets.·The·programs·prints·out·only·values·for·landmarks·that·are
10 available·and·have·location·values·in·both·sets10 available·and·have·location·values·in·both·sets
11 Options:11 Options:
12 ··-i,·--in-file-1=(input,·required);·io12 ··-i,·--in-file-1=(required,·input);·io
13 ······input·landmark·set·1.·For·supported·file·types·see·Plugin_type:13 ······input·landmark·set·1.·For·supported·file·types·see·Plugin_type:
14 ······3dlandmarklist/io14 ······3dlandmarklist/io
15 ··-o,·--in-file-2=(input,·required);·io15 ··-o,·--in-file-2=(required,·input);·io
16 ······input·landmark·set·2.·For·supported·file·types·see·Plugin_type:16 ······input·landmark·set·2.·For·supported·file·types·see·Plugin_type:
17 ······3dlandmarklist/io17 ······3dlandmarklist/io
18 Help·&·Info18 Help·&·Info
19 ··-V,·--verbose=warning;·dict19 ··-V,·--verbose=warning;·dict
20 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.20 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
21 ······Supported·priorities·starting·at·lowest·level·are:21 ······Supported·priorities·starting·at·lowest·level·are:
22 ······trace:···Function·call·trace22 ······trace:···Function·call·trace
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dlandmarks-transform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dlandmarksdistances.html"·title="mia-3dlandmarks-distances"><link·rel="next"·href="Secmia3dnonrigidreg.html"·title="mia-3dnonrigidreg"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dlandmarks-transform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarksdistances.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidreg.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dlandmarkstransform"></a>mia-3dlandmarks-transform</h3></div></div></div><h4><a·name="idp12055"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dlandmarks-transform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dlandmarks-transform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dlandmarksdistances.html"·title="mia-3dlandmarks-distances"><link·rel="next"·href="Secmia3dnonrigidreg.html"·title="mia-3dnonrigidreg"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dlandmarks-transform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarksdistances.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidreg.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dlandmarkstransform"></a>mia-3dlandmarks-transform</h3></div></div></div><h4><a·name="idp12055"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dlandmarks-transform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12066"></a>Description:</h4><p·class="description">Transform·the·locations·of·the·landmarks·by·means·of·a·given·3D·transformation.·Note,·landmark·transformations·do·the·inverse·of·an·image·transformation·(in·a·manner·of·speaking),·i.e.·given·a·transformation·V(x)·in·an·image·transformation·the·pixel·intensity·at·x·is·set·to·the·original·intensity·at·V(x),·while·a·landmark·at·x·is·moved·to·V(x).</p><h4><a·name="idp12068"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·landmark·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dlandmarklistio.html"·title="Plugin·type:·3dlandmarklist/io">Plugin·type:·3dlandmarklist/io</a></p></dd><dt><span·class="term">-o,·-[·...·truncated·by·diffoscope;·len:·301,·SHA:·afe5c5108168fe5ee4f082e3734c5c41b30ab431186cd4d67b8250014ef33597·...·]);·io</span></dt><dd><p>transformation·file.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp12085"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12136"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12142"></a>Example:</h4><p>Transform·the·landmarks·given·in·input.lmx·by·applyning·the·transfromation·stored·in·trans.v·and·store·the·result·in·output.lmx</p><pre·class="screen">mia-3dlandmarks-transform·-i·input.lmx·-t·trans.v··-o·output.lmx</pre><h4><a·name="idp12145"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarksdistances.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidreg.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dlandmarks-distances </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dnonrigidreg</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12066"></a>Description:</h4><p·class="description">Transform·the·locations·of·the·landmarks·by·means·of·a·given·3D·transformation.·Note,·landmark·transformations·do·the·inverse·of·an·image·transformation·(in·a·manner·of·speaking),·i.e.·given·a·transformation·V(x)·in·an·image·transformation·the·pixel·intensity·at·x·is·set·to·the·original·intensity·at·V(x),·while·a·landmark·at·x·is·moved·to·V(x).</p><h4><a·name="idp12068"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·landmark·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dlandmarklistio.html"·title="Plugin·type:·3dlandmarklist/io">Plugin·type:·3dlandmarklist/io</a></p></dd><dt><span·class="term">-o,·-[·...·truncated·by·diffoscope;·len:·301,·SHA:·7a43dfc82b1534416486bcc95be1398dcca049c6b33000ae07c77cc1a8144705·...·]);·io</span></dt><dd><p>transformation·file.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp12085"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12136"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12142"></a>Example:</h4><p>Transform·the·landmarks·given·in·input.lmx·by·applyning·the·transfromation·stored·in·trans.v·and·store·the·result·in·output.lmx</p><pre·class="screen">mia-3dlandmarks-transform·-i·input.lmx·-t·trans.v··-o·output.lmx</pre><h4><a·name="idp12145"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarksdistances.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidreg.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dlandmarks-distances </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dnonrigidreg</td></tr></table></div></body></html>
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7 Description:7 Description:
8 Transform·the·locations·of·the·landmarks·by·means·of·a·given·3D·transformation.8 Transform·the·locations·of·the·landmarks·by·means·of·a·given·3D·transformation.
9 Note,·landmark·transformations·do·the·inverse·of·an·image·transformation·(in·a9 Note,·landmark·transformations·do·the·inverse·of·an·image·transformation·(in·a
10 manner·of·speaking),·i.e.·given·a·transformation·V(x)·in·an·image10 manner·of·speaking),·i.e.·given·a·transformation·V(x)·in·an·image
11 transformation·the·pixel·intensity·at·x·is·set·to·the·original·intensity·at·V11 transformation·the·pixel·intensity·at·x·is·set·to·the·original·intensity·at·V
12 (x),·while·a·landmark·at·x·is·moved·to·V(x).12 (x),·while·a·landmark·at·x·is·moved·to·V(x).
13 Options:13 Options:
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······input·landmark·set.·For·supported·file·types·see·Plugin_type:15 ······input·landmark·set.·For·supported·file·types·see·Plugin_type:
16 ······3dlandmarklist/io16 ······3dlandmarklist/io
17 ··-o,·--out-file=(required,·output);·io17 ··-o,·--out-file=(required,·output);·io
18 ······output·landmark·set.·For·supported·file·types·see·Plugin_type:18 ······output·landmark·set.·For·supported·file·types·see·Plugin_type:
19 ······3dlandmarklist/io19 ······3dlandmarklist/io
20 ··-t,·--transformation=(input,·required);·io20 ··-t,·--transformation=(required,·input);·io
21 ······transformation·file.·For·supported·file·types·see·Plugin_type:21 ······transformation·file.·For·supported·file·types·see·Plugin_type:
22 ······3dtransform/io22 ······3dtransform/io
23 Help·&·Info23 Help·&·Info
24 ··-V,·--verbose=warning;·dict24 ··-V,·--verbose=warning;·dict
25 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.25 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
26 ······Supported·priorities·starting·at·lowest·level·are:26 ······Supported·priorities·starting·at·lowest·level·are:
27 ······trace:···Function·call·trace27 ······trace:···Function·call·trace
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./usr/share/doc/mia-2.4/userref/Secmia3dlerp.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dlerp</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3disosurfacefromstack.html"·title="mia-3disosurface-from-stack"><link·rel="next"·href="Secmia3dmaskseeded.html"·title="mia-3dmaskseeded"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dlerp</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromstack.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dmaskseeded.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dlerp"></a>mia-3dlerp</h3></div></div></div><h4><a·name="idp10700"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dlerp</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-p·<em·class="replaceable"><code>vfloat</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dlerp</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3disosurfacefromstack.html"·title="mia-3disosurface-from-stack"><link·rel="next"·href="Secmia3dmaskseeded.html"·title="mia-3dmaskseeded"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dlerp</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromstack.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dmaskseeded.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dlerp"></a>mia-3dlerp</h3></div></div></div><h4><a·name="idp10700"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dlerp</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-p·<em·class="replaceable"><code>vfloat</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp10713"></a>Description:</h4><p·class="description">merge·two·images·by·linear·combination.</p><h4><a·name="idp10715"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--first=(input,·required);·io</span></dt><dd><p>first·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-2,·--second=(input,·requi[·...·truncated·by·diffoscope;·len:·3,·SHA:·b1f51a511f1da0cd348b8f8598db32e61cb963e5fc69e2b41485bf99590ed75a·...·]);·io</span></dt><dd><p>second·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>linearly·interpolated·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-p,·--positions=(required);·vfloat</span></dt><dd><p>image·series·positions·(first,·target,·second)</p></dd></dl></div><h4><a·name="idp10736"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10787"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10793"></a>Test</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--selftest=(</span></dt><dd><p>run·a·self·test·of·the·program</p></dd></dl></div><h4><a·name="idp10799"></a>Example:</h4><p>Combine·image·inputA.v·and·inputB.v·by·using·position·coordinates·4,·7,·and·9.·This·means·the·output·pixel·values·will·be·evaluated·according·to3 ········...]</p></div><h4><a·name="idp10713"></a>Description:</h4><p·class="description">merge·two·images·by·linear·combination.</p><h4><a·name="idp10715"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--first=(required,·input);·io</span></dt><dd><p>first·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-2,·--second=(required,·in[·...·truncated·by·diffoscope;·len:·3,·SHA:·373cb2c6d4fe2778441d4f0266505b699fa518d002e5793b87f9b48836de3f62·...·]);·io</span></dt><dd><p>second·input·image·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>linearly·interpolated·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-p,·--positions=(required);·vfloat</span></dt><dd><p>image·series·positions·(first,·target,·second)</p></dd></dl></div><h4><a·name="idp10736"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10787"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10793"></a>Test</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--selftest=(</span></dt><dd><p>run·a·self·test·of·the·program</p></dd></dl></div><h4><a·name="idp10799"></a>Example:</h4><p>Combine·image·inputA.v·and·inputB.v·by·using·position·coordinates·4,·7,·and·9.·This·means·the·output·pixel·values·will·be·evaluated·according·to
  
4 ····(9-7)/(9-4)·*·A·+·(7-4)/(9-4)·*·B··4 ····(9-7)/(9-4)·*·A·+·(7-4)/(9-4)·*·B··
  
5 The·result·image·will·be·written·to·output.v</p><pre·class="screen">mia-3dlerp·-1·inputA.v·-2·inputB.v·-p·4,7,9·-o·output.v</pre><h4><a·name="idp10802"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromstack.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dmaskseeded.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3disosurface-from-stack </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dmaskseeded</td></tr></table></div></body></html>5 The·result·image·will·be·written·to·output.v</p><pre·class="screen">mia-3dlerp·-1·inputA.v·-2·inputB.v·-p·4,7,9·-o·output.v</pre><h4><a·name="idp10802"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromstack.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dmaskseeded.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3disosurface-from-stack </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dmaskseeded</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dlerp4 mia-3dlerp
5 Sysnopis:5 Sysnopis:
6 mia-3dlerp·{-1·io}·{-2·io}·{-o·io}·{-p·vfloat}·[·options·...]6 mia-3dlerp·{-1·io}·{-2·io}·{-o·io}·{-p·vfloat}·[·options·...]
7 Description:7 Description:
8 merge·two·images·by·linear·combination.8 merge·two·images·by·linear·combination.
9 Options:9 Options:
10 ··-1,·--first=(input,·required);·io10 ··-1,·--first=(required,·input);·io
11 ······first·input·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io11 ······first·input·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io
12 ··-2,·--second=(input,·required);·io12 ··-2,·--second=(required,·input);·io
13 ······second·input·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······second·input·image·.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······linearly·interpolated·image.·For·supported·file·types·see·Plugin_type:15 ······linearly·interpolated·image.·For·supported·file·types·see·Plugin_type:
16 ······3dimage/io16 ······3dimage/io
17 ··-p,·--positions=(required);·vfloat17 ··-p,·--positions=(required);·vfloat
18 ······image·series·positions·(first,·target,·second)18 ······image·series·positions·(first,·target,·second)
19 Help·&·Info19 Help·&·Info
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./usr/share/doc/mia-2.4/userref/Secmia3dmany2onenonrigid.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dmany2one-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="next"·href="Secmia3dmotioncompicanonrigid.html"·title="mia-3dmotioncompica-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dmany2one-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof3Dimages.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dmotioncompicanonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dmany2onenonrigid"></a>mia-3dmany2one-nonrigid</h3></div></div></div><h4><a·name="idp12880"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dmany2one-nonrigid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dmany2one-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="next"·href="Secmia3dmotioncompicanonrigid.html"·title="mia-3dmotioncompica-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dmany2one-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof3Dimages.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dmotioncompicanonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dmany2onenonrigid"></a>mia-3dmany2one-nonrigid</h3></div></div></div><h4><a·name="idp12880"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dmany2one-nonrigid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp12890"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·image·series·by·registereing·all·images·to·a·user-selected·reference.</p><h4><a·name="idp12892"></a>Options:</h4><h4><a·name="idp12893"></a>7 ········...]</p></div><h4><a·name="idp12890"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·image·series·by·registereing·all·images·to·a·user-selected·reference.</p><h4><a·name="idp12892"></a>Options:</h4><h4><a·name="idp12893"></a>
8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·perfusion·data·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>file·name·for·registered·files.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp12905"></a>8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·perfusion·data·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>file·name·for·registered·files.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp12905"></a>
9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd></dl></div><h4><a·name="idp12924"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12975"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12981"></a>Example:</h4><p>Register·the·images·given·as·numbered·files·imagesXXXX.v·by·optimizing·a·spline·based·transformation·with·a·coefficient·rate·of·16·pixel·using··a·weighted·combination·of·normalized·gradient·fields·and·SSD·as·cost·measure,·and·penalize·the·transformation·by·using·divcurl·with·aweight·of·2.0.·Store·the·resultsing·images·in·registeredXXXX.v.</p><pre·class="screen">mia-3dmany2one-nonrigid·-i·images0000.v·-o··registered%04d.v·-F·spline:rate=16·image:cost=[ngf:eval=ds],weight=2.0·image:cost=ssd,weight=0.1·divcurl:weight=2.0</pre><h4><a·name="idp12984"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof3Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dmotioncompicanonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Registration·of·series·of·3D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dmotioncompica-nonrigid</td></tr></table></div></body></html>9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd></dl></div><h4><a·name="idp12924"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12975"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12981"></a>Example:</h4><p>Register·the·images·given·as·numbered·files·imagesXXXX.v·by·optimizing·a·spline·based·transformation·with·a·coefficient·rate·of·16·pixel·using··a·weighted·combination·of·normalized·gradient·fields·and·SSD·as·cost·measure,·and·penalize·the·transformation·by·using·divcurl·with·aweight·of·2.0.·Store·the·resultsing·images·in·registeredXXXX.v.</p><pre·class="screen">mia-3dmany2one-nonrigid·-i·images0000.v·-o··registered%04d.v·-F·spline:rate=16·image:cost=[ngf:eval=ds],weight=2.0·image:cost=ssd,weight=0.1·divcurl:weight=2.0</pre><h4><a·name="idp12984"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="SecRegistrationofseriesof3Dimages.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dmotioncompicanonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">Registration·of·series·of·3D·images </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dmotioncompica-nonrigid</td></tr></table></div></body></html>
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6 mia-3dmany2one-nonrigid·{-i·io}·[·options·...]·[·Plugin_type:_3dimage/fullcost6 mia-3dmany2one-nonrigid·{-i·io}·[·options·...]·[·Plugin_type:_3dimage/fullcost
7 ...]7 ...]
8 Description:8 Description:
9 This·program·runs·the·non-rigid·registration·of·an·image·series·by·registereing9 This·program·runs·the·non-rigid·registration·of·an·image·series·by·registereing
10 all·images·to·a·user-selected·reference.10 all·images·to·a·user-selected·reference.
11 Options:11 Options:
12 ·File-IO12 ·File-IO
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·perfusion·data·set.·For·supported·file·types·see·Plugin_type:14 ······input·perfusion·data·set.·For·supported·file·types·see·Plugin_type:
15 ······3dimage/io15 ······3dimage/io
16 ··-o,·--out-file=(output);·io16 ··-o,·--out-file=(output);·io
17 ······file·name·for·registered·files.·For·supported·file·types·see·Plugin_type:17 ······file·name·for·registered·files.·For·supported·file·types·see·Plugin_type:
18 ······3dimage/io18 ······3dimage/io
19 ·Registration19 ·Registration
20 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING20 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dmaskseeded</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dlerp.html"·title="mia-3dlerp"><link·rel="next"·href="Secmia3dproposeboundingbox.html"·title="mia-3dpropose-boundingbox"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dmaskseeded</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dlerp.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dproposeboundingbox.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dmaskseeded"></a>mia-3dmaskseeded</h3></div></div></div><h4><a·name="idp10806"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dmaskseeded</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dmaskseeded</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dlerp.html"·title="mia-3dlerp"><link·rel="next"·href="Secmia3dproposeboundingbox.html"·title="mia-3dpropose-boundingbox"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dmaskseeded</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dlerp.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dproposeboundingbox.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dmaskseeded"></a>mia-3dmaskseeded</h3></div></div></div><h4><a·name="idp10806"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dmaskseeded</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp10815"></a>Description:</h4><p·class="description">3D·image·segmentation·based·on·region·growing·from·a·seed·point.·Neighboring·points·are·added,·either·when·their·intensity·is·equal·or·higher·than·that·of·the·seed·point,·or·of·the·intensity·is·lower·or·equal·then·that·of·the·neighoring·point.·After·region·growing·is·finished,·this·mask·is·used·to·zero·out·the·region·in·the·original·image·yielding·the·resulting·image.·</p><h4><a·name="idp10817"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-s,·--seed=[0,0,0];·3dbounds</span></dt><dd><p>seed·point</p></dd><dt><span·class="term">-n,·--neighborhood=6n;·factory</span></dt><dd><p>neighborhood·shape.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></p></dd></dl></div><h4><a·name="idp10838"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10889"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10895"></a>Example:</h4><p>Run·a·region·growing·on·input.v·starting·at·point·&lt;10,23,21&gt;·and·use·the·18n·neighbourhood.</p><pre·class="screen">mia-3dmaskseeded·-i·image.v·-o·masked.v·-s·'&lt;10,23,21&gt;'·-n·18n</pre><h4><a·name="idp10898"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dlerp.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dproposeboundingbox.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dlerp </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dpropose-boundingbox</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp10815"></a>Description:</h4><p·class="description">3D·image·segmentation·based·on·region·growing·from·a·seed·point.·Neighboring·points·are·added,·either·when·their·intensity·is·equal·or·higher·than·that·of·the·seed·point,·or·of·the·intensity·is·lower·or·equal·then·that·of·the·neighoring·point.·After·region·growing·is·finished,·this·mask·is·used·to·zero·out·the·region·in·the·original·image·yielding·the·resulting·image.·</p><h4><a·name="idp10817"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image(s)·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-s,·--seed=[0,0,0];·3dbounds</span></dt><dd><p>seed·point</p></dd><dt><span·class="term">-n,·--neighborhood=6n;·factory</span></dt><dd><p>neighborhood·shape.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimageshape.html"·title="Plugin·type:·3dimage/shape">Plugin·type:·3dimage/shape</a></p></dd></dl></div><h4><a·name="idp10838"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10889"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10895"></a>Example:</h4><p>Run·a·region·growing·on·input.v·starting·at·point·&lt;10,23,21&gt;·and·use·the·18n·neighbourhood.</p><pre·class="screen">mia-3dmaskseeded·-i·image.v·-o·masked.v·-s·'&lt;10,23,21&gt;'·-n·18n</pre><h4><a·name="idp10898"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dlerp.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dproposeboundingbox.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dlerp </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dpropose-boundingbox</td></tr></table></div></body></html>
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7 Description:7 Description:
8 3D·image·segmentation·based·on·region·growing·from·a·seed·point.·Neighboring8 3D·image·segmentation·based·on·region·growing·from·a·seed·point.·Neighboring
9 points·are·added,·either·when·their·intensity·is·equal·or·higher·than·that·of9 points·are·added,·either·when·their·intensity·is·equal·or·higher·than·that·of
10 the·seed·point,·or·of·the·intensity·is·lower·or·equal·then·that·of·the10 the·seed·point,·or·of·the·intensity·is·lower·or·equal·then·that·of·the
11 neighoring·point.·After·region·growing·is·finished,·this·mask·is·used·to·zero11 neighoring·point.·After·region·growing·is·finished,·this·mask·is·used·to·zero
12 out·the·region·in·the·original·image·yielding·the·resulting·image.12 out·the·region·in·the·original·image·yielding·the·resulting·image.
13 Options:13 Options:
14 ··-i,·--in-file=(input,·required);·io14 ··-i,·--in-file=(required,·input);·io
15 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:15 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
16 ······3dimage/io16 ······3dimage/io
17 ··-o,·--out-file=(required,·output);·io17 ··-o,·--out-file=(required,·output);·io
18 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see18 ······output·image(s)·that·have·been·filtered.·For·supported·file·types·see
19 ······Plugin_type:_3dimage/io19 ······Plugin_type:_3dimage/io
20 ··-s,·--seed=[0,0,0];·3dbounds20 ··-s,·--seed=[0,0,0];·3dbounds
21 ······seed·point21 ······seed·point
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dmotioncompica-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="Secmia3dmany2onenonrigid.html"·title="mia-3dmany2one-nonrigid"><link·rel="next"·href="Secmia3dprealignnonrigid.html"·title="mia-3dprealign-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dmotioncompica-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dmany2onenonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dprealignnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dmotioncompicanonrigid"></a>mia-3dmotioncompica-nonrigid</h3></div></div></div><h4><a·name="idp12988"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dmotioncompica-nonrigid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dmotioncompica-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="Secmia3dmany2onenonrigid.html"·title="mia-3dmany2one-nonrigid"><link·rel="next"·href="Secmia3dprealignnonrigid.html"·title="mia-3dprealign-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dmotioncompica-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dmany2onenonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dprealignnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dmotioncompicanonrigid"></a>mia-3dmotioncompica-nonrigid</h3></div></div></div><h4><a·name="idp12988"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dmotioncompica-nonrigid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12997"></a>Description:</h4><p·class="description">This·program·implements·a·3D·version·of·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012</a></p><p·class="description">.</p><h4><a·name="idp13001"></a>Options:</h4><h4><a·name="idp13002"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·images·of·consecutively·numbered·filed·(nameXXXX.ext).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·name·(as·C·format·string·including·a·%04d·in·order·to·define·the·file·numbering).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">--save-refs=STRING</span></dt><dd><p>save·reference·images,·the·given·string·is·used·as·file·name·base,·the·number·pattern·follows·the·input·images,·and·the·output·format·is·always·'vista'</p></dd><dt><span·class="term">--save-regs=STRING</span></dt><dd><p>save·intermediate·registered·images,·the·given·string·is·used·as·file·name·base,·the·number·pattern·follows·the·input·images,·and·the·output·format·is·always·'vista'</p></dd><dt><span·class="term">--save-coeffs=STRING</span></dt><dd><p>save·mixing·matrix·to·a·text·file</p></dd><dt><span·class="term">--save-features=STRING</span></dt><dd><p>save·feature·images·as·PNG</p></dd></dl></div><h4><a·name="idp13030"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13081"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--no-normalize</span></dt><dd><p>don't·normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd></dl></div><h4><a·name="idp13108"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13114"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-a,·--start-c-rate=32;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=20;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd,;·stringSTRING</span></dt><dd><p>image·cost</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp13148"></a>Example:</h4><p>Register·the·perfusion·series·given·in·images·imagesXXXX.v·by·using·4-class·ICA·estimation.·Skip·two·images·at·the·beginning,·use·at·most·4·registration·threads,·a·nlopt·based·optimizer·and·otherwiese·use·the·default·parameters.·Store·the·result·in·registeredXXXX.v·</p><pre·class="screen">mia-3dmotioncompica-nonrigid·-i·images0000.v·-o··registered%04d.v··-k·2·-C·4·-t·4·-O·nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300</pre><h4><a·name="idp13151"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dmany2onenonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dprealignnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dmany2one-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dprealign-nonrigid</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12997"></a>Description:</h4><p·class="description">This·program·implements·a·3D·version·of·the·motion·compensation·algorithm·described·in·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1016/j.media.2012.02.004"·target="_top">Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012</a></p><p·class="description">.</p><h4><a·name="idp13001"></a>Options:</h4><h4><a·name="idp13002"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·images·of·consecutively·numbered·filed·(nameXXXX.ext).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·name·(as·C·format·string·including·a·%04d·in·order·to·define·the·file·numbering).·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">--save-refs=STRING</span></dt><dd><p>save·reference·images,·the·given·string·is·used·as·file·name·base,·the·number·pattern·follows·the·input·images,·and·the·output·format·is·always·'vista'</p></dd><dt><span·class="term">--save-regs=STRING</span></dt><dd><p>save·intermediate·registered·images,·the·given·string·is·used·as·file·name·base,·the·number·pattern·follows·the·input·images,·and·the·output·format·is·always·'vista'</p></dd><dt><span·class="term">--save-coeffs=STRING</span></dt><dd><p>save·mixing·matrix·to·a·text·file</p></dd><dt><span·class="term">--save-features=STRING</span></dt><dd><p>save·feature·images·as·PNG</p></dd></dl></div><h4><a·name="idp13030"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13081"></a>ICA</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--fastica=internal;·factory</span></dt><dd><p>FastICA·implementationto·be·used.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypefasticaimplementation.html"·title="Plugin·type:·fastica/implementation">Plugin·type:·fastica/implementation</a></p></dd><dt><span·class="term">-C,·--components=0;·ulong</span></dt><dd><p>ICA·components·0·=·automatic·estimation</p></dd><dt><span·class="term">--no-normalize</span></dt><dd><p>don't·normalized·ICs</p></dd><dt><span·class="term">--no-meanstrip</span></dt><dd><p>don't·strip·the·mean·from·the·mixing·curves</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·images·at·the·beginning·of·the·series·e.g.·because·as·they·are·of·other·modalities</p></dd><dt><span·class="term">-m,·--max-ica-iter=400;·ulong</span></dt><dd><p>maximum·number·of·iterations·in·ICA</p></dd></dl></div><h4><a·name="idp13108"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13114"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·stringSTRING</span></dt><dd><p>Optimizer·used·for·minimization</p></dd><dt><span·class="term">-a,·--start-c-rate=32;·double</span></dt><dd><p>start·coefficinet·rate·in·spines,·gets·divided·by·--c-rate-divider·with·every·pass</p></dd><dt><span·class="term">--c-rate-divider=4;·double</span></dt><dd><p>cofficient·rate·divider·for·each·pass</p></dd><dt><span·class="term">-d,·--start-divcurl=20;·double</span></dt><dd><p>start·divcurl·weight,·gets·divided·by·--divcurl-divider·with·every·pass</p></dd><dt><span·class="term">--divcurl-divider=4;·double</span></dt><dd><p>divcurl·weight·scaling·with·each·new·pass</p></dd><dt><span·class="term">-w,·--imagecost=image:weight=1,cost=ssd,;·stringSTRING</span></dt><dd><p>image·cost</p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·ulong</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp13148"></a>Example:</h4><p>Register·the·perfusion·series·given·in·images·imagesXXXX.v·by·using·4-class·ICA·estimation.·Skip·two·images·at·the·beginning,·use·at·most·4·registration·threads,·a·nlopt·based·optimizer·and·otherwiese·use·the·default·parameters.·Store·the·result·in·registeredXXXX.v·</p><pre·class="screen">mia-3dmotioncompica-nonrigid·-i·images0000.v·-o··registered%04d.v··-k·2·-C·4·-t·4·-O·nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300</pre><h4><a·name="idp13151"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dmany2onenonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dprealignnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dmany2one-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dprealign-nonrigid</td></tr></table></div></body></html>
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9 described·in9 described·in
10 Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion10 Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion
11 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using11 Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using
12 Independent_Component_Analysis"_Medical_Image_Analysis,_201212 Independent_Component_Analysis"_Medical_Image_Analysis,_2012
13 .13 .
14 Options:14 Options:
15 File-IO15 File-IO
16 ··-i,·--in-file=(input,·required);·io16 ··-i,·--in-file=(required,·input);·io
17 ······input·images·of·consecutively·numbered·filed·(nameXXXX.ext).·For17 ······input·images·of·consecutively·numbered·filed·(nameXXXX.ext).·For
18 ······supported·file·types·see·Plugin_type:_3dimage/io18 ······supported·file·types·see·Plugin_type:_3dimage/io
19 ··-o,·--out-file=(required,·output);·io19 ··-o,·--out-file=(required,·output);·io
20 ······output·image·name·(as·C·format·string·including·a·%04d·in·order·to·define20 ······output·image·name·(as·C·format·string·including·a·%04d·in·order·to·define
21 ······the·file·numbering).·For·supported·file·types·see·Plugin_type:_3dimage/io21 ······the·file·numbering).·For·supported·file·types·see·Plugin_type:_3dimage/io
22 ··--save-refs=STRING22 ··--save-refs=STRING
23 ······save·reference·images,·the·given·string·is·used·as·file·name·base,·the23 ······save·reference·images,·the·given·string·is·used·as·file·name·base,·the
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dnonrigidreg</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dlandmarkstransform.html"·title="mia-3dlandmarks-transform"><link·rel="next"·href="Secmia3dnonrigidregalt.html"·title="mia-3dnonrigidreg-alt"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dnonrigidreg</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarkstransform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidregalt.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dnonrigidreg"></a>mia-3dnonrigidreg</h3></div></div></div><h4><a·name="idp12149"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dnonrigidreg</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dnonrigidreg</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dlandmarkstransform.html"·title="mia-3dlandmarks-transform"><link·rel="next"·href="Secmia3dnonrigidregalt.html"·title="mia-3dnonrigidreg-alt"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dnonrigidreg</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarkstransform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidregalt.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dnonrigidreg"></a>mia-3dnonrigidreg</h3></div></div></div><h4><a·name="idp12149"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dnonrigidreg</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp12163"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·3D·images.</p><h4><a·name="idp12165"></a>Options:</h4><h4><a·name="idp12166"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12217"></a>IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(input,·required);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output);·io</span></dt><dd><p>registered·output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--transformation=(output);·io</span></dt><dd><p>output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp12239"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12245"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=spline:rate=10;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd></dl></div><h4><a·name="idp12261"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·by·using·a·spline·transformation·with·a·coefficient·rate·of·5··and·write·the·registered·image·to·reg.v.·Use·two·multiresolution·levels,·ssd·as·image·cost·function·and·divcurl·weighted·by·10.0·as·transformation·smoothness·penalty.·</p><pre·class="screen">mia-3dnonrigidreg·-i·test.v·-r·ref.v·-o·reg.v·-l·2·-f·spline:rate=3··image:cost=ssd·divcurl:weight=10</pre><h4><a·name="idp12264"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarkstransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidregalt.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dlandmarks-transform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dnonrigidreg-alt</td></tr></table></div></body></html>7 ········...]</p></div><h4><a·name="idp12163"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·3D·images.</p><h4><a·name="idp12165"></a>Options:</h4><h4><a·name="idp12166"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12217"></a>IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(required,·input);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output);·io</span></dt><dd><p>registered·output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--transformation=(output);·io</span></dt><dd><p>output·transformation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp12239"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12245"></a>Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-l,·--levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=spline:rate=10;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd></dl></div><h4><a·name="idp12261"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·by·using·a·spline·transformation·with·a·coefficient·rate·of·5··and·write·the·registered·image·to·reg.v.·Use·two·multiresolution·levels,·ssd·as·image·cost·function·and·divcurl·weighted·by·10.0·as·transformation·smoothness·penalty.·</p><pre·class="screen">mia-3dnonrigidreg·-i·test.v·-r·ref.v·-o·reg.v·-l·2·-f·spline:rate=3··image:cost=ssd·divcurl:weight=10</pre><h4><a·name="idp12264"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dlandmarkstransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dnonrigidregalt.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dlandmarks-transform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dnonrigidreg-alt</td></tr></table></div></body></html>
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25 ··-h,·--help=();·bool25 ··-h,·--help=();·bool
26 ······print·this·help26 ······print·this·help
27 ··-?,·--usage=();·bool27 ··-?,·--usage=();·bool
28 ······print·a·short·help28 ······print·a·short·help
29 ··--version=();·bool29 ··--version=();·bool
30 ······print·the·version·number·and·exit30 ······print·the·version·number·and·exit
31 IO31 IO
32 ··-i,·--in-image=(input,·required);·io32 ··-i,·--in-image=(required,·input);·io
33 ······test·image.·For·supported·file·types·see·Plugin_type:_3dimage/io33 ······test·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
34 ··-r,·--ref-image=(input,·required);·io34 ··-r,·--ref-image=(required,·input);·io
35 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io35 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
36 ··-o,·--out-image=(required,·output);·io36 ··-o,·--out-image=(required,·output);·io
37 ······registered·output·image.·For·supported·file·types·see·Plugin_type:37 ······registered·output·image.·For·supported·file·types·see·Plugin_type:
38 ······3dimage/io38 ······3dimage/io
39 ··-t,·--transformation=(output);·io39 ··-t,·--transformation=(output);·io
40 ······output·transformation.·For·supported·file·types·see·Plugin_type:40 ······output·transformation.·For·supported·file·types·see·Plugin_type:
41 ······3dtransform/io41 ······3dtransform/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dprealign-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="Secmia3dmotioncompicanonrigid.html"·title="mia-3dmotioncompica-nonrigid"><link·rel="next"·href="Secmia3dserialnonrigid.html"·title="mia-3dserial-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dprealign-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dmotioncompicanonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dserialnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dprealignnonrigid"></a>mia-3dprealign-nonrigid</h3></div></div></div><h4><a·name="idp13155"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dprealign-nonrigid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dprealign-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="Secmia3dmotioncompicanonrigid.html"·title="mia-3dmotioncompica-nonrigid"><link·rel="next"·href="Secmia3dserialnonrigid.html"·title="mia-3dserial-nonrigid"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dprealign-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dmotioncompicanonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dserialnonrigid.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dprealignnonrigid"></a>mia-3dprealign-nonrigid</h3></div></div></div><h4><a·name="idp13155"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dprealign-nonrigid</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp13164"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·image·series·by·first·registering·an·already·aligned·subset·of·the·images·to·one·reference,·and·then·by·registering·the·remaining·images·by·using·synthetic·references.·This·is·a·3D·version·of·</p><p·class="citation"><a·class="ulink"·href="http://dx.doi.org/10.1109/TMI.2010.2049270"·target="_top">G.·Wollny,·M-J·Ledesma-Cabryo,·P.Kellman,·and·A.Santos,·"Exploiting·Quasiperiodicity·in·Motion·Correction·of·Free-Breathing,"·IEEE·Transactions·on·Medical·Imaging,·29(8),·2010.</a></p><h4><a·name="idp13168"></a>Options:</h4><h4><a·name="idp13169"></a>3 ········...]</p></div><h4><a·name="idp13164"></a>Description:</h4><p·class="description">This·program·runs·the·non-rigid·registration·of·an·image·series·by·first·registering·an·already·aligned·subset·of·the·images·to·one·reference,·and·then·by·registering·the·remaining·images·by·using·synthetic·references.·This·is·a·3D·version·of·</p><p·class="citation"><a·class="ulink"·href="http://dx.doi.org/10.1109/TMI.2010.2049270"·target="_top">G.·Wollny,·M-J·Ledesma-Cabryo,·P.Kellman,·and·A.Santos,·"Exploiting·Quasiperiodicity·in·Motion·Correction·of·Free-Breathing,"·IEEE·Transactions·on·Medical·Imaging,·29(8),·2010.</a></p><h4><a·name="idp13168"></a>Options:</h4><h4><a·name="idp13169"></a>
4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·images·following·the·naming·pattern·nameXXXX.ext.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>file·name·base·for·registered·files·given·as·C-format·string.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">--save-references</span></dt><dd><p>Save·synthetic·references·to·files·refXXXX.v</p></dd></dl></div><h4><a·name="idp13185"></a>4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·images·following·the·naming·pattern·nameXXXX.ext.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>file·name·base·for·registered·files·given·as·C-format·string.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">--save-references</span></dt><dd><p>Save·synthetic·references·to·files·refXXXX.v</p></dd></dl></div><h4><a·name="idp13185"></a>
5 Preconditions·&amp;·Preprocessing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--preskip=20;·ulong</span></dt><dd><p>Skip·images·at·the·beginning+skip·of·the·series·when·searching·for·high·contrats·image</p></dd><dt><span·class="term">--postskip=2;·ulong</span></dt><dd><p>Skip·images·at·the·end·of·the·series·when·searching·for·high·contrats·image</p></dd><dt><span·class="term">--max-candidates=20;·ulong</span></dt><dd><p>maximum·number·of·candidates·for·global·reference·image</p></dd><dt><span·class="term">-S,·--cost-series=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Const·function·to·use·for·the·analysis·of·the·series.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a></p></dd><dt><span·class="term">--ref-idx=STRING</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-R,·--global-reference=-1;·int</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-D,·--max-subset-delta=0;·ulong</span></dt><dd><p>Maximum·delta·between·two·elements·of·the·prealigned·subset</p></dd></dl></div><h4><a·name="idp13220"></a>5 Preconditions·&amp;·Preprocessing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--preskip=20;·ulong</span></dt><dd><p>Skip·images·at·the·beginning+skip·of·the·series·when·searching·for·high·contrats·image</p></dd><dt><span·class="term">--postskip=2;·ulong</span></dt><dd><p>Skip·images·at·the·end·of·the·series·when·searching·for·high·contrats·image</p></dd><dt><span·class="term">--max-candidates=20;·ulong</span></dt><dd><p>maximum·number·of·candidates·for·global·reference·image</p></dd><dt><span·class="term">-S,·--cost-series=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Const·function·to·use·for·the·analysis·of·the·series.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a></p></dd><dt><span·class="term">--ref-idx=STRING</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-R,·--global-reference=-1;·int</span></dt><dd><p>save·reference·index·number·to·this·file</p></dd><dt><span·class="term">-D,·--max-subset-delta=0;·ulong</span></dt><dd><p>Maximum·delta·between·two·elements·of·the·prealigned·subset</p></dd></dl></div><h4><a·name="idp13220"></a>
6 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.01;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mr-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-1,·--cost-subset=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Cost·function·for·registration·during·the·subset·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a></p></dd><dt><span·class="term">-2,·--cost-final=image:cost=ssd;·factory</span></dt><dd><p>Cost·function·for·registration·during·the·final·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a></p></dd></dl></div><h4><a·name="idp13246"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13297"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13303"></a>Example:</h4><p>Register·the·image·series·given·by·images·imageXXXX.v·by·optimizing·a·spline·based·transformation·with·a·coefficient·rate·of·16·pixel,·skipping·two·images·at·the·beginning·and·using·normalized·gradient·fields·as·initial·cost·measure·and·SSD·as·final·measure.·Penalize·the·transformation·by·using·divcurl·with·aweight·of·2.0.·As·optimizer·an·nlopt·based·newton·method·is·used.</p><pre·class="screen">mia-3dprealign-nonrigid·mia-3dprealign-nonrigid··-i·imageXXXX.v·-o·registered·-t·vista·-k·2-F·spline:rate=16,penalty=[divcurl:weight=2]·-1·image:cost=[ngf:eval=ds]·-2·image:cost=ssd·-O·nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300</pre><h4><a·name="idp13306"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dmotioncompicanonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dserialnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dmotioncompica-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dserial-nonrigid</td></tr></table></div></body></html>6 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.01;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mr-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-1,·--cost-subset=image:cost=[ngf:eval=ds];·factory</span></dt><dd><p>Cost·function·for·registration·during·the·subset·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a></p></dd><dt><span·class="term">-2,·--cost-final=image:cost=ssd;·factory</span></dt><dd><p>Cost·function·for·registration·during·the·final·registration.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a></p></dd></dl></div><h4><a·name="idp13246"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13297"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13303"></a>Example:</h4><p>Register·the·image·series·given·by·images·imageXXXX.v·by·optimizing·a·spline·based·transformation·with·a·coefficient·rate·of·16·pixel,·skipping·two·images·at·the·beginning·and·using·normalized·gradient·fields·as·initial·cost·measure·and·SSD·as·final·measure.·Penalize·the·transformation·by·using·divcurl·with·aweight·of·2.0.·As·optimizer·an·nlopt·based·newton·method·is·used.</p><pre·class="screen">mia-3dprealign-nonrigid·mia-3dprealign-nonrigid··-i·imageXXXX.v·-o·registered·-t·vista·-k·2-F·spline:rate=16,penalty=[divcurl:weight=2]·-1·image:cost=[ngf:eval=ds]·-2·image:cost=ssd·-O·nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300</pre><h4><a·name="idp13306"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dmotioncompicanonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dserialnonrigid.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dmotioncompica-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dserial-nonrigid</td></tr></table></div></body></html>
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10 by·registering·the·remaining·images·by·using·synthetic·references.·This·is·a·3D10 by·registering·the·remaining·images·by·using·synthetic·references.·This·is·a·3D
11 version·of11 version·of
12 G._Wollny,_M-J_Ledesma-Cabryo,_P.Kellman,_and_A.Santos,_"Exploiting12 G._Wollny,_M-J_Ledesma-Cabryo,_P.Kellman,_and_A.Santos,_"Exploiting
13 Quasiperiodicity_in_Motion_Correction_of_Free-Breathing,"_IEEE_Transactions_on13 Quasiperiodicity_in_Motion_Correction_of_Free-Breathing,"_IEEE_Transactions_on
14 Medical_Imaging,_29(8),_2010.14 Medical_Imaging,_29(8),_2010.
15 Options:15 Options:
16 ·File-IO16 ·File-IO
17 ··-i,·--in-file=(input,·required);·io17 ··-i,·--in-file=(required,·input);·io
18 ······input·images·following·the·naming·pattern·nameXXXX.ext.·For·supported18 ······input·images·following·the·naming·pattern·nameXXXX.ext.·For·supported
19 ······file·types·see·Plugin_type:_3dimage/io19 ······file·types·see·Plugin_type:_3dimage/io
20 ··-o,·--out-file=(required,·output);·io20 ··-o,·--out-file=(required,·output);·io
21 ······file·name·base·for·registered·files·given·as·C-format·string.·For21 ······file·name·base·for·registered·files·given·as·C-format·string.·For
22 ······supported·file·types·see·Plugin_type:_3dimage/io22 ······supported·file·types·see·Plugin_type:_3dimage/io
23 ··--save-references23 ··--save-references
24 ······Save·synthetic·references·to·files·refXXXX.v24 ······Save·synthetic·references·to·files·refXXXX.v
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dpropose-boundingbox</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dmaskseeded.html"·title="mia-3dmaskseeded"><link·rel="next"·href="Secmia3dsegmentahmed.html"·title="mia-3dsegment-ahmed"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dpropose-boundingbox</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dmaskseeded.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentahmed.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dproposeboundingbox"></a>mia-3dpropose-boundingbox</h3></div></div></div><h4><a·name="idp10902"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dpropose-boundingbox</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dpropose-boundingbox</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dmaskseeded.html"·title="mia-3dmaskseeded"><link·rel="next"·href="Secmia3dsegmentahmed.html"·title="mia-3dsegment-ahmed"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dpropose-boundingbox</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dmaskseeded.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentahmed.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dproposeboundingbox"></a>mia-3dpropose-boundingbox</h3></div></div></div><h4><a·name="idp10902"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dpropose-boundingbox</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp10909"></a>Description:</h4><p·class="description">This·program·evaluates·a·box·that·contains·all·the·pixels·of·a·given·mask·image.·If·the·input·image·is·not·a·binary·image,·a·pre-filter·must·be·applied·that·converts·the·imput·image·into·a·mask.</p><h4><a·name="idp10911"></a>Options:</h4><h4><a·name="idp10912"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp10919"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10970"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-f,·--filter=</span></dt><dd><p>Filter·to·be·applied·to·the·image·before·the·bounding·box·is·evaluated.·Must·return·a·bit-valued·image..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a></p></dd><dt><span·class="term">-p,·--padding=0;·uint·in·[0,·inf)</span></dt><dd><p>Padding·of·boundaries.</p></dd></dl></div><h4><a·name="idp10981"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10987"></a>Example:</h4><p>Evaluate·a·bounding·box·with·boundary·padding·of·5·of·a·mask·resulting·from·a·binarization·with·a·minimum·value·10.10·and·a·boundary·padding·of·5·from·image·image.v·.</p><pre·class="screen">mia-3dpropose-boundingbox·-i·image.v·-f·binarize:min=10·-p·5</pre><h4><a·name="idp10990"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dmaskseeded.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentahmed.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dmaskseeded </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dsegment-ahmed</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp10909"></a>Description:</h4><p·class="description">This·program·evaluates·a·box·that·contains·all·the·pixels·of·a·given·mask·image.·If·the·input·image·is·not·a·binary·image,·a·pre-filter·must·be·applied·that·converts·the·imput·image·into·a·mask.</p><h4><a·name="idp10911"></a>Options:</h4><h4><a·name="idp10912"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp10919"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp10970"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-f,·--filter=</span></dt><dd><p>Filter·to·be·applied·to·the·image·before·the·bounding·box·is·evaluated.·Must·return·a·bit-valued·image..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a></p></dd><dt><span·class="term">-p,·--padding=0;·uint·in·[0,·inf)</span></dt><dd><p>Padding·of·boundaries.</p></dd></dl></div><h4><a·name="idp10981"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp10987"></a>Example:</h4><p>Evaluate·a·bounding·box·with·boundary·padding·of·5·of·a·mask·resulting·from·a·binarization·with·a·minimum·value·10.10·and·a·boundary·padding·of·5·from·image·image.v·.</p><pre·class="screen">mia-3dpropose-boundingbox·-i·image.v·-f·binarize:min=10·-p·5</pre><h4><a·name="idp10990"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dmaskseeded.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentahmed.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dmaskseeded </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dsegment-ahmed</td></tr></table></div></body></html>
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6 mia-3dpropose-boundingbox·{-i·io}·[·options·...]6 mia-3dpropose-boundingbox·{-i·io}·[·options·...]
7 Description:7 Description:
8 This·program·evaluates·a·box·that·contains·all·the·pixels·of·a·given·mask8 This·program·evaluates·a·box·that·contains·all·the·pixels·of·a·given·mask
9 image.·If·the·input·image·is·not·a·binary·image,·a·pre-filter·must·be·applied9 image.·If·the·input·image·is·not·a·binary·image,·a·pre-filter·must·be·applied
10 that·converts·the·imput·image·into·a·mask.10 that·converts·the·imput·image·into·a·mask.
11 Options:11 Options:
12 File-IO12 File-IO
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:14 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
15 ······3dimage/io15 ······3dimage/io
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
19 ······Supported·priorities·starting·at·lowest·level·are:19 ······Supported·priorities·starting·at·lowest·level·are:
20 ······trace:···Function·call·trace20 ······trace:···Function·call·trace
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3drigidreg</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dnonrigidregalt.html"·title="mia-3dnonrigidreg-alt"><link·rel="next"·href="Secmia3dtransform.html"·title="mia-3dtransform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3drigidreg</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dnonrigidregalt.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3drigidreg"></a>mia-3drigidreg</h3></div></div></div><h4><a·name="idp12365"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3drigidreg</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3drigidreg</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dnonrigidregalt.html"·title="mia-3dnonrigidreg-alt"><link·rel="next"·href="Secmia3dtransform.html"·title="mia-3dtransform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3drigidreg</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dnonrigidregalt.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3drigidreg"></a>mia-3drigidreg</h3></div></div></div><h4><a·name="idp12365"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3drigidreg</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12376"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·3D·images.·The·transformation·is·not·penalized,·therefore,·one·should·only·use·translation,·rigid,·or·affine·transformations·as·target·and·run·mia-3dnonrigidreg·of·nonrigid·registration·is·to·be·achieved.</p><h4><a·name="idp12378"></a>Options:</h4><h4><a·name="idp12379"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(input,·required);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(input,·required);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output);·io</span></dt><dd><p>registered·output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--transformation=(output);·io</span></dt><dd><p>transformation·output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>cost·function.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd><dt><span·class="term">-l,·--levels=3;·ulong</span></dt><dd><p>multigrid·levels</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=rigid;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd></dl></div><h4><a·name="idp12420"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12471"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12477"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·affine·and·write·the·registered·image·to·reg.v.·Use·two·multiresolution·levels·and·ssd·as·cost·function.</p><pre·class="screen">mia-3drigidreg·-i·test.v·-r·ref.v·-o·reg.v·-l·2·-f·affine·-c·ssd</pre><h4><a·name="idp12480"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dnonrigidregalt.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dnonrigidreg-alt </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dtransform</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12376"></a>Description:</h4><p·class="description">This·program·implements·the·registration·of·two·gray·scale·3D·images.·The·transformation·is·not·penalized,·therefore,·one·should·only·use·translation,·rigid,·or·affine·transformations·as·target·and·run·mia-3dnonrigidreg·of·nonrigid·registration·is·to·be·achieved.</p><h4><a·name="idp12378"></a>Options:</h4><h4><a·name="idp12379"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-image=(required,·input);·io</span></dt><dd><p>test·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--ref-image=(required,·input);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-image=(required,·output);·io</span></dt><dd><p>registered·output·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-t,·--transformation=(output);·io</span></dt><dd><p>transformation·output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-c,·--cost=ssd;·factory</span></dt><dd><p>cost·function.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagecost.html"·title="Plugin·type:·3dimage/cost">Plugin·type:·3dimage/cost</a></p></dd><dt><span·class="term">-l,·--levels=3;·ulong</span></dt><dd><p>multigrid·levels</p></dd><dt><span·class="term">-O,·--optimizer=gsl:opt=simplex,step=1.0;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-f,·--transForm=rigid;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd></dl></div><h4><a·name="idp12420"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12471"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12477"></a>Example:</h4><p>Register·image·test.v·to·image·ref.v·affine·and·write·the·registered·image·to·reg.v.·Use·two·multiresolution·levels·and·ssd·as·cost·function.</p><pre·class="screen">mia-3drigidreg·-i·test.v·-r·ref.v·-o·reg.v·-l·2·-f·affine·-c·ssd</pre><h4><a·name="idp12480"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dnonrigidregalt.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dnonrigidreg-alt </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dtransform</td></tr></table></div></body></html>
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7 Description:7 Description:
8 This·program·implements·the·registration·of·two·gray·scale·3D·images.·The8 This·program·implements·the·registration·of·two·gray·scale·3D·images.·The
9 transformation·is·not·penalized,·therefore,·one·should·only·use·translation,9 transformation·is·not·penalized,·therefore,·one·should·only·use·translation,
10 rigid,·or·affine·transformations·as·target·and·run·mia-3dnonrigidreg·of10 rigid,·or·affine·transformations·as·target·and·run·mia-3dnonrigidreg·of
11 nonrigid·registration·is·to·be·achieved.11 nonrigid·registration·is·to·be·achieved.
12 Options:12 Options:
13 File·I/O13 File·I/O
14 ··-i,·--in-image=(input,·required);·io14 ··-i,·--in-image=(required,·input);·io
15 ······test·image.·For·supported·file·types·see·Plugin_type:_3dimage/io15 ······test·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
16 ··-r,·--ref-image=(input,·required);·io16 ··-r,·--ref-image=(required,·input);·io
17 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io17 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
18 ··-o,·--out-image=(required,·output);·io18 ··-o,·--out-image=(required,·output);·io
19 ······registered·output·image.·For·supported·file·types·see·Plugin_type:19 ······registered·output·image.·For·supported·file·types·see·Plugin_type:
20 ······3dimage/io20 ······3dimage/io
21 ··-t,·--transformation=(output);·io21 ··-t,·--transformation=(output);·io
22 ······transformation·output·file·name.·For·supported·file·types·see·Plugin22 ······transformation·output·file·name.·For·supported·file·types·see·Plugin
23 ······type:_3dtransform/io23 ······type:_3dtransform/io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dsegment-ahmed</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dproposeboundingbox.html"·title="mia-3dpropose-boundingbox"><link·rel="next"·href="Secmia3dsegmentlocalcmeans.html"·title="mia-3dsegment-local-cmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dsegment-ahmed</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dproposeboundingbox.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentlocalcmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dsegmentahmed"></a>mia-3dsegment-ahmed</h3></div></div></div><h4><a·name="idp10994"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dsegment-ahmed</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-c·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dsegment-ahmed</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dproposeboundingbox.html"·title="mia-3dpropose-boundingbox"><link·rel="next"·href="Secmia3dsegmentlocalcmeans.html"·title="mia-3dsegment-local-cmeans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dsegment-ahmed</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dproposeboundingbox.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentlocalcmeans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dsegmentahmed"></a>mia-3dsegment-ahmed</h3></div></div></div><h4><a·name="idp10994"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dsegment-ahmed</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-c·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11003"></a>Description:</h4><p·class="description">This·program·implements·a·variation·of·the·paper:</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/42.996338"·target="_top">Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,</a></p><p·class="description">·changes·are:·p=2,·and·exp</p><h4><a·name="idp11007"></a>Options:</h4><h4><a·name="idp11008"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--class-file=(required,·output);·io</span></dt><dd><p>class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-b,·--out-file=(output);·io</span></dt><dd><p>Bias·corrected·image·will·be·of·the·same·type·like·the·input·image.·If·this·parameter·is·not·given,·then·the·bias·correction·will·not·be·applied..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp11025"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11076"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-C,·--class-centres=</span></dt><dd><p>initial·class·centers,·this·parameter·overrides·'no-of-clases'.</p></dd><dt><span·class="term">-s,·--spread=64;·float</span></dt><dd><p>spread·parameter·describing·the·strength·of·mattar·distinction</p></dd></dl></div><h4><a·name="idp11090"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11096"></a>Example:</h4><p>Run·a·5-class·segmentation·over·input·image·input.v·and·store·the·class·probability·images·in·cls.v.</p><pre·class="screen">mia-3dsegment-ahmed·-i·input.v·-a·5·-o·cls.v</pre><h4><a·name="idp11099"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dproposeboundingbox.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentlocalcmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dpropose-boundingbox </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dsegment-local-cmeans</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11003"></a>Description:</h4><p·class="description">This·program·implements·a·variation·of·the·paper:</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.1109/42.996338"·target="_top">Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,</a></p><p·class="description">·changes·are:·p=2,·and·exp</p><h4><a·name="idp11007"></a>Options:</h4><h4><a·name="idp11008"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-c,·--class-file=(required,·output);·io</span></dt><dd><p>class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-b,·--out-file=(output);·io</span></dt><dd><p>Bias·corrected·image·will·be·of·the·same·type·like·the·input·image.·If·this·parameter·is·not·given,·then·the·bias·correction·will·not·be·applied..·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp11025"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11076"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-n,·--no-of-classes=3;·int</span></dt><dd><p>number·of·classes</p></dd><dt><span·class="term">-C,·--class-centres=</span></dt><dd><p>initial·class·centers,·this·parameter·overrides·'no-of-clases'.</p></dd><dt><span·class="term">-s,·--spread=64;·float</span></dt><dd><p>spread·parameter·describing·the·strength·of·mattar·distinction</p></dd></dl></div><h4><a·name="idp11090"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11096"></a>Example:</h4><p>Run·a·5-class·segmentation·over·input·image·input.v·and·store·the·class·probability·images·in·cls.v.</p><pre·class="screen">mia-3dsegment-ahmed·-i·input.v·-a·5·-o·cls.v</pre><h4><a·name="idp11099"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dproposeboundingbox.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dsegmentlocalcmeans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dpropose-boundingbox </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dsegment-local-cmeans</td></tr></table></div></body></html>
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8 This·program·implements·a·variation·of·the·paper:8 This·program·implements·a·variation·of·the·paper:
9 Mohamed_N._Ahmed_et._al,_"A_Modified_Fuzzy_C-Means_Algorithm_for_Bias_Field9 Mohamed_N._Ahmed_et._al,_"A_Modified_Fuzzy_C-Means_Algorithm_for_Bias_Field
10 estimation_and_Segmentation_of_MRI_Data",_IEEE_Trans._on_Medical_Imaging,_Vol.10 estimation_and_Segmentation_of_MRI_Data",_IEEE_Trans._on_Medical_Imaging,_Vol.
11 21,_No._3,_March_2002,11 21,_No._3,_March_2002,
12 changes·are:·p=2,·and·exp12 changes·are:·p=2,·and·exp
13 Options:13 Options:
14 File-IO14 File-IO
15 ··-i,·--in-file=(input,·required);·io15 ··-i,·--in-file=(required,·input);·io
16 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_3dimage/16 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_3dimage/
17 ······io17 ······io
18 ··-c,·--class-file=(required,·output);·io18 ··-c,·--class-file=(required,·output);·io
19 ······class·probability·images,·the·image·type·must·support·multiple·images·and19 ······class·probability·images,·the·image·type·must·support·multiple·images·and
20 ······floating·point·values.·For·supported·file·types·see·Plugin_type:_3dimage/20 ······floating·point·values.·For·supported·file·types·see·Plugin_type:_3dimage/
21 ······io21 ······io
22 ··-b,·--out-file=(output);·io22 ··-b,·--out-file=(output);·io
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dsegment-local-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dsegmentahmed.html"·title="mia-3dsegment-ahmed"><link·rel="next"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dsegment-local-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dsegmentahmed.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dsegmentlocalcmeans"></a>mia-3dsegment-local-cmeans</h3></div></div></div><h4><a·name="idp11103"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dsegment-local-cmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dsegment-local-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"><link·rel="prev"·href="Secmia3dsegmentahmed.html"·title="mia-3dsegment-ahmed"><link·rel="next"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dsegment-local-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dsegmentahmed.html">Prev</a> </td><th·width="60%"·align="center">Analysis,·filtering,·combining,·and·segmentation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dsegmentlocalcmeans"></a>mia-3dsegment-local-cmeans</h3></div></div></div><h4><a·name="idp11103"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dsegment-local-cmeans</code>··{-i·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp11110"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·3D·image·by·applying·a·localized·c-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·c-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·c-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.·This·program·implements·algorithm·described·in:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.7717/peerj.4374"·target="_top">Dunmore·CJ,·Wollny·G,·Skinner·MM.·(2018)·MIA-Clustering:·a·novel·method·for·segmentation·of·paleontological·material.·PeerJ·6:e4374.</a></p><h4><a·name="idp11114"></a>Options:</h4><h4><a·name="idp11115"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-G,·--out-global-crisp=(output);·io</span></dt><dd><p>class·label·image·based·on·global·segmentation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-C,·--class-prob=(output);·io</span></dt><dd><p>class·probability·image·file,·filetype·must·support·floating·point·multi-frame·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp11137"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11188"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-g,·--grid-spacing=15;·int·in·[3,·inf)</span></dt><dd><p>Spacing·of·the·grid·used·to·modulate·the·intensity·inhomogeneities</p></dd><dt><span·class="term">-c,·--cmeans=kmeans:nc=3;·factory</span></dt><dd><p>c-means·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd><dt><span·class="term">-e,·--c-means-epsilon=0.0001;·float·in·(0,·inf)</span></dt><dd><p>c-means·breaking·condition·for·update·tolerance</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.02;·double·in·[0,·1)</span></dt><dd><p>threshhold·to·ignore·classes·when·initializing·the·local·cmeans·from·the·global·one.</p></dd><dt><span·class="term">-B,·--ignore-background</span></dt><dd><p>Don't·take·background·probablities·into·account·when·desiding·whether·classes·are·to·be·ignored</p></dd><dt><span·class="term">-L,·--label-threshold=0;·float·in·[0,·1]</span></dt><dd><p>for·values·&lt;=·0.5:·create·segmentation·based·on·highest·class·probability,·labels·start·at·0.·For·values·&gt;0.5:·create·labels·only·for·voxels·with·a·class·probability·higher·than·the·given·value,·labels·start·at·1·and·voxels·without·an·according·class·probability·are·set·to·0;·this·output·is·suitable·for·the·seeded·watershed·filter.</p></dd></dl></div><h4><a·name="idp11215"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11221"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-3dsegment-local-cmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp11224"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dsegmentahmed.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dsegment-ahmed </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration,·Comparison,·and·Transformation·of·3D·images</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp11110"></a>Description:</h4><p·class="description">This·program·runs·the·segmentation·of·a·3D·image·by·applying·a·localized·c-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·c-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·c-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.·This·program·implements·algorithm·described·in:·</p><p·class="citation"><a·class="ulink"·href="https://doi.org/10.7717/peerj.4374"·target="_top">Dunmore·CJ,·Wollny·G,·Skinner·MM.·(2018)·MIA-Clustering:·a·novel·method·for·segmentation·of·paleontological·material.·PeerJ·6:e4374.</a></p><h4><a·name="idp11114"></a>Options:</h4><h4><a·name="idp11115"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>image·to·be·segmented.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(output);·io</span></dt><dd><p>class·label·image·based·on·merging·local·labels.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-G,·--out-global-crisp=(output);·io</span></dt><dd><p>class·label·image·based·on·global·segmentation.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-C,·--class-prob=(output);·io</span></dt><dd><p>class·probability·image·file,·filetype·must·support·floating·point·multi-frame·images.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp11137"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp11188"></a>Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-g,·--grid-spacing=15;·int·in·[3,·inf)</span></dt><dd><p>Spacing·of·the·grid·used·to·modulate·the·intensity·inhomogeneities</p></dd><dt><span·class="term">-c,·--cmeans=kmeans:nc=3;·factory</span></dt><dd><p>c-means·initializer.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dcmeans.html"·title="Plugin·type:·1d/cmeans">Plugin·type:·1d/cmeans</a></p></dd><dt><span·class="term">-e,·--c-means-epsilon=0.0001;·float·in·(0,·inf)</span></dt><dd><p>c-means·breaking·condition·for·update·tolerance</p></dd><dt><span·class="term">-t,·--relative-cluster-threshold=0.02;·double·in·[0,·1)</span></dt><dd><p>threshhold·to·ignore·classes·when·initializing·the·local·cmeans·from·the·global·one.</p></dd><dt><span·class="term">-B,·--ignore-background</span></dt><dd><p>Don't·take·background·probablities·into·account·when·desiding·whether·classes·are·to·be·ignored</p></dd><dt><span·class="term">-L,·--label-threshold=0;·float·in·[0,·1]</span></dt><dd><p>for·values·&lt;=·0.5:·create·segmentation·based·on·highest·class·probability,·labels·start·at·0.·For·values·&gt;0.5:·create·labels·only·for·voxels·with·a·class·probability·higher·than·the·given·value,·labels·start·at·1·and·voxels·without·an·according·class·probability·are·set·to·0;·this·output·is·suitable·for·the·seeded·watershed·filter.</p></dd></dl></div><h4><a·name="idp11215"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp11221"></a>Example:</h4><p>Run·the·segmentation·on·image·test.png·using·three·classes,·local·regions·of·40·pixels·(grid·width·20·pixels),·and·a·class·ignore·threshold·of·0.01.</p><pre·class="screen">mia-3dsegment-local-cmeans·-i·test.png·-o·label.png·-n·3·-g·20·-t·0.01</pre><h4><a·name="idp11224"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dsegmentahmed.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dsegment-ahmed </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration,·Comparison,·and·Transformation·of·3D·images</td></tr></table></div></body></html>
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12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain12 including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain
13 more·pixels·than·a·given·threshold.·This·program·implements·algorithm·described13 more·pixels·than·a·given·threshold.·This·program·implements·algorithm·described
14 in:14 in:
15 Dunmore_CJ,_Wollny_G,_Skinner_MM._(2018)_MIA-Clustering:_a_novel_method_for15 Dunmore_CJ,_Wollny_G,_Skinner_MM._(2018)_MIA-Clustering:_a_novel_method_for
16 segmentation_of_paleontological_material._PeerJ_6:e4374.16 segmentation_of_paleontological_material._PeerJ_6:e4374.
17 Options:17 Options:
18 File-IO18 File-IO
19 ··-i,·--in-file=(input,·required);·io19 ··-i,·--in-file=(required,·input);·io
20 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_3dimage/20 ······image·to·be·segmented.·For·supported·file·types·see·Plugin_type:_3dimage/
21 ······io21 ······io
22 ··-o,·--out-file=(output);·io22 ··-o,·--out-file=(output);·io
23 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types23 ······class·label·image·based·on·merging·local·labels.·For·supported·file·types
24 ······see·Plugin_type:_3dimage/io24 ······see·Plugin_type:_3dimage/io
25 ··-G,·--out-global-crisp=(output);·io25 ··-G,·--out-global-crisp=(output);·io
26 ······class·label·image·based·on·global·segmentation.·For·supported·file·types26 ······class·label·image·based·on·global·segmentation.·For·supported·file·types
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dserial-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="Secmia3dprealignnonrigid.html"·title="mia-3dprealign-nonrigid"><link·rel="next"·href="SecToolsfortheAnalysisof3Dimageseries.html"·title="Tools·for·the·Analysis·of·3D·image·series"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dserial-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dprealignnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof3Dimageseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dserialnonrigid"></a>mia-3dserial-nonrigid</h3></div></div></div><h4><a·name="idp13310"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dserial-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dserial-nonrigid</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"><link·rel="prev"·href="Secmia3dprealignnonrigid.html"·title="mia-3dprealign-nonrigid"><link·rel="next"·href="SecToolsfortheAnalysisof3Dimageseries.html"·title="Tools·for·the·Analysis·of·3D·image·series"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dserial-nonrigid</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dprealignnonrigid.html">Prev</a> </td><th·width="60%"·align="center">Registration·of·series·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof3Dimageseries.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dserialnonrigid"></a>mia-3dserial-nonrigid</h3></div></div></div><h4><a·name="idp13310"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dserial-nonrigid</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a>5 ············<a·class="xref"·href="SecPlugintype3dimagefullcost.html"·title="Plugin·type:·3dimage/fullcost">Plugin·type:·3dimage/fullcost</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp13320"></a>Description:</h4><p·class="description">This·program·runs·the·image·registration·of·a·consecutively·numbered·image·series.·The·registration·is·run·in·a·serial·manner,·this·is,·only·images·in·temporal·succession·(i.e.·consecutive·numbers)·are·registered,·and·the·obtained·transformations·are·applied·accumulated·to·reach·full·registration.·</p><h4><a·name="idp13322"></a>Options:</h4><h4><a·name="idp13323"></a>7 ········...]</p></div><h4><a·name="idp13320"></a>Description:</h4><p·class="description">This·program·runs·the·image·registration·of·a·consecutively·numbered·image·series.·The·registration·is·run·in·a·serial·manner,·this·is,·only·images·in·temporal·succession·(i.e.·consecutive·numbers)·are·registered,·and·the·obtained·transformations·are·applied·accumulated·to·reach·full·registration.·</p><h4><a·name="idp13322"></a>Options:</h4><h4><a·name="idp13323"></a>
8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(output);·string</span></dt><dd><p>file·name·for·registered·fiels</p></dd></dl></div><h4><a·name="idp13333"></a>8 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·perfusion·data·set</p></dd><dt><span·class="term">-o,·--out-file=(output);·string</span></dt><dd><p>file·name·for·registered·fiels</p></dd></dl></div><h4><a·name="idp13333"></a>
9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd></dl></div><h4><a·name="idp13353"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13404"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13410"></a>Example:</h4><p>Run·a·serial·registration·of·images·inputXXXX.v·(X·digit)·to·reference·image·20·and·store·the·result·in·regXXXX.v.·Optimize·the·sum·of·squared·differences·and·spline·transformations·with·coefficient·rate·10.</p><pre·class="screen">mia-3dserial-nonrigid·-i·input0000.v·-o·'reg%04d.v'·-f·spline:rate=10·-r·20·ssd</pre><h4><a·name="idp13413"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dprealignnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof3Dimageseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dprealign-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Tools·for·the·Analysis·of·3D·image·series</td></tr></table></div></body></html>9 Registration</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-O,·--optimizer=gsl:opt=gd,step=0.1;·factory</span></dt><dd><p>Optimizer·used·for·minimization.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintypeminimizersinglecost.html"·title="Plugin·type:·minimizer/singlecost">Plugin·type:·minimizer/singlecost</a></p></dd><dt><span·class="term">-l,·--mg-levels=3;·ulong</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-f,·--transForm=spline;·factory</span></dt><dd><p>transformation·type.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagetransform.html"·title="Plugin·type:·3dimage/transform">Plugin·type:·3dimage/transform</a></p></dd><dt><span·class="term">-r,·--ref=-1;·int</span></dt><dd><p>reference·frame·(-1·==·use·image·in·the·middle)</p></dd></dl></div><h4><a·name="idp13353"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13404"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13410"></a>Example:</h4><p>Run·a·serial·registration·of·images·inputXXXX.v·(X·digit)·to·reference·image·20·and·store·the·result·in·regXXXX.v.·Optimize·the·sum·of·squared·differences·and·spline·transformations·with·coefficient·rate·10.</p><pre·class="screen">mia-3dserial-nonrigid·-i·input0000.v·-o·'reg%04d.v'·-f·spline:rate=10·-r·20·ssd</pre><h4><a·name="idp13413"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dprealignnonrigid.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationofseriesof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecToolsfortheAnalysisof3Dimageseries.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dprealign-nonrigid </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Tools·for·the·Analysis·of·3D·image·series</td></tr></table></div></body></html>
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8 Description:8 Description:
9 This·program·runs·the·image·registration·of·a·consecutively·numbered·image9 This·program·runs·the·image·registration·of·a·consecutively·numbered·image
10 series.·The·registration·is·run·in·a·serial·manner,·this·is,·only·images·in10 series.·The·registration·is·run·in·a·serial·manner,·this·is,·only·images·in
11 temporal·succession·(i.e.·consecutive·numbers)·are·registered,·and·the·obtained11 temporal·succession·(i.e.·consecutive·numbers)·are·registered,·and·the·obtained
12 transformations·are·applied·accumulated·to·reach·full·registration.12 transformations·are·applied·accumulated·to·reach·full·registration.
13 Options:13 Options:
14 ·File-IO14 ·File-IO
15 ··-i,·--in-file=(input,·required);·string15 ··-i,·--in-file=(required,·input);·string
16 ······input·perfusion·data·set16 ······input·perfusion·data·set
17 ··-o,·--out-file=(output);·string17 ··-o,·--out-file=(output);·string
18 ······file·name·for·registered·fiels18 ······file·name·for·registered·fiels
19 ·Registration19 ·Registration
20 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·factory20 ··-O,·--optimizer=gsl:opt=gd,step=0.1;·factory
21 ······Optimizer·used·for·minimization.·For·supported·plug-ins·see·Plugin_type:21 ······Optimizer·used·for·minimization.·For·supported·plug-ins·see·Plugin_type:
22 ······minimizer/singlecost22 ······minimizer/singlecost
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dseries-track-intensity</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsfortheAnalysisof3Dimageseries.html"·title="Tools·for·the·Analysis·of·3D·image·series"><link·rel="prev"·href="Secmia3devaltransformquantity.html"·title="mia-3deval-transformquantity"><link·rel="next"·href="Secmia3dtrackpixelmovement.html"·title="mia-3dtrackpixelmovement"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dseries-track-intensity</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3devaltransformquantity.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·the·Analysis·of·3D·image·series</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dtrackpixelmovement.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dseriestrackintensity"></a>mia-3dseries-track-intensity</h3></div></div></div><h4><a·name="idp13538"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dseries-track-intensity</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dseries-track-intensity</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsfortheAnalysisof3Dimageseries.html"·title="Tools·for·the·Analysis·of·3D·image·series"><link·rel="prev"·href="Secmia3devaltransformquantity.html"·title="mia-3deval-transformquantity"><link·rel="next"·href="Secmia3dtrackpixelmovement.html"·title="mia-3dtrackpixelmovement"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dseries-track-intensity</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3devaltransformquantity.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·the·Analysis·of·3D·image·series</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dtrackpixelmovement.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dseriestrackintensity"></a>mia-3dseries-track-intensity</h3></div></div></div><h4><a·name="idp13538"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dseries-track-intensity</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp13547"></a>Description:</h4><p·class="description">This·program·tracks·the·intensity·of·a·pixel·at·the·given·coordinates.</p><h4><a·name="idp13549"></a>Options:</h4><h4><a·name="idp13550"></a>3 ········...]</p></div><h4><a·name="idp13547"></a>Description:</h4><p·class="description">This·program·tracks·the·intensity·of·a·pixel·at·the·given·coordinates.</p><h4><a·name="idp13549"></a>Options:</h4><h4><a·name="idp13550"></a>
4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·perfusion·data·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>file·name·for·output·intensity·slopes</p></dd></dl></div><h4><a·name="idp13561"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13612"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13618"></a>Example:</h4><p>Evaluate·the·intensity-time·curves·at·points·&lt;12,13,14&gt;·and·&lt;222,113,214&gt;</p><pre·class="screen">mia-3dseries-track-intensity·-i·images0000.v·-o·curves.txt·'&lt;12,13,14&gt;'·'&lt;222,113,214&gt;'</pre><h4><a·name="idp13621"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3devaltransformquantity.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof3Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dtrackpixelmovement.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3deval-transformquantity </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dtrackpixelmovement</td></tr></table></div></body></html>4 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·perfusion·data·set.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>file·name·for·output·intensity·slopes</p></dd></dl></div><h4><a·name="idp13561"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13612"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13618"></a>Example:</h4><p>Evaluate·the·intensity-time·curves·at·points·&lt;12,13,14&gt;·and·&lt;222,113,214&gt;</p><pre·class="screen">mia-3dseries-track-intensity·-i·images0000.v·-o·curves.txt·'&lt;12,13,14&gt;'·'&lt;222,113,214&gt;'</pre><h4><a·name="idp13621"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3devaltransformquantity.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof3Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dtrackpixelmovement.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3deval-transformquantity </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dtrackpixelmovement</td></tr></table></div></body></html>
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4 mia-3dseries-track-intensity4 mia-3dseries-track-intensity
5 Sysnopis:5 Sysnopis:
6 mia-3dseries-track-intensity·{-i·io}·{-o·string}·[·options·...]6 mia-3dseries-track-intensity·{-i·io}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·tracks·the·intensity·of·a·pixel·at·the·given·coordinates.8 This·program·tracks·the·intensity·of·a·pixel·at·the·given·coordinates.
9 Options:9 Options:
10 ·File-IO10 ·File-IO
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·perfusion·data·set.·For·supported·file·types·see·Plugin_type:12 ······input·perfusion·data·set.·For·supported·file·types·see·Plugin_type:
13 ······3dimage/io13 ······3dimage/io
14 ··-o,·--out-file=(required,·output);·string14 ··-o,·--out-file=(required,·output);·string
15 ······file·name·for·output·intensity·slopes15 ······file·name·for·output·intensity·slopes
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dtrackpixelmovement</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsfortheAnalysisof3Dimageseries.html"·title="Tools·for·the·Analysis·of·3D·image·series"><link·rel="prev"·href="Secmia3dseriestrackintensity.html"·title="mia-3dseries-track-intensity"><link·rel="next"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dtrackpixelmovement</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dseriestrackintensity.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·the·Analysis·of·3D·image·series</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecMiscellaneousprograms.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dtrackpixelmovement"></a>mia-3dtrackpixelmovement</h3></div></div></div><h4><a·name="idp13625"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dtrackpixelmovement</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dtrackpixelmovement</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecToolsfortheAnalysisof3Dimageseries.html"·title="Tools·for·the·Analysis·of·3D·image·series"><link·rel="prev"·href="Secmia3dseriestrackintensity.html"·title="mia-3dseries-track-intensity"><link·rel="next"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dtrackpixelmovement</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dseriestrackintensity.html">Prev</a> </td><th·width="60%"·align="center">Tools·for·the·Analysis·of·3D·image·series</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecMiscellaneousprograms.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dtrackpixelmovement"></a>mia-3dtrackpixelmovement</h3></div></div></div><h4><a·name="idp13625"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dtrackpixelmovement</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp13636"></a>Description:</h4><p·class="description">Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using·image·registration.·The·pixel·data·is·given·in·CSV·format3 ········...]</p></div><h4><a·name="idp13636"></a>Description:</h4><p·class="description">Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using·image·registration.·The·pixel·data·is·given·in·CSV·format
4 ···id;time;x;y;z;reserved4 ···id;time;x;y;z;reserved
  
5 The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and·the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.</p><h4><a·name="idp13638"></a>Options:</h4><h4><a·name="idp13639"></a>5 The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and·the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.</p><h4><a·name="idp13638"></a>Options:</h4><h4><a·name="idp13639"></a>
6 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·point·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·point·set</p></dd><dt><span·class="term">-t,·--transformation=(input,·required);·io</span></dt><dd><p>transformation·describing·the·monitored·change.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp13654"></a>6 File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·point·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·point·set</p></dd><dt><span·class="term">-t,·--transformation=(required,·input);·io</span></dt><dd><p>transformation·describing·the·monitored·change.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd></dl></div><h4><a·name="idp13654"></a>
7 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--time-step=1;·float</span></dt><dd><p>time·step·to·use·for·the·position·update</p></dd></dl></div><h4><a·name="idp13660"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13711"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13717"></a>Example:</h4><p>This·program·evaluated·the·changed·position·of·pixels·given·in·input.csv,·by·using··a·time·step·of·2.0·time·units·and·the·transformation·change.v3df,·and·writes·the·updated·positions·to·updated.csv.</p><pre·class="screen">mia-3dtrackpixelmovement·-i·input.csv·-o·output.cvs·--time-step·2.0·--transformation·change.v3df</pre><h4><a·name="idp13720"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dseriestrackintensity.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof3Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecMiscellaneousprograms.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dseries-track-intensity </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Miscellaneous·programs</td></tr></table></div></body></html>7 Parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-T,·--time-step=1;·float</span></dt><dd><p>time·step·to·use·for·the·position·update</p></dd></dl></div><h4><a·name="idp13660"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp13711"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp13717"></a>Example:</h4><p>This·program·evaluated·the·changed·position·of·pixels·given·in·input.csv,·by·using··a·time·step·of·2.0·time·units·and·the·transformation·change.v3df,·and·writes·the·updated·positions·to·updated.csv.</p><pre·class="screen">mia-3dtrackpixelmovement·-i·input.csv·-o·output.cvs·--time-step·2.0·--transformation·change.v3df</pre><h4><a·name="idp13720"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dseriestrackintensity.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecToolsfortheAnalysisof3Dimageseries.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecMiscellaneousprograms.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dseries-track-intensity </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Miscellaneous·programs</td></tr></table></div></body></html>
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7 Description:7 Description:
8 Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using8 Track·the·position·of·a·pixel·by·means·of·a·transformation·obtained·by·using
9 image·registration.·The·pixel·data·is·given·in·CSV·format9 image·registration.·The·pixel·data·is·given·in·CSV·format
10 id;time;x;y;z;reserved·The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and10 id;time;x;y;z;reserved·The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and
11 the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.11 the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.
12 Options:12 Options:
13 ·File-IO13 ·File-IO
14 ··-i,·--in-file=(input,·required);·string14 ··-i,·--in-file=(required,·input);·string
15 ······input·point·set15 ······input·point·set
16 ··-o,·--out-file=(required,·output);·string16 ··-o,·--out-file=(required,·output);·string
17 ······output·point·set17 ······output·point·set
18 ··-t,·--transformation=(input,·required);·io18 ··-t,·--transformation=(required,·input);·io
19 ······transformation·describing·the·monitored·change.·For·supported·file·types19 ······transformation·describing·the·monitored·change.·For·supported·file·types
20 ······see·Plugin_type:_3dtransform/io20 ······see·Plugin_type:_3dtransform/io
21 ·Parameters21 ·Parameters
22 ··-T,·--time-step=1;·float22 ··-T,·--time-step=1;·float
23 ······time·step·to·use·for·the·position·update23 ······time·step·to·use·for·the·position·update
24 Help·&·Info24 Help·&·Info
25 ··-V,·--verbose=warning;·dict25 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dtransform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3drigidreg.html"·title="mia-3drigidreg"><link·rel="next"·href="Secmia3dtransform2vf.html"·title="mia-3dtransform2vf"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dtransform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3drigidreg.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform2vf.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dtransform"></a>mia-3dtransform</h3></div></div></div><h4><a·name="idp12484"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dtransform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dtransform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3drigidreg.html"·title="mia-3drigidreg"><link·rel="next"·href="Secmia3dtransform2vf.html"·title="mia-3dtransform2vf"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dtransform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3drigidreg.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform2vf.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dtransform"></a>mia-3dtransform</h3></div></div></div><h4><a·name="idp12484"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dtransform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-t·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12495"></a>Description:</h4><p·class="description">Transform·a·3D·image·by·applying·a·given·3D·transformation.</p><h4><a·name="idp12497"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output)[·...·truncated·by·diffoscope;·len:·250,·SHA:·89658e0b165100db6b64cd3494ba52bbd8945b1a2c964fa982b05b9d7aa05413·...·]);·io</span></dt><dd><p>transformation·file.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-p,·--interpolator=STRING</span></dt><dd><p>override·the·interpolator·provided·by·the·transformation</p></dd><dt><span·class="term">-b,·--boundary=mirror;·stringSTRING</span></dt><dd><p>override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·also·overridden.</p></dd></dl></div><h4><a·name="idp12522"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12573"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12579"></a>Example:</h4><p>Transform·an·image·input.v·by·the·transfromation·stored·in·trans.v·by·using·nearest·neighbour·interpolation·ans·store·the·result·in·output.v</p><pre·class="screen">mia-3dtransform·-i·input.v·-t·trans.v··-o·output.v··-p·bspline:d=0</pre><h4><a·name="idp12582"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3drigidreg.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform2vf.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3drigidreg </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dtransform2vf</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12495"></a>Description:</h4><p·class="description">Transform·a·3D·image·by·applying·a·given·3D·transformation.</p><h4><a·name="idp12497"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output)[·...·truncated·by·diffoscope;·len:·250,·SHA:·01b5fec394ed73f829dfcc013ed831382355530782783e39f094f3bfae8e503e·...·]);·io</span></dt><dd><p>transformation·file.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-p,·--interpolator=STRING</span></dt><dd><p>override·the·interpolator·provided·by·the·transformation</p></dd><dt><span·class="term">-b,·--boundary=mirror;·stringSTRING</span></dt><dd><p>override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·also·overridden.</p></dd></dl></div><h4><a·name="idp12522"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12573"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12579"></a>Example:</h4><p>Transform·an·image·input.v·by·the·transfromation·stored·in·trans.v·by·using·nearest·neighbour·interpolation·ans·store·the·result·in·output.v</p><pre·class="screen">mia-3dtransform·-i·input.v·-t·trans.v··-o·output.v··-p·bspline:d=0</pre><h4><a·name="idp12582"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3drigidreg.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dtransform2vf.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3drigidreg </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dtransform2vf</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-3dtransform4 mia-3dtransform
5 Sysnopis:5 Sysnopis:
6 mia-3dtransform·{-i·io}·{-o·io}·{-t·io}·[·options·...]6 mia-3dtransform·{-i·io}·{-o·io}·{-t·io}·[·options·...]
7 Description:7 Description:
8 Transform·a·3D·image·by·applying·a·given·3D·transformation.8 Transform·a·3D·image·by·applying·a·given·3D·transformation.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io11 ······input·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······transformed·image.·For·supported·file·types·see·Plugin_type:_3dimage/io13 ······transformed·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
14 ··-t,·--transformation=(input,·required);·io14 ··-t,·--transformation=(required,·input);·io
15 ······transformation·file.·For·supported·file·types·see·Plugin_type:15 ······transformation·file.·For·supported·file·types·see·Plugin_type:
16 ······3dtransform/io16 ······3dtransform/io
17 ··-p,·--interpolator=STRING17 ··-p,·--interpolator=STRING
18 ······override·the·interpolator·provided·by·the·transformation18 ······override·the·interpolator·provided·by·the·transformation
19 ··-b,·--boundary=mirror;·stringSTRING19 ··-b,·--boundary=mirror;·stringSTRING
20 ······override·the·boundary·conditions·provided·by·the·transformation.·This·is20 ······override·the·boundary·conditions·provided·by·the·transformation.·This·is
21 ······only·used·if·the·interpolator·is·also·overridden.21 ······only·used·if·the·interpolator·is·also·overridden.
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./usr/share/doc/mia-2.4/userref/Secmia3dtransform2vf.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dtransform2vf</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dtransform.html"·title="mia-3dtransform"><link·rel="next"·href="Secmia3dvf2transform.html"·title="mia-3dvf2transform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dtransform2vf</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dtransform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dvf2transform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dtransform2vf"></a>mia-3dtransform2vf</h3></div></div></div><h4><a·name="idp12586"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dtransform2vf</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dtransform2vf</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dtransform.html"·title="mia-3dtransform"><link·rel="next"·href="Secmia3dvf2transform.html"·title="mia-3dvf2transform"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dtransform2vf</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dtransform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dvf2transform.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dtransform2vf"></a>mia-3dtransform2vf</h3></div></div></div><h4><a·name="idp12586"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dtransform2vf</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12595"></a>Description:</h4><p·class="description">Create·a·3D·vector·field·from·a·given·transformation.·The·output·vector·field·will·have·the·dimesions·as·given·in·the·transformation·description.</p><h4><a·name="idp12597"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·transformation·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd></dl></div><h4><a·name="idp12609"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12660"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12666"></a>Example:</h4><p>Transform·the·input·transformation·trans.v3df·to·a·vector·field·field.vtk.</p><pre·class="screen">mia-3dtransform2vf·-i·trans.v3df···-o·field.vtk</pre><h4><a·name="idp12669"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dtransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dvf2transform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dtransform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dvf2transform</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12595"></a>Description:</h4><p·class="description">Create·a·3D·vector·field·from·a·given·transformation.·The·output·vector·field·will·have·the·dimesions·as·given·in·the·transformation·description.</p><h4><a·name="idp12597"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·transformation·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd></dl></div><h4><a·name="idp12609"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12660"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12666"></a>Example:</h4><p>Transform·the·input·transformation·trans.v3df·to·a·vector·field·field.vtk.</p><pre·class="screen">mia-3dtransform2vf·-i·trans.v3df···-o·field.vtk</pre><h4><a·name="idp12669"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dtransform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dvf2transform.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dtransform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dvf2transform</td></tr></table></div></body></html>
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4 mia-3dtransform2vf4 mia-3dtransform2vf
5 Sysnopis:5 Sysnopis:
6 mia-3dtransform2vf·{-i·io}·{-o·io}·[·options·...]6 mia-3dtransform2vf·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Create·a·3D·vector·field·from·a·given·transformation.·The·output·vector·field8 Create·a·3D·vector·field·from·a·given·transformation.·The·output·vector·field
9 will·have·the·dimesions·as·given·in·the·transformation·description.9 will·have·the·dimesions·as·given·in·the·transformation·description.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·io11 ··-i,·--in-file=(required,·input);·io
12 ······input·transformation·.·For·supported·file·types·see·Plugin_type:12 ······input·transformation·.·For·supported·file·types·see·Plugin_type:
13 ······3dtransform/io13 ······3dtransform/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·vector·field·.·For·supported·file·types·see·Plugin_type:_3dvf/io15 ······output·vector·field·.·For·supported·file·types·see·Plugin_type:_3dvf/io
16 Help·&·Info16 Help·&·Info
17 ··-V,·--verbose=warning;·dict17 ··-V,·--verbose=warning;·dict
18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.18 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dvf2transform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dtransform2vf.html"·title="mia-3dtransform2vf"><link·rel="next"·href="Secmia3dvfcompare.html"·title="mia-3dvfcompare"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dvf2transform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dtransform2vf.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dvfcompare.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dvf2transform"></a>mia-3dvf2transform</h3></div></div></div><h4><a·name="idp12673"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dvf2transform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dvf2transform</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dtransform2vf.html"·title="mia-3dtransform2vf"><link·rel="next"·href="Secmia3dvfcompare.html"·title="mia-3dvfcompare"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dvf2transform</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dtransform2vf.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmia3dvfcompare.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dvf2transform"></a>mia-3dvf2transform</h3></div></div></div><h4><a·name="idp12673"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dvf2transform</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12682"></a>Description:</h4><p·class="description">Creates·a·3D·transformation·from·a·vector·field.·The·input·vector·field·is·simply·encapsulated·into·the·transformation·file·format.·The·boundary·conditions·and·the·image·interpolator·kernel·can·be·set·at·the·command·line.</p><h4><a·name="idp12684"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·transformation·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-k,·--imgkernel=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel·which·is·used·when·the·transformation·is·applied·to·an·image.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">-b,·--imgboundary=mirror;·factory</span></dt><dd><p>Boundary·condition·applied·when·the·transformation·is·used·to·transform·an·image.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinebc.html"·title="Plugin·type:·1d/splinebc">Plugin·type:·1d/splinebc</a></p></dd></dl></div><h4><a·name="idp12706"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12757"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12763"></a>Example:</h4><p>Transform·the·input·vector·field·field.vtk·to·the·transformation·trans.v3df·and·specify·zero·boundary·conditions·and·b-splines·of·degree·2·for·image·interpolation.</p><pre·class="screen">mia-3dvf2transform·-i·field.vtk·-o·trans.v3df·--imgkernel·bspline:d=2·--imgboundary·zero</pre><h4><a·name="idp12766"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dtransform2vf.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dvfcompare.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dtransform2vf </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dvfcompare</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12682"></a>Description:</h4><p·class="description">Creates·a·3D·transformation·from·a·vector·field.·The·input·vector·field·is·simply·encapsulated·into·the·transformation·file·format.·The·boundary·conditions·and·the·image·interpolator·kernel·can·be·set·at·the·command·line.</p><h4><a·name="idp12684"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·transformation·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·vector·field·.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dtransformio.html"·title="Plugin·type:·3dtransform/io">Plugin·type:·3dtransform/io</a></p></dd><dt><span·class="term">-k,·--imgkernel=bspline:d=3;·factory</span></dt><dd><p>image·interpolator·kernel·which·is·used·when·the·transformation·is·applied·to·an·image.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinekernel.html"·title="Plugin·type:·1d/splinekernel">Plugin·type:·1d/splinekernel</a></p></dd><dt><span·class="term">-b,·--imgboundary=mirror;·factory</span></dt><dd><p>Boundary·condition·applied·when·the·transformation·is·used·to·transform·an·image.·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype1dsplinebc.html"·title="Plugin·type:·1d/splinebc">Plugin·type:·1d/splinebc</a></p></dd></dl></div><h4><a·name="idp12706"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12757"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12763"></a>Example:</h4><p>Transform·the·input·vector·field·field.vtk·to·the·transformation·trans.v3df·and·specify·zero·boundary·conditions·and·b-splines·of·degree·2·for·image·interpolation.</p><pre·class="screen">mia-3dvf2transform·-i·field.vtk·-o·trans.v3df·--imgkernel·bspline:d=2·--imgboundary·zero</pre><h4><a·name="idp12766"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dtransform2vf.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmia3dvfcompare.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dtransform2vf </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-3dvfcompare</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-3dvf2transform·{-i·io}·{-o·io}·[·options·...]6 mia-3dvf2transform·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 Creates·a·3D·transformation·from·a·vector·field.·The·input·vector·field·is8 Creates·a·3D·transformation·from·a·vector·field.·The·input·vector·field·is
9 simply·encapsulated·into·the·transformation·file·format.·The·boundary9 simply·encapsulated·into·the·transformation·file·format.·The·boundary
10 conditions·and·the·image·interpolator·kernel·can·be·set·at·the·command·line.10 conditions·and·the·image·interpolator·kernel·can·be·set·at·the·command·line.
11 Options:11 Options:
12 ··-i,·--in-file=(input,·required);·io12 ··-i,·--in-file=(required,·input);·io
13 ······input·transformation·.·For·supported·file·types·see·Plugin_type:_3dvf/io13 ······input·transformation·.·For·supported·file·types·see·Plugin_type:_3dvf/io
14 ··-o,·--out-file=(required,·output);·io14 ··-o,·--out-file=(required,·output);·io
15 ······output·vector·field·.·For·supported·file·types·see·Plugin_type:15 ······output·vector·field·.·For·supported·file·types·see·Plugin_type:
16 ······3dtransform/io16 ······3dtransform/io
17 ··-k,·--imgkernel=bspline:d=3;·factory17 ··-k,·--imgkernel=bspline:d=3;·factory
18 ······image·interpolator·kernel·which·is·used·when·the·transformation·is18 ······image·interpolator·kernel·which·is·used·when·the·transformation·is
19 ······applied·to·an·image.·For·supported·plug-ins·see·Plugin_type:_1d/19 ······applied·to·an·image.·For·supported·plug-ins·see·Plugin_type:_1d/
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dvfcompare</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dvf2transform.html"·title="mia-3dvf2transform"><link·rel="next"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dvfcompare</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dvf2transform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof3Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dvfcompare"></a>mia-3dvfcompare</h3></div></div></div><h4><a·name="idp12770"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dvfcompare</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-3dvfcompare</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecRegistrationComparisonandTransformationof3Dimages.html"·title="Registration,·Comparison,·and·Transformation·of·3D·images"><link·rel="prev"·href="Secmia3dvf2transform.html"·title="mia-3dvf2transform"><link·rel="next"·href="SecRegistrationofseriesof3Dimages.html"·title="Registration·of·series·of·3D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-3dvfcompare</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dvf2transform.html">Prev</a> </td><th·width="60%"·align="center">Registration,·Comparison,·and·Transformation·of·3D·images</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof3Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmia3dvfcompare"></a>mia-3dvfcompare</h3></div></div></div><h4><a·name="idp12770"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-3dvfcompare</code>··{-1·<em·class="replaceable"><code>io</code></em>}·{-2·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp12779"></a>Description:</h4><p·class="description">Compare·two·vector·fields·and·print·the·out·the·difference·norm·per·pixel·to·cout·it·it·is·larger·than·delta.</p><h4><a·name="idp12781"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--in-file-1=(input,·required);·io</span></dt><dd><p>input·vector·field·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-2,·--in-file-2=(input,·required);·io</span></dt><dd><p>input·vector·field·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-d,·--delta=0;·float</span></dt><dd><p>Maximum·difference·between·vector·to·be·ignored</p></dd></dl></div><h4><a·name="idp12797"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12848"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12854"></a>Example:</h4><p>Compare·vector·fields·vf1.v·and·vf2.v·and·print·out·all·differences·above·0.01.</p><pre·class="screen">mia-3dvfcompare·-1·vf1.v·-2·vf2.v·-d·0.01</pre><h4><a·name="idp12857"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dvf2transform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof3Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dvf2transform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration·of·series·of·3D·images</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp12779"></a>Description:</h4><p·class="description">Compare·two·vector·fields·and·print·the·out·the·difference·norm·per·pixel·to·cout·it·it·is·larger·than·delta.</p><h4><a·name="idp12781"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-1,·--in-file-1=(required,·input);·io</span></dt><dd><p>input·vector·field·1.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-2,·--in-file-2=(required,·input);·io</span></dt><dd><p>input·vector·field·2.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dvfio.html"·title="Plugin·type:·3dvf/io">Plugin·type:·3dvf/io</a></p></dd><dt><span·class="term">-d,·--delta=0;·float</span></dt><dd><p>Maximum·difference·between·vector·to·be·ignored</p></dd></dl></div><h4><a·name="idp12797"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp12848"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp12854"></a>Example:</h4><p>Compare·vector·fields·vf1.v·and·vf2.v·and·print·out·all·differences·above·0.01.</p><pre·class="screen">mia-3dvfcompare·-1·vf1.v·-2·vf2.v·-d·0.01</pre><h4><a·name="idp12857"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dvf2transform.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecRegistrationComparisonandTransformationof3Dimages.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecRegistrationofseriesof3Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dvf2transform </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Registration·of·series·of·3D·images</td></tr></table></div></body></html>
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4 mia-3dvfcompare4 mia-3dvfcompare
5 Sysnopis:5 Sysnopis:
6 mia-3dvfcompare·{-1·io}·{-2·io}·[·options·...]6 mia-3dvfcompare·{-1·io}·{-2·io}·[·options·...]
7 Description:7 Description:
8 Compare·two·vector·fields·and·print·the·out·the·difference·norm·per·pixel·to8 Compare·two·vector·fields·and·print·the·out·the·difference·norm·per·pixel·to
9 cout·it·it·is·larger·than·delta.9 cout·it·it·is·larger·than·delta.
10 Options:10 Options:
11 ··-1,·--in-file-1=(input,·required);·io11 ··-1,·--in-file-1=(required,·input);·io
12 ······input·vector·field·1.·For·supported·file·types·see·Plugin_type:_3dvf/io12 ······input·vector·field·1.·For·supported·file·types·see·Plugin_type:_3dvf/io
13 ··-2,·--in-file-2=(input,·required);·io13 ··-2,·--in-file-2=(required,·input);·io
14 ······input·vector·field·2.·For·supported·file·types·see·Plugin_type:_3dvf/io14 ······input·vector·field·2.·For·supported·file·types·see·Plugin_type:_3dvf/io
15 ··-d,·--delta=0;·float15 ··-d,·--delta=0;·float
16 ······Maximum·difference·between·vector·to·be·ignored16 ······Maximum·difference·between·vector·to·be·ignored
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
20 ······Supported·priorities·starting·at·lowest·level·are:20 ······Supported·priorities·starting·at·lowest·level·are:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmia3dvectorfieldcreate.html"·title="mia-3dvectorfieldcreate"><link·rel="next"·href="Secmiafilenumberpattern.html"·title="mia-filenumberpattern"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dvectorfieldcreate.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiafilenumberpattern.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiacmeans"></a>mia-cmeans</h3></div></div></div><h4><a·name="idp14026"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-cmeans</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-cmeans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmia3dvectorfieldcreate.html"·title="mia-3dvectorfieldcreate"><link·rel="next"·href="Secmiafilenumberpattern.html"·title="mia-filenumberpattern"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-cmeans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dvectorfieldcreate.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiafilenumberpattern.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiacmeans"></a>mia-cmeans</h3></div></div></div><h4><a·name="idp14026"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-cmeans</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14035"></a>Description:</h4><p·class="description">This·Program·reads·a·histogram·from·stdin·and·evaluates·a·cmeans·classification·of·the·intensity·values·into·the·given·number·of·classes.</p><h4><a·name="idp14037"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·file·name·containing·the·histogram</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name·to·store·probabilities</p></dd><dt><span·class="term">-n,·--nclasses=3;·int</span></dt><dd><p>number·of·classes·to·partition·into</p></dd><dt><span·class="term">-m,·--max-iter=100;·int</span></dt><dd><p>maximum·number·of·iterations</p></dd><dt><span·class="term">-e,·--even-start</span></dt><dd><p>start·with·centers·evenly·distributed·over·the·histogram</p></dd><dt><span·class="term">-c,·--class-centers=</span></dt><dd><p>initial·class·centers</p></dd><dt><span·class="term">-a,·--auto</span></dt><dd><p>atomatic·adaption·of·variance·(experimental)</p></dd><dt><span·class="term">-t,·--cut-histo</span></dt><dd><p>cut·empty·histogram·at·the·end·</p></dd><dt><span·class="term">-k,·--variance=1;·double</span></dt><dd><p>variance·parameter</p></dd><dt><span·class="term">--self-test</span></dt><dd><p>run·self·test</p></dd></dl></div><h4><a·name="idp14079"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14130"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14136"></a>Example:</h4><p>3 ········...]</p></div><h4><a·name="idp14035"></a>Description:</h4><p·class="description">This·Program·reads·a·histogram·from·stdin·and·evaluates·a·cmeans·classification·of·the·intensity·values·into·the·given·number·of·classes.</p><h4><a·name="idp14037"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·file·name·containing·the·histogram</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name·to·store·probabilities</p></dd><dt><span·class="term">-n,·--nclasses=3;·int</span></dt><dd><p>number·of·classes·to·partition·into</p></dd><dt><span·class="term">-m,·--max-iter=100;·int</span></dt><dd><p>maximum·number·of·iterations</p></dd><dt><span·class="term">-e,·--even-start</span></dt><dd><p>start·with·centers·evenly·distributed·over·the·histogram</p></dd><dt><span·class="term">-c,·--class-centers=</span></dt><dd><p>initial·class·centers</p></dd><dt><span·class="term">-a,·--auto</span></dt><dd><p>atomatic·adaption·of·variance·(experimental)</p></dd><dt><span·class="term">-t,·--cut-histo</span></dt><dd><p>cut·empty·histogram·at·the·end·</p></dd><dt><span·class="term">-k,·--variance=1;·double</span></dt><dd><p>variance·parameter</p></dd><dt><span·class="term">--self-test</span></dt><dd><p>run·self·test</p></dd></dl></div><h4><a·name="idp14079"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14130"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14136"></a>Example:</h4><p>
4 ····</p><pre·class="screen">mia-cmeans·</pre><h4><a·name="idp14139"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dvectorfieldcreate.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiafilenumberpattern.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dvectorfieldcreate </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-filenumberpattern</td></tr></table></div></body></html>4 ····</p><pre·class="screen">mia-cmeans·</pre><h4><a·name="idp14139"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dvectorfieldcreate.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiafilenumberpattern.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dvectorfieldcreate </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-filenumberpattern</td></tr></table></div></body></html>
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4 mia-cmeans4 mia-cmeans
5 Sysnopis:5 Sysnopis:
6 mia-cmeans·{-i·string}·{-o·string}·[·options·...]6 mia-cmeans·{-i·string}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·Program·reads·a·histogram·from·stdin·and·evaluates·a·cmeans·classification8 This·Program·reads·a·histogram·from·stdin·and·evaluates·a·cmeans·classification
9 of·the·intensity·values·into·the·given·number·of·classes.9 of·the·intensity·values·into·the·given·number·of·classes.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·string11 ··-i,·--in-file=(required,·input);·string
12 ······input·file·name·containing·the·histogram12 ······input·file·name·containing·the·histogram
13 ··-o,·--out-file=(required,·output);·string13 ··-o,·--out-file=(required,·output);·string
14 ······output·file·name·to·store·probabilities14 ······output·file·name·to·store·probabilities
15 ··-n,·--nclasses=3;·int15 ··-n,·--nclasses=3;·int
16 ······number·of·classes·to·partition·into16 ······number·of·classes·to·partition·into
17 ··-m,·--max-iter=100;·int17 ··-m,·--max-iter=100;·int
18 ······maximum·number·of·iterations18 ······maximum·number·of·iterations
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./usr/share/doc/mia-2.4/userref/Secmiafilenumberpattern.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-filenumberpattern</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmiacmeans.html"·title="mia-cmeans"><link·rel="next"·href="Secmialabelsort.html"·title="mia-labelsort"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-filenumberpattern</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiacmeans.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmialabelsort.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiafilenumberpattern"></a>mia-filenumberpattern</h3></div></div></div><h4><a·name="idp14143"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-filenumberpattern</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-filenumberpattern</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmiacmeans.html"·title="mia-cmeans"><link·rel="next"·href="Secmialabelsort.html"·title="mia-labelsort"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-filenumberpattern</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiacmeans.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmialabelsort.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiafilenumberpattern"></a>mia-filenumberpattern</h3></div></div></div><h4><a·name="idp14143"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-filenumberpattern</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14150"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·a·extract·the·number·pattern·for·file012312.ext·type·file·names.</p><h4><a·name="idp14152"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·image·example·name</p></dd></dl></div><h4><a·name="idp14158"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14209"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14215"></a>Example:</h4><p>3 ········...]</p></div><h4><a·name="idp14150"></a>Description:</h4><p·class="description">This·program·is·used·to·extract·a·extract·the·number·pattern·for·file012312.ext·type·file·names.</p><h4><a·name="idp14152"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·image·example·name</p></dd></dl></div><h4><a·name="idp14158"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14209"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14215"></a>Example:</h4><p>
4 ····</p><pre·class="screen">mia-filenumberpattern·</pre><h4><a·name="idp14218"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiacmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmialabelsort.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-cmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-labelsort</td></tr></table></div></body></html>4 ····</p><pre·class="screen">mia-filenumberpattern·</pre><h4><a·name="idp14218"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiacmeans.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmialabelsort.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-cmeans </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-labelsort</td></tr></table></div></body></html>
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4 mia-filenumberpattern4 mia-filenumberpattern
5 Sysnopis:5 Sysnopis:
6 mia-filenumberpattern·{-i·string}·[·options·...]6 mia-filenumberpattern·{-i·string}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·extract·a·extract·the·number·pattern·for·file012312.ext8 This·program·is·used·to·extract·a·extract·the·number·pattern·for·file012312.ext
9 type·file·names.9 type·file·names.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·string11 ··-i,·--in-file=(required,·input);·string
12 ······input·image·example·name12 ······input·image·example·name
13 Help·&·Info13 Help·&·Info
14 ··-V,·--verbose=warning;·dict14 ··-V,·--verbose=warning;·dict
15 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.15 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
16 ······Supported·priorities·starting·at·lowest·level·are:16 ······Supported·priorities·starting·at·lowest·level·are:
17 ······trace:···Function·call·trace17 ······trace:···Function·call·trace
18 ······debug:···Debug·output18 ······debug:···Debug·output
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./usr/share/doc/mia-2.4/userref/Secmialabelsort.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-labelsort</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmiafilenumberpattern.html"·title="mia-filenumberpattern"><link·rel="next"·href="Secmiamyowavelettest.html"·title="mia-myowavelettest"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-labelsort</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiafilenumberpattern.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiamyowavelettest.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmialabelsort"></a>mia-labelsort</h3></div></div></div><h4><a·name="idp14222"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-labelsort</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-labelsort</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmiafilenumberpattern.html"·title="mia-filenumberpattern"><link·rel="next"·href="Secmiamyowavelettest.html"·title="mia-myowavelettest"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-labelsort</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiafilenumberpattern.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiamyowavelettest.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmialabelsort"></a>mia-labelsort</h3></div></div></div><h4><a·name="idp14222"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-labelsort</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14231"></a>Description:</h4><p·class="description">This·program·is·used·create·a·mapping·based·on·a·histogram·that·puts·the·intensities·with·high·values·at·the·beginning·of·the·histogram.·The·main·use·case·will·be·to·sort·labels·of·connected·components·in·out-of-core·image·processing.</p><h4><a·name="idp14233"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·file·name·containing·the·histogram</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name·to·store·probabilities</p></dd></dl></div><h4><a·name="idp14243"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14294"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14300"></a>Example:</h4><p>3 ········...]</p></div><h4><a·name="idp14231"></a>Description:</h4><p·class="description">This·program·is·used·create·a·mapping·based·on·a·histogram·that·puts·the·intensities·with·high·values·at·the·beginning·of·the·histogram.·The·main·use·case·will·be·to·sort·labels·of·connected·components·in·out-of-core·image·processing.</p><h4><a·name="idp14233"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·file·name·containing·the·histogram</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·file·name·to·store·probabilities</p></dd></dl></div><h4><a·name="idp14243"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14294"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14300"></a>Example:</h4><p>
4 ····</p><pre·class="screen">mia-labelsort·</pre><h4><a·name="idp14303"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiafilenumberpattern.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiamyowavelettest.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-filenumberpattern </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-myowavelettest</td></tr></table></div></body></html>4 ····</p><pre·class="screen">mia-labelsort·</pre><h4><a·name="idp14303"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiafilenumberpattern.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiamyowavelettest.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-filenumberpattern </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-myowavelettest</td></tr></table></div></body></html>
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6 mia-labelsort·{-i·string}·{-o·string}·[·options·...]6 mia-labelsort·{-i·string}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·create·a·mapping·based·on·a·histogram·that·puts·the8 This·program·is·used·create·a·mapping·based·on·a·histogram·that·puts·the
9 intensities·with·high·values·at·the·beginning·of·the·histogram.·The·main·use9 intensities·with·high·values·at·the·beginning·of·the·histogram.·The·main·use
10 case·will·be·to·sort·labels·of·connected·components·in·out-of-core·image10 case·will·be·to·sort·labels·of·connected·components·in·out-of-core·image
11 processing.11 processing.
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·string13 ··-i,·--in-file=(required,·input);·string
14 ······input·file·name·containing·the·histogram14 ······input·file·name·containing·the·histogram
15 ··-o,·--out-file=(required,·output);·string15 ··-o,·--out-file=(required,·output);·string
16 ······output·file·name·to·store·probabilities16 ······output·file·name·to·store·probabilities
17 Help·&·Info17 Help·&·Info
18 ··-V,·--verbose=warning;·dict18 ··-V,·--verbose=warning;·dict
19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.19 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
20 ······Supported·priorities·starting·at·lowest·level·are:20 ······Supported·priorities·starting·at·lowest·level·are:
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-mesh-deformable-model</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="Secmia3disosurfacefromvolume.html"·title="mia-3disosurface-from-volume"><link·rel="next"·href="Secmiameshtomaskimage.html"·title="mia-mesh-to-maskimage"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-mesh-deformable-model</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromvolume.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshtomaskimage.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiameshdeformablemodel"></a>mia-mesh-deformable-model</h3></div></div></div><h4><a·name="idp14649"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-mesh-deformable-model</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-mesh-deformable-model</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="Secmia3disosurfacefromvolume.html"·title="mia-3disosurface-from-volume"><link·rel="next"·href="Secmiameshtomaskimage.html"·title="mia-mesh-to-maskimage"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-mesh-deformable-model</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromvolume.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshtomaskimage.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiameshdeformablemodel"></a>mia-mesh-deformable-model</h3></div></div></div><h4><a·name="idp14649"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-mesh-deformable-model</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14660"></a>Description:</h4><p·class="description">This·program·runs·a·deformable·model·to·adapt·a·mesh·to·an·iso-value·within·a·given·image.·&lt;FIXME:·Reference&gt;</p><h4><a·name="idp14662"></a>Options:</h4><h4><a·name="idp14663"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·mesh·to·be·adapted.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·out[·...·truncated·by·diffoscope;·len:·256,·SHA:·758ad1e738c780bd6a7fa304dda8ee9f9ed9365487987aa6734e98989a1b41ca·...·]);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp14680"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14731"></a>Model·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--smoothing-weight=0.04;·float·in·[0,·inf)</span></dt><dd><p>Weight·of·the·inner·force·used·to·smooth·the·mesh</p></dd><dt><span·class="term">--gradient-weight=0.04;·float</span></dt><dd><p>Weight·of·the·gradient·force·drive·the·mesh·deformation.·Use·a·negative·value·to·invert·the·search·direction.</p></dd><dt><span·class="term">--intensity-weight=0.02;·float·in·[0,·inf)</span></dt><dd><p>Weight·of·the·force·resulting·from·the·intensity·difference·at·the·vertex·position·versus·the·reference·intensity·'iso'.</p></dd><dt><span·class="term">--intensity-scaling=1;·float·in·(0,·inf)</span></dt><dd><p>Scaling·of·the·raw·intensity·difference.</p></dd><dt><span·class="term">-s,·--iso=64;·float</span></dt><dd><p>Intensity·value·the·mesh·verices·should·adapt·to.</p></dd></dl></div><h4><a·name="idp14753"></a>Preprocessing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--image-smoothing=gauss:w=2;·factory</span></dt><dd><p>Prefilter·to·smooth·the·reference·image..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a></p></dd></dl></div><h4><a·name="idp14760"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd><dt><span·class="term">-m,·--maxiter=200;·uint·in·(0,·inf)</span></dt><dd><p>Maximum·number·of·iterations.</p></dd><dt><span·class="term">-e,·--epsilon=0.001;·float·in·(0,·inf)</span></dt><dd><p>Stop·iteration·when·the·maximum·shift·of·the·vertices·falls·below·this·value</p></dd><dt><span·class="term">--reorient</span></dt><dd><p>Reorientate·the·mesh·triangles</p></dd></dl></div><h4><a·name="idp14778"></a>Example:</h4><p>Run·the·deforemable·model·on·input.vmesh·with·200·iterations·adapting·to·a·value·of·128·in·the·image·ref.v·and·save·the·result·to·deformed.vmesh</p><pre·class="screen">mia-mesh-deformable-model·-i·input.vmesh·-o·deformed.vmesh·--iso·128·--maxiter·200</pre><h4><a·name="idp14781"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromvolume.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshtomaskimage.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3disosurface-from-volume </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-mesh-to-maskimage</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp14660"></a>Description:</h4><p·class="description">This·program·runs·a·deformable·model·to·adapt·a·mesh·to·an·iso-value·within·a·given·image.·&lt;FIXME:·Reference&gt;</p><h4><a·name="idp14662"></a>Options:</h4><h4><a·name="idp14663"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·mesh·to·be·adapted.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·out[·...·truncated·by·diffoscope;·len:·256,·SHA:·53316edcef87d49a2cf04d5ba7e9fbf718fcc1dc7a7a2e68d672cba2b5841e93·...·]);·io</span></dt><dd><p>reference·image.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp14680"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14731"></a>Model·parameters</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--smoothing-weight=0.04;·float·in·[0,·inf)</span></dt><dd><p>Weight·of·the·inner·force·used·to·smooth·the·mesh</p></dd><dt><span·class="term">--gradient-weight=0.04;·float</span></dt><dd><p>Weight·of·the·gradient·force·drive·the·mesh·deformation.·Use·a·negative·value·to·invert·the·search·direction.</p></dd><dt><span·class="term">--intensity-weight=0.02;·float·in·[0,·inf)</span></dt><dd><p>Weight·of·the·force·resulting·from·the·intensity·difference·at·the·vertex·position·versus·the·reference·intensity·'iso'.</p></dd><dt><span·class="term">--intensity-scaling=1;·float·in·(0,·inf)</span></dt><dd><p>Scaling·of·the·raw·intensity·difference.</p></dd><dt><span·class="term">-s,·--iso=64;·float</span></dt><dd><p>Intensity·value·the·mesh·verices·should·adapt·to.</p></dd></dl></div><h4><a·name="idp14753"></a>Preprocessing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--image-smoothing=gauss:w=2;·factory</span></dt><dd><p>Prefilter·to·smooth·the·reference·image..·For·supported·plug-ins·see·<a·class="xref"·href="SecPlugintype3dimagefilter.html"·title="Plugin·type:·3dimage/filter">Plugin·type:·3dimage/filter</a></p></dd></dl></div><h4><a·name="idp14760"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd><dt><span·class="term">-m,·--maxiter=200;·uint·in·(0,·inf)</span></dt><dd><p>Maximum·number·of·iterations.</p></dd><dt><span·class="term">-e,·--epsilon=0.001;·float·in·(0,·inf)</span></dt><dd><p>Stop·iteration·when·the·maximum·shift·of·the·vertices·falls·below·this·value</p></dd><dt><span·class="term">--reorient</span></dt><dd><p>Reorientate·the·mesh·triangles</p></dd></dl></div><h4><a·name="idp14778"></a>Example:</h4><p>Run·the·deforemable·model·on·input.vmesh·with·200·iterations·adapting·to·a·value·of·128·in·the·image·ref.v·and·save·the·result·to·deformed.vmesh</p><pre·class="screen">mia-mesh-deformable-model·-i·input.vmesh·-o·deformed.vmesh·--iso·128·--maxiter·200</pre><h4><a·name="idp14781"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3disosurfacefromvolume.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshtomaskimage.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3disosurface-from-volume </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-mesh-to-maskimage</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-mesh-deformable-model·{-i·io}·{-o·io}·{-r·io}·[·options·...]6 mia-mesh-deformable-model·{-i·io}·{-o·io}·{-r·io}·[·options·...]
7 Description:7 Description:
8 This·program·runs·a·deformable·model·to·adapt·a·mesh·to·an·iso-value·within·a8 This·program·runs·a·deformable·model·to·adapt·a·mesh·to·an·iso-value·within·a
9 given·image.·<FIXME:·Reference>9 given·image.·<FIXME:·Reference>
10 Options:10 Options:
11 File·I/O11 File·I/O
12 ··-i,·--in-file=(input,·required);·io12 ··-i,·--in-file=(required,·input);·io
13 ······input·mesh·to·be·adapted.·For·supported·file·types·see·Plugin_type:_mesh/13 ······input·mesh·to·be·adapted.·For·supported·file·types·see·Plugin_type:_mesh/
14 ······io14 ······io
15 ··-o,·--out-file=(required,·output);·io15 ··-o,·--out-file=(required,·output);·io
16 ······output·mesh·that·has·been·deformed.·For·supported·file·types·see·Plugin16 ······output·mesh·that·has·been·deformed.·For·supported·file·types·see·Plugin
17 ······type:_mesh/io17 ······type:_mesh/io
18 ··-r,·--ref-file=(input,·required);·io18 ··-r,·--ref-file=(required,·input);·io
19 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io19 ······reference·image.·For·supported·file·types·see·Plugin_type:_3dimage/io
20 Help·&·Info20 Help·&·Info
21 ··-V,·--verbose=warning;·dict21 ··-V,·--verbose=warning;·dict
22 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.22 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
23 ······Supported·priorities·starting·at·lowest·level·are:23 ······Supported·priorities·starting·at·lowest·level·are:
24 ······trace:···Function·call·trace24 ······trace:···Function·call·trace
25 ······debug:···Debug·output25 ······debug:···Debug·output
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-meshdistance-to-stackmask</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="Secmiameshtomaskimage.html"·title="mia-mesh-to-maskimage"><link·rel="next"·href="Secmiameshfilter.html"·title="mia-meshfilter"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-meshdistance-to-stackmask</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiameshtomaskimage.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshfilter.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiameshdistancetostackmask"></a>mia-meshdistance-to-stackmask</h3></div></div></div><h4><a·name="idp14887"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-meshdistance-to-stackmask</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-meshdistance-to-stackmask</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="Secmiameshtomaskimage.html"·title="mia-mesh-to-maskimage"><link·rel="next"·href="Secmiameshfilter.html"·title="mia-meshfilter"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-meshdistance-to-stackmask</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiameshtomaskimage.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshfilter.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiameshdistancetostackmask"></a>mia-meshdistance-to-stackmask</h3></div></div></div><h4><a·name="idp14887"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-meshdistance-to-stackmask</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-r·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14898"></a>Description:</h4><p·class="description">This·program·takes·a·binary·masks·and·a·triangular·mesh·as·input·and·evaluates·the·distance·of·the·mesh·vertices·to·the·binary·maskand·stores·the·result·in·a·new·mesh.</p><h4><a·name="idp14900"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-mesh=(input,·required);·io</span></dt><dd><p>input·mesh.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-r,·--ref-mask=(input,·required);·io</span></dt><dd><p>reference·binary·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-mesh=(required,·output);·io</span></dt><dd><p>output·mesh.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd></dl></div><h4><a·name="idp14917"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14968"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14974"></a>Example:</h4><p>Evaluate·the·distance·of·the·mask·given·in·the·images·maskXXXX.png·to·the·mesh·given·in·mesh.v·and·save·the·result·to·mesh-dist.v</p><pre·class="screen">mia-meshdistance-to-stackmask·-i·mesh.v·-r·maskXXXX.png·-o·mesh-dist.v</pre><h4><a·name="idp14977"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiameshtomaskimage.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshfilter.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-mesh-to-maskimage </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-meshfilter</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp14898"></a>Description:</h4><p·class="description">This·program·takes·a·binary·masks·and·a·triangular·mesh·as·input·and·evaluates·the·distance·of·the·mesh·vertices·to·the·binary·maskand·stores·the·result·in·a·new·mesh.</p><h4><a·name="idp14900"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-mesh=(required,·input);·io</span></dt><dd><p>input·mesh.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-r,·--ref-mask=(required,·input);·io</span></dt><dd><p>reference·binary·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-mesh=(required,·output);·io</span></dt><dd><p>output·mesh.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd></dl></div><h4><a·name="idp14917"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14968"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14974"></a>Example:</h4><p>Evaluate·the·distance·of·the·mask·given·in·the·images·maskXXXX.png·to·the·mesh·given·in·mesh.v·and·save·the·result·to·mesh-dist.v</p><pre·class="screen">mia-meshdistance-to-stackmask·-i·mesh.v·-r·maskXXXX.png·-o·mesh-dist.v</pre><h4><a·name="idp14977"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiameshtomaskimage.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshfilter.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-mesh-to-maskimage </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-meshfilter</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-meshdistance-to-stackmask·{-i·io}·{-r·io}·{-o·io}·[·options·...]6 mia-meshdistance-to-stackmask·{-i·io}·{-r·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·takes·a·binary·masks·and·a·triangular·mesh·as·input·and·evaluates8 This·program·takes·a·binary·masks·and·a·triangular·mesh·as·input·and·evaluates
9 the·distance·of·the·mesh·vertices·to·the·binary·maskand·stores·the·result·in·a9 the·distance·of·the·mesh·vertices·to·the·binary·maskand·stores·the·result·in·a
10 new·mesh.10 new·mesh.
11 Options:11 Options:
12 ··-i,·--in-mesh=(input,·required);·io12 ··-i,·--in-mesh=(required,·input);·io
13 ······input·mesh.·For·supported·file·types·see·Plugin_type:_mesh/io13 ······input·mesh.·For·supported·file·types·see·Plugin_type:_mesh/io
14 ··-r,·--ref-mask=(input,·required);·io14 ··-r,·--ref-mask=(required,·input);·io
15 ······reference·binary·mask.·For·supported·file·types·see·Plugin_type:_2dimage/15 ······reference·binary·mask.·For·supported·file·types·see·Plugin_type:_2dimage/
16 ······io16 ······io
17 ··-o,·--out-mesh=(required,·output);·io17 ··-o,·--out-mesh=(required,·output);·io
18 ······output·mesh.·For·supported·file·types·see·Plugin_type:_mesh/io18 ······output·mesh.·For·supported·file·types·see·Plugin_type:_mesh/io
19 Help·&·Info19 Help·&·Info
20 ··-V,·--verbose=warning;·dict20 ··-V,·--verbose=warning;·dict
21 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.21 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
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2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]·[3 ········...]·[
4 ··········<em·class="replaceable"><code>4 ··········<em·class="replaceable"><code>
5 ············<a·class="xref"·href="SecPlugintypemeshfilter.html"·title="Plugin·type:·mesh/filter">Plugin·type:·mesh/filter</a>5 ············<a·class="xref"·href="SecPlugintypemeshfilter.html"·title="Plugin·type:·mesh/filter">Plugin·type:·mesh/filter</a>
6 ··········</code></em>6 ··········</code></em>
7 ········...]</p></div><h4><a·name="idp14993"></a>Description:</h4><p·class="description">This·program·runs·a·series·filters·on·a·given·input·mesh.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run7 ········...]</p></div><h4><a·name="idp14993"></a>Description:</h4><p·class="description">This·program·runs·a·series·filters·on·a·given·input·mesh.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run
8 ···'mia-plugin-help·mesh/filter'8 ···'mia-plugin-help·mesh/filter'
9 from·the·command·line</p><h4><a·name="idp14995"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·mesh·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mesh·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd></dl></div><h4><a·name="idp15007"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp15058"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp15064"></a>Example:</h4><p>Run·an·isotropic·scaling·on·input.vmesh·to·fit·it·into·the·box·defined·by·the·corners·&lt;0,0,0&gt;·-·&lt;128,128,128&gt;·and·save·the·result·to·output.vmesh</p><pre·class="screen">mia-meshfilter·-i·input.vmesh·-o·output.vmesh·scale:strategy=iso-fitbox,box-start=[&lt;0,0,0&gt;],box-end=[&lt;128,128,128&gt;]</pre><h4><a·name="idp15067"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiameshdistancetostackmask.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecHelp.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-meshdistance-to-stackmask </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Help</td></tr></table></div></body></html>9 from·the·command·line</p><h4><a·name="idp14995"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·mesh·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·mesh·that·have·been·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd></dl></div><h4><a·name="idp15007"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp15058"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp15064"></a>Example:</h4><p>Run·an·isotropic·scaling·on·input.vmesh·to·fit·it·into·the·box·defined·by·the·corners·&lt;0,0,0&gt;·-·&lt;128,128,128&gt;·and·save·the·result·to·output.vmesh</p><pre·class="screen">mia-meshfilter·-i·input.vmesh·-o·output.vmesh·scale:strategy=iso-fitbox,box-start=[&lt;0,0,0&gt;],box-end=[&lt;128,128,128&gt;]</pre><h4><a·name="idp15067"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiameshdistancetostackmask.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecHelp.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-meshdistance-to-stackmask </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Help</td></tr></table></div></body></html>
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6 mia-meshfilter·{-i·io}·{-o·io}·[·options·...]·[·Plugin_type:_mesh/filter·...]6 mia-meshfilter·{-i·io}·{-o·io}·[·options·...]·[·Plugin_type:_mesh/filter·...]
7 Description:7 Description:
8 This·program·runs·a·series·filters·on·a·given·input·mesh.·The·filters·are·given8 This·program·runs·a·series·filters·on·a·given·input·mesh.·The·filters·are·given
9 as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they9 as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they
10 are·given.·To·obtain·a·list·of·available·filters·you·may·run·'mia-plugin-help10 are·given.·To·obtain·a·list·of·available·filters·you·may·run·'mia-plugin-help
11 mesh/filter'·from·the·command·line11 mesh/filter'·from·the·command·line
12 Options:12 Options:
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·mesh·to·be·filtered.·For·supported·file·types·see·Plugin_type:14 ······input·mesh·to·be·filtered.·For·supported·file·types·see·Plugin_type:
15 ······mesh/io15 ······mesh/io
16 ··-o,·--out-file=(required,·output);·io16 ··-o,·--out-file=(required,·output);·io
17 ······output·mesh·that·have·been·filtered.·For·supported·file·types·see·Plugin17 ······output·mesh·that·have·been·filtered.·For·supported·file·types·see·Plugin
18 ······type:_mesh/io18 ······type:_mesh/io
19 Help·&·Info19 Help·&·Info
20 ··-V,·--verbose=warning;·dict20 ··-V,·--verbose=warning;·dict
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-mesh-to-maskimage</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="Secmiameshdeformablemodel.html"·title="mia-mesh-deformable-model"><link·rel="next"·href="Secmiameshdistancetostackmask.html"·title="mia-meshdistance-to-stackmask"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-mesh-to-maskimage</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiameshdeformablemodel.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshdistancetostackmask.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiameshtomaskimage"></a>mia-mesh-to-maskimage</h3></div></div></div><h4><a·name="idp14785"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-mesh-to-maskimage</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-mesh-to-maskimage</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"><link·rel="prev"·href="Secmiameshdeformablemodel.html"·title="mia-mesh-deformable-model"><link·rel="next"·href="Secmiameshdistancetostackmask.html"·title="mia-meshdistance-to-stackmask"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-mesh-to-maskimage</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiameshdeformablemodel.html">Prev</a> </td><th·width="60%"·align="center">Creation,·analysis,·and·filtering·of·triangular·3D·meshes</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiameshdistancetostackmask.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiameshtomaskimage"></a>mia-mesh-to-maskimage</h3></div></div></div><h4><a·name="idp14785"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-mesh-to-maskimage</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14794"></a>Description:</h4><p·class="description">This·program·converts·a·3D·mesh·into·a·binary·mask·comprising·the·mesh·surface.·The·output·image·size·is·either·given·on·the·command·line·or·deducted·from·the·mesh·dimensions.</p><h4><a·name="idp14796"></a>Options:</h4><h4><a·name="idp14797"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·mesh·to·be·adapted.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·containing·the·binary·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp14809"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14860"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14866"></a>Properties</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--origin=[0,0,0];·3dfvector</span></dt><dd><p>coordinate·of·pixel·at·index·0,0,0</p></dd><dt><span·class="term">--spacing=[1,1,1];·3dfvector</span></dt><dd><p>voxel·spacing·in·the·output·image,·all·values·must·be·positive.</p></dd><dt><span·class="term">--size=[0,0,0];·3dbounds</span></dt><dd><p>size·of·the·output·image·(0,0,0·=·deduct)</p></dd></dl></div><h4><a·name="idp14880"></a>Example:</h4><p>The·input·mesh·input.vmesh·is·converted·into·the·binary·mask·mask.v.·The·image·size·is·set·to·50,50,50·and·the·size·is·obtained·automatically·to·include·the·whole·mesh</p><pre·class="screen">mia-mesh-to-maskimage·-i·input.vmesh·-o·mask.v·--origin·0,0,0</pre><h4><a·name="idp14883"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiameshdeformablemodel.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshdistancetostackmask.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-mesh-deformable-model </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-meshdistance-to-stackmask</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp14794"></a>Description:</h4><p·class="description">This·program·converts·a·3D·mesh·into·a·binary·mask·comprising·the·mesh·surface.·The·output·image·size·is·either·given·on·the·command·line·or·deducted·from·the·mesh·dimensions.</p><h4><a·name="idp14796"></a>Options:</h4><h4><a·name="idp14797"></a>File·I/O</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·mesh·to·be·adapted.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintypemeshio.html"·title="Plugin·type:·mesh/io">Plugin·type:·mesh/io</a></p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·image·containing·the·binary·mask.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd></dl></div><h4><a·name="idp14809"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14860"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14866"></a>Properties</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--origin=[0,0,0];·3dfvector</span></dt><dd><p>coordinate·of·pixel·at·index·0,0,0</p></dd><dt><span·class="term">--spacing=[1,1,1];·3dfvector</span></dt><dd><p>voxel·spacing·in·the·output·image,·all·values·must·be·positive.</p></dd><dt><span·class="term">--size=[0,0,0];·3dbounds</span></dt><dd><p>size·of·the·output·image·(0,0,0·=·deduct)</p></dd></dl></div><h4><a·name="idp14880"></a>Example:</h4><p>The·input·mesh·input.vmesh·is·converted·into·the·binary·mask·mask.v.·The·image·size·is·set·to·50,50,50·and·the·size·is·obtained·automatically·to·include·the·whole·mesh</p><pre·class="screen">mia-mesh-to-maskimage·-i·input.vmesh·-o·mask.v·--origin·0,0,0</pre><h4><a·name="idp14883"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiameshdeformablemodel.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiameshdistancetostackmask.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-mesh-deformable-model </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-meshdistance-to-stackmask</td></tr></table></div></body></html>
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6 mia-mesh-to-maskimage·{-i·io}·{-o·io}·[·options·...]6 mia-mesh-to-maskimage·{-i·io}·{-o·io}·[·options·...]
7 Description:7 Description:
8 This·program·converts·a·3D·mesh·into·a·binary·mask·comprising·the·mesh·surface.8 This·program·converts·a·3D·mesh·into·a·binary·mask·comprising·the·mesh·surface.
9 The·output·image·size·is·either·given·on·the·command·line·or·deducted·from·the9 The·output·image·size·is·either·given·on·the·command·line·or·deducted·from·the
10 mesh·dimensions.10 mesh·dimensions.
11 Options:11 Options:
12 File·I/O12 File·I/O
13 ··-i,·--in-file=(input,·required);·io13 ··-i,·--in-file=(required,·input);·io
14 ······input·mesh·to·be·adapted.·For·supported·file·types·see·Plugin_type:_mesh/14 ······input·mesh·to·be·adapted.·For·supported·file·types·see·Plugin_type:_mesh/
15 ······io15 ······io
16 ··-o,·--out-file=(required,·output);·io16 ··-o,·--out-file=(required,·output);·io
17 ······output·image·containing·the·binary·mask.·For·supported·file·types·see17 ······output·image·containing·the·binary·mask.·For·supported·file·types·see
18 ······Plugin_type:_3dimage/io18 ······Plugin_type:_3dimage/io
19 Help·&·Info19 Help·&·Info
20 ··-V,·--verbose=warning;·dict20 ··-V,·--verbose=warning;·dict
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./usr/share/doc/mia-2.4/userref/Secmiamultihist.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-multihist</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia3ddistance.html"·title="mia-3ddistance"><link·rel="next"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-multihist</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3ddistance.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiamultihist"></a>mia-multihist</h3></div></div></div><h4><a·name="idp8963"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-multihist</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-multihist</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html"·title="Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)"><link·rel="prev"·href="Secmia3ddistance.html"·title="mia-3ddistance"><link·rel="next"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·3D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-multihist</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3ddistance.html">Prev</a> </td><th·width="60%"·align="center">Processing·of·series·of·2D·images·in·a·3D·fashion·(out-of-core)</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiamultihist"></a>mia-multihist</h3></div></div></div><h4><a·name="idp8963"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-multihist</code>··{-i·<em·class="replaceable"><code>io</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp8972"></a>Description:</h4><p·class="description">This·program·evaluates·the·histogram·over·a·series·of·2D·images</p><h4><a·name="idp8974"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-histogram=(required,·output);·string</span></dt><dd><p>output·file·name</p></dd><dt><span·class="term">--min=0;·float</span></dt><dd><p>minimum·of·histogram·range</p></dd><dt><span·class="term">--max=65535;·float</span></dt><dd><p>maximum·of·histogram·range</p></dd><dt><span·class="term">--bins=65536;·ulong</span></dt><dd><p>number·of·histogram·bins,·set·to·zero·to·create·a·bin·for·each·intensity·value·available·in·the·input·data.·In·this·case·the·histogram·range·is·also·evaluated·automatically</p></dd></dl></div><h4><a·name="idp8997"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9048"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9054"></a>Example:</h4><p>Evaluate·the·histogram·over·all·consecutively·numbered·images·that·follow·the·numbering·pattern·inputXXXX.exr·and·store·the·output·histogram·in·histo.txt.·Use·the·range·[0,256]·and·64·bins.</p><pre·class="screen">mia-multihist·-i·input0000.exr·-o·histo.txt·--min·0·--max·256·--bins·64</pre><h4><a·name="idp9057"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3ddistance.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3ddistance </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Analysis,·filtering,·combining,·and·segmentation·of·3D·images</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp8972"></a>Description:</h4><p·class="description">This·program·evaluates·the·histogram·over·a·series·of·2D·images</p><h4><a·name="idp8974"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·io</span></dt><dd><p>input·image(s)·to·be·filtered.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-o,·--out-histogram=(required,·output);·string</span></dt><dd><p>output·file·name</p></dd><dt><span·class="term">--min=0;·float</span></dt><dd><p>minimum·of·histogram·range</p></dd><dt><span·class="term">--max=65535;·float</span></dt><dd><p>maximum·of·histogram·range</p></dd><dt><span·class="term">--bins=65536;·ulong</span></dt><dd><p>number·of·histogram·bins,·set·to·zero·to·create·a·bin·for·each·intensity·value·available·in·the·input·data.·In·this·case·the·histogram·range·is·also·evaluated·automatically</p></dd></dl></div><h4><a·name="idp8997"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp9048"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp9054"></a>Example:</h4><p>Evaluate·the·histogram·over·all·consecutively·numbered·images·that·follow·the·numbering·pattern·inputXXXX.exr·and·store·the·output·histogram·in·histo.txt.·Use·the·range·[0,256]·and·64·bins.</p><pre·class="screen">mia-multihist·-i·input0000.exr·-o·histo.txt·--min·0·--max·256·--bins·64</pre><h4><a·name="idp9057"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3ddistance.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3ddistance </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Analysis,·filtering,·combining,·and·segmentation·of·3D·images</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-multihist4 mia-multihist
5 Sysnopis:5 Sysnopis:
6 mia-multihist·{-i·io}·{-o·string}·[·options·...]6 mia-multihist·{-i·io}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·evaluates·the·histogram·over·a·series·of·2D·images8 This·program·evaluates·the·histogram·over·a·series·of·2D·images
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·io10 ··-i,·--in-file=(required,·input);·io
11 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:11 ······input·image(s)·to·be·filtered.·For·supported·file·types·see·Plugin_type:
12 ······2dimage/io12 ······2dimage/io
13 ··-o,·--out-histogram=(required,·output);·string13 ··-o,·--out-histogram=(required,·output);·string
14 ······output·file·name14 ······output·file·name
15 ··--min=0;·float15 ··--min=0;·float
16 ······minimum·of·histogram·range16 ······minimum·of·histogram·range
17 ··--max=65535;·float17 ··--max=65535;·float
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-myowavelettest</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmialabelsort.html"·title="mia-labelsort"><link·rel="next"·href="Secmiawavelettrans.html"·title="mia-wavelettrans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-myowavelettest</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmialabelsort.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiawavelettrans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiamyowavelettest"></a>mia-myowavelettest</h3></div></div></div><h4><a·name="idp14307"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-myowavelettest</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-myowavelettest</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmialabelsort.html"·title="mia-labelsort"><link·rel="next"·href="Secmiawavelettrans.html"·title="mia-wavelettrans"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-myowavelettest</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmialabelsort.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiawavelettrans.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiamyowavelettest"></a>mia-myowavelettest</h3></div></div></div><h4><a·name="idp14307"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-myowavelettest</code>··{-i·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14314"></a>Description:</h4><p·class="description">This·program·runs·the·wavelet·based·slope-statistics·on·the·mixing·matrix·of·a·ICA·perfusion·series.</p><h4><a·name="idp14316"></a>Options:</h4><h4><a·name="idp14317"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·data·set</p></dd></dl></div><h4><a·name="idp14323"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14374"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14380"></a>Example:</h4><p>3 ········...]</p></div><h4><a·name="idp14314"></a>Description:</h4><p·class="description">This·program·runs·the·wavelet·based·slope-statistics·on·the·mixing·matrix·of·a·ICA·perfusion·series.</p><h4><a·name="idp14316"></a>Options:</h4><h4><a·name="idp14317"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·data·set</p></dd></dl></div><h4><a·name="idp14323"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14374"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14380"></a>Example:</h4><p>
4 ····</p><pre·class="screen">mia-myowavelettest·</pre><h4><a·name="idp14383"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmialabelsort.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiawavelettrans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-labelsort </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-wavelettrans</td></tr></table></div></body></html>4 ····</p><pre·class="screen">mia-myowavelettest·</pre><h4><a·name="idp14383"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmialabelsort.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiawavelettrans.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-labelsort </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-wavelettrans</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-myowavelettest·{-i·string}·[·options·...]6 mia-myowavelettest·{-i·string}·[·options·...]
7 Description:7 Description:
8 This·program·runs·the·wavelet·based·slope-statistics·on·the·mixing·matrix·of·a8 This·program·runs·the·wavelet·based·slope-statistics·on·the·mixing·matrix·of·a
9 ICA·perfusion·series.9 ICA·perfusion·series.
10 Options:10 Options:
11 File-IO11 File-IO
12 ··-i,·--in-file=(input,·required);·string12 ··-i,·--in-file=(required,·input);·string
13 ······input·data·set13 ······input·data·set
14 Help·&·Info14 Help·&·Info
15 ··-V,·--verbose=warning;·dict15 ··-V,·--verbose=warning;·dict
16 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.16 ······verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.
17 ······Supported·priorities·starting·at·lowest·level·are:17 ······Supported·priorities·starting·at·lowest·level·are:
18 ······trace:···Function·call·trace18 ······trace:···Function·call·trace
19 ······debug:···Debug·output19 ······debug:···Debug·output
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-raw2image</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia3dimageselect.html"·title="mia-3dimageselect"><link·rel="next"·href="Secmiaraw2volume.html"·title="mia-raw2volume"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-raw2image</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimageselect.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiaraw2volume.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiaraw2image"></a>mia-raw2image</h3></div></div></div><h4><a·name="idp614"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-raw2image</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-s·<em·class="replaceable"><code>2dbounds</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-raw2image</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmia3dimageselect.html"·title="mia-3dimageselect"><link·rel="next"·href="Secmiaraw2volume.html"·title="mia-raw2volume"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-raw2image</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmia3dimageselect.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="Secmiaraw2volume.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiaraw2image"></a>mia-raw2image</h3></div></div></div><h4><a·name="idp614"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-raw2image</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-s·<em·class="replaceable"><code>2dbounds</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp625"></a>Description:</h4><p·class="description">This·program·is·used·to·convert·raw·data·to·a·2D·file·format.</p><h4><a·name="idp627"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·file·name</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--repn=ubyte;·dict</span></dt><dd><p>input·pixel·type·</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--big-endian</span></dt><dd><p>input·data·is·big·endian</p></dd><dt><span·class="term">-f,·--scale=[1,1];·2dfvector</span></dt><dd><p>scale·of·input·pixels·&lt;FX,FY&gt;</p></dd><dt><span·class="term">-s,·--size=(required);·2dbounds</span></dt><dd><p>size·of·input·&lt;NX,NY&gt;</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·number·of·bytes·from·beginning·of·file</p></dd></dl></div><h4><a·name="idp699"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp750"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp756"></a>Example:</h4><p>Convert·a·data·set·data.raw·of·size·&lt;10,20&gt;·of·short·integer·data·with·a·pixel·size·of·&lt;1.2,·2.3&gt;·to·a·PNG·file·image.png</p><pre·class="screen">mia-raw2image·-i·data.raw·-o·image.png·-s·'&lt;10,20&gt;'·-k·'&lt;1.2,2.3&gt;'·-r·ushort</pre><h4><a·name="idp759"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimageselect.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiaraw2volume.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimageselect </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-raw2volume</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp625"></a>Description:</h4><p·class="description">This·program·is·used·to·convert·raw·data·to·a·2D·file·format.</p><h4><a·name="idp627"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·file·name</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype2dimageio.html"·title="Plugin·type:·2dimage/io">Plugin·type:·2dimage/io</a></p></dd><dt><span·class="term">-r,·--repn=ubyte;·dict</span></dt><dd><p>input·pixel·type·</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--big-endian</span></dt><dd><p>input·data·is·big·endian</p></dd><dt><span·class="term">-f,·--scale=[1,1];·2dfvector</span></dt><dd><p>scale·of·input·pixels·&lt;FX,FY&gt;</p></dd><dt><span·class="term">-s,·--size=(required);·2dbounds</span></dt><dd><p>size·of·input·&lt;NX,NY&gt;</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·number·of·bytes·from·beginning·of·file</p></dd></dl></div><h4><a·name="idp699"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp750"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp756"></a>Example:</h4><p>Convert·a·data·set·data.raw·of·size·&lt;10,20&gt;·of·short·integer·data·with·a·pixel·size·of·&lt;1.2,·2.3&gt;·to·a·PNG·file·image.png</p><pre·class="screen">mia-raw2image·-i·data.raw·-o·image.png·-s·'&lt;10,20&gt;'·-k·'&lt;1.2,2.3&gt;'·-r·ushort</pre><h4><a·name="idp759"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmia3dimageselect.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="Secmiaraw2volume.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-3dimageselect </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> mia-raw2volume</td></tr></table></div></body></html>
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3 ===============================================================================3 ===============================================================================
4 mia-raw2image4 mia-raw2image
5 Sysnopis:5 Sysnopis:
6 mia-raw2image·{-i·string}·{-o·io}·{-s·2dbounds}·[·options·...]6 mia-raw2image·{-i·string}·{-o·io}·{-s·2dbounds}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·convert·raw·data·to·a·2D·file·format.8 This·program·is·used·to·convert·raw·data·to·a·2D·file·format.
9 Options:9 Options:
10 ··-i,·--in-file=(input,·required);·string10 ··-i,·--in-file=(required,·input);·string
11 ······input·file·name11 ······input·file·name
12 ··-o,·--out-file=(required,·output);·io12 ··-o,·--out-file=(required,·output);·io
13 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io13 ······output·file·name.·For·supported·file·types·see·Plugin_type:_2dimage/io
14 ··-r,·--repn=ubyte;·dict14 ··-r,·--repn=ubyte;·dict
15 ······input·pixel·type15 ······input·pixel·type
16 ······bit:····binary·data16 ······bit:····binary·data
17 ······sbyte:··signed·8·bit17 ······sbyte:··signed·8·bit
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./usr/share/doc/mia-2.4/userref/Secmiaraw2volume.html
    
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-raw2volume</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmiaraw2image.html"·title="mia-raw2image"><link·rel="next"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-raw2volume</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiaraw2image.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiaraw2volume"></a>mia-raw2volume</h3></div></div></div><h4><a·name="idp763"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-raw2volume</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-s·<em·class="replaceable"><code>3dbounds</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-raw2volume</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecImageconversion.html"·title="Image·conversion"><link·rel="prev"·href="Secmiaraw2image.html"·title="mia-raw2image"><link·rel="next"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html"·title="Analysis,·filtering,·combining,·and·segmentation·of·2D·images"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-raw2volume</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiaraw2image.html">Prev</a> </td><th·width="60%"·align="center">Image·conversion</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiaraw2volume"></a>mia-raw2volume</h3></div></div></div><h4><a·name="idp763"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-raw2volume</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>io</code></em>}·{-s·<em·class="replaceable"><code>3dbounds</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp774"></a>Description:</h4><p·class="description">This·program·is·used·to·convert·raw·data·into·3D·images·with·apropriate·metadata.</p><h4><a·name="idp776"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·file·name</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--repn=ubyte;·dict</span></dt><dd><p>input·pixel·type·</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--big-endian</span></dt><dd><p>input·data·is·big·endian</p></dd><dt><span·class="term">-f,·--scale=[1,1,1];·3dfvector</span></dt><dd><p>scale·of·input·voxels·&lt;FX,FY,FZ&gt;</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·number·of·bytes·from·beginning·of·file</p></dd><dt><span·class="term">-s,·--size=(required);·3dbounds</span></dt><dd><p>size·of·input·&lt;NX,NY,NZ&gt;</p></dd></dl></div><h4><a·name="idp848"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp899"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp905"></a>Example:</h4><p>pixel·size·of·&lt;1.2,·2.3,·3.4&gt;·to·an·Analyze·file·image.hdr</p><pre·class="screen">mia-raw2volume·-i·data.raw·-o·image.hdr·-s·"&lt;10,20,30&gt;"·-k·"&lt;1.2,2.3,3.4&gt;"·-r·ushort</pre><h4><a·name="idp908"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiaraw2image.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-raw2image </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Analysis,·filtering,·combining,·and·segmentation·of·2D·images</td></tr></table></div></body></html>3 ········...]</p></div><h4><a·name="idp774"></a>Description:</h4><p·class="description">This·program·is·used·to·convert·raw·data·into·3D·images·with·apropriate·metadata.</p><h4><a·name="idp776"></a>Options:</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·file·name</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·io</span></dt><dd><p>output·file·name.·For·supported·file·types·see·<a·class="xref"·href="SecPlugintype3dimageio.html"·title="Plugin·type:·3dimage/io">Plugin·type:·3dimage/io</a></p></dd><dt><span·class="term">-r,·--repn=ubyte;·dict</span></dt><dd><p>input·pixel·type·</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">bit:</td><td·align="left"·valign="top">binary·data</td></tr><tr><td·align="left"·valign="top">sbyte:</td><td·align="left"·valign="top">signed·8·bit</td></tr><tr><td·align="left"·valign="top">ubyte:</td><td·align="left"·valign="top">unsigned·8·bit</td></tr><tr><td·align="left"·valign="top">sshort:</td><td·align="left"·valign="top">signed·16·bit</td></tr><tr><td·align="left"·valign="top">ushort:</td><td·align="left"·valign="top">unsigned·16·bit</td></tr><tr><td·align="left"·valign="top">sint:</td><td·align="left"·valign="top">signed·32·bit</td></tr><tr><td·align="left"·valign="top">uint:</td><td·align="left"·valign="top">unsigned·32·bit</td></tr><tr><td·align="left"·valign="top">slong:</td><td·align="left"·valign="top">signed·64·bit</td></tr><tr><td·align="left"·valign="top">ulong:</td><td·align="left"·valign="top">unsigned·64·bit</td></tr><tr><td·align="left"·valign="top">float:</td><td·align="left"·valign="top">floating·point·32·bit</td></tr><tr><td·align="left"·valign="top">double:</td><td·align="left"·valign="top">floating·point·64·bit</td></tr><tr><td·align="left"·valign="top">none:</td><td·align="left"·valign="top">no·pixel·type·defined</td></tr></tbody></table></div></dd><dt><span·class="term">-b,·--big-endian</span></dt><dd><p>input·data·is·big·endian</p></dd><dt><span·class="term">-f,·--scale=[1,1,1];·3dfvector</span></dt><dd><p>scale·of·input·voxels·&lt;FX,FY,FZ&gt;</p></dd><dt><span·class="term">-k,·--skip=0;·ulong</span></dt><dd><p>skip·number·of·bytes·from·beginning·of·file</p></dd><dt><span·class="term">-s,·--size=(required);·3dbounds</span></dt><dd><p>size·of·input·&lt;NX,NY,NZ&gt;</p></dd></dl></div><h4><a·name="idp848"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp899"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp905"></a>Example:</h4><p>pixel·size·of·&lt;1.2,·2.3,·3.4&gt;·to·an·Analyze·file·image.hdr</p><pre·class="screen">mia-raw2volume·-i·data.raw·-o·image.hdr·-s·"&lt;10,20,30&gt;"·-k·"&lt;1.2,2.3,3.4&gt;"·-r·ushort</pre><h4><a·name="idp908"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiaraw2image.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecImageconversion.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-raw2image </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Analysis,·filtering,·combining,·and·segmentation·of·2D·images</td></tr></table></div></body></html>
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4 mia-raw2volume4 mia-raw2volume
5 Sysnopis:5 Sysnopis:
6 mia-raw2volume·{-i·string}·{-o·io}·{-s·3dbounds}·[·options·...]6 mia-raw2volume·{-i·string}·{-o·io}·{-s·3dbounds}·[·options·...]
7 Description:7 Description:
8 This·program·is·used·to·convert·raw·data·into·3D·images·with·apropriate8 This·program·is·used·to·convert·raw·data·into·3D·images·with·apropriate
9 metadata.9 metadata.
10 Options:10 Options:
11 ··-i,·--in-file=(input,·required);·string11 ··-i,·--in-file=(required,·input);·string
12 ······input·file·name12 ······input·file·name
13 ··-o,·--out-file=(required,·output);·io13 ··-o,·--out-file=(required,·output);·io
14 ······output·file·name.·For·supported·file·types·see·Plugin_type:_3dimage/io14 ······output·file·name.·For·supported·file·types·see·Plugin_type:_3dimage/io
15 ··-r,·--repn=ubyte;·dict15 ··-r,·--repn=ubyte;·dict
16 ······input·pixel·type16 ······input·pixel·type
17 ······bit:····binary·data17 ······bit:····binary·data
18 ······sbyte:··signed·8·bit18 ······sbyte:··signed·8·bit
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1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-wavelettrans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmiamyowavelettest.html"·title="mia-myowavelettest"><link·rel="next"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-wavelettrans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiamyowavelettest.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiawavelettrans"></a>mia-wavelettrans</h3></div></div></div><h4><a·name="idp14387"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-wavelettrans</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[1 <html><head><meta·http-equiv="Content-Type"·content="text/html;·charset=ISO-8859-1"><title>mia-wavelettrans</title><link·rel="stylesheet"·type="text/css"·href="progref.css"><meta·name="generator"·content="DocBook·XSL·Stylesheets·Vsnapshot"><link·rel="home"·href="index.html"·title="Mia·Program·Reference"><link·rel="up"·href="SecMiscellaneousprograms.html"·title="Miscellaneous·programs"><link·rel="prev"·href="Secmiamyowavelettest.html"·title="mia-myowavelettest"><link·rel="next"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html"·title="Creation,·analysis,·and·filtering·of·triangular·3D·meshes"></head><body·bgcolor="white"·text="black"·link="#0000FF"·vlink="#840084"·alink="#0000FF"><div·class="navheader"><table·width="100%"·summary="Navigation·header"><tr><th·colspan="3"·align="center">mia-wavelettrans</th></tr><tr><td·width="20%"·align="left"><a·accesskey="p"·href="Secmiamyowavelettest.html">Prev</a> </td><th·width="60%"·align="center">Miscellaneous·programs</th><td·width="20%"·align="right"> <a·accesskey="n"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Next</a></td></tr></table><hr></div><div·class="section"><div·class="titlepage"><div><div><h3·class="title"><a·name="Secmiawavelettrans"></a>mia-wavelettrans</h3></div></div></div><h4><a·name="idp14387"></a>Sysnopis:</h4><div·class="cmdsynopsis"><p><code·class="command">mia-wavelettrans</code>··{-i·<em·class="replaceable"><code>string</code></em>}·{-o·<em·class="replaceable"><code>string</code></em>}·[
2 ··········<em·class="replaceable"><code>options</code></em>2 ··········<em·class="replaceable"><code>options</code></em>
3 ········...]</p></div><h4><a·name="idp14396"></a>Description:</h4><p·class="description">This·program·runs·the·a·column-wise·discret·wavelet·forward·transform·on·the·data·given·by·an·input·text·file.</p><h4><a·name="idp14398"></a>Options:</h4><h4><a·name="idp14399"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(input,·required);·string</span></dt><dd><p>input·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·data·set</p></dd><dt><span·class="term">-s,·--save-wave=(output);·string</span></dt><dd><p>base·name·of·the·output·files·that·will·store·the·wavelet·coefficients·as·matrix</p></dd></dl></div><h4><a·name="idp14413"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14464"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14470"></a>Wavelet</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-w,·--wavelet=c-daubechies;·dict</span></dt><dd><p>wavelet·to·be·used</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">haar:</td><td·align="left"·valign="top">HAAR·wavelet</td></tr><tr><td·align="left"·valign="top">c-haar:</td><td·align="left"·valign="top">HAAR·wavelet·(centered)</td></tr><tr><td·align="left"·valign="top">daubechies:</td><td·align="left"·valign="top">Daubechies·wavelet</td></tr><tr><td·align="left"·valign="top">c-daubechies:</td><td·align="left"·valign="top">Daubechies·wavelet·(centered)</td></tr><tr><td·align="left"·valign="top">bspline:</td><td·align="left"·valign="top">B-Spline·wavelet</td></tr><tr><td·align="left"·valign="top">c-bspline:</td><td·align="left"·valign="top">B-Spline·wavelet·(centered)</td></tr></tbody></table></div></dd><dt><span·class="term">-m,·--member=10;·int</span></dt><dd><p>wavelet·member·ID</p></dd></dl></div><h4><a·name="idp14503"></a>Example:</h4><p>3 ········...]</p></div><h4><a·name="idp14396"></a>Description:</h4><p·class="description">This·program·runs·the·a·column-wise·discret·wavelet·forward·transform·on·the·data·given·by·an·input·text·file.</p><h4><a·name="idp14398"></a>Options:</h4><h4><a·name="idp14399"></a>File-IO</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-i,·--in-file=(required,·input);·string</span></dt><dd><p>input·data·set</p></dd><dt><span·class="term">-o,·--out-file=(required,·output);·string</span></dt><dd><p>output·data·set</p></dd><dt><span·class="term">-s,·--save-wave=(output);·string</span></dt><dd><p>base·name·of·the·output·files·that·will·store·the·wavelet·coefficients·as·matrix</p></dd></dl></div><h4><a·name="idp14413"></a>Help·&amp;·Info</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-V,·--verbose=warning;·dict</span></dt><dd><p>verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">trace:</td><td·align="left"·valign="top">Function·call·trace</td></tr><tr><td·align="left"·valign="top">debug:</td><td·align="left"·valign="top">Debug·output</td></tr><tr><td·align="left"·valign="top">info:</td><td·align="left"·valign="top">Low·level·messages</td></tr><tr><td·align="left"·valign="top">message:</td><td·align="left"·valign="top">Normal·messages</td></tr><tr><td·align="left"·valign="top">warning:</td><td·align="left"·valign="top">Warnings</td></tr><tr><td·align="left"·valign="top">fail:</td><td·align="left"·valign="top">Report·test·failures</td></tr><tr><td·align="left"·valign="top">error:</td><td·align="left"·valign="top">Report·errors</td></tr><tr><td·align="left"·valign="top">fatal:</td><td·align="left"·valign="top">Report·only·fatal·errors</td></tr></tbody></table></div></dd><dt><span·class="term">--copyright=();·bool</span></dt><dd><p>print·copyright·information</p></dd><dt><span·class="term">-h,·--help=();·bool</span></dt><dd><p>print·this·help</p></dd><dt><span·class="term">-?,·--usage=();·bool</span></dt><dd><p>print·a·short·help</p></dd><dt><span·class="term">--version=();·bool</span></dt><dd><p>print·the·version·number·and·exit</p></dd></dl></div><h4><a·name="idp14464"></a>Processing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">--threads=-1;·int</span></dt><dd><p>Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(-1:·automatic·estimation).</p></dd></dl></div><h4><a·name="idp14470"></a>Wavelet</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-w,·--wavelet=c-daubechies;·dict</span></dt><dd><p>wavelet·to·be·used</p><div·class="informaltable"><table·class="informaltable"·border="0"><colgroup><col·class="c1"><col·class="c2"></colgroup><tbody><tr><td·align="left"·valign="top">haar:</td><td·align="left"·valign="top">HAAR·wavelet</td></tr><tr><td·align="left"·valign="top">c-haar:</td><td·align="left"·valign="top">HAAR·wavelet·(centered)</td></tr><tr><td·align="left"·valign="top">daubechies:</td><td·align="left"·valign="top">Daubechies·wavelet</td></tr><tr><td·align="left"·valign="top">c-daubechies:</td><td·align="left"·valign="top">Daubechies·wavelet·(centered)</td></tr><tr><td·align="left"·valign="top">bspline:</td><td·align="left"·valign="top">B-Spline·wavelet</td></tr><tr><td·align="left"·valign="top">c-bspline:</td><td·align="left"·valign="top">B-Spline·wavelet·(centered)</td></tr></tbody></table></div></dd><dt><span·class="term">-m,·--member=10;·int</span></dt><dd><p>wavelet·member·ID</p></dd></dl></div><h4><a·name="idp14503"></a>Example:</h4><p>
4 ····</p><pre·class="screen">mia-wavelettrans·</pre><h4><a·name="idp14506"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiamyowavelettest.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-myowavelettest </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Creation,·analysis,·and·filtering·of·triangular·3D·meshes</td></tr></table></div></body></html>4 ····</p><pre·class="screen">mia-wavelettrans·</pre><h4><a·name="idp14506"></a>Author(s):</h4><p>Gert·Wollny</p></div><div·class="navfooter"><hr><table·width="100%"·summary="Navigation·footer"><tr><td·width="40%"·align="left"><a·accesskey="p"·href="Secmiamyowavelettest.html">Prev</a> </td><td·width="20%"·align="center"><a·accesskey="u"·href="SecMiscellaneousprograms.html">Up</a></td><td·width="40%"·align="right"> <a·accesskey="n"·href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Next</a></td></tr><tr><td·width="40%"·align="left"·valign="top">mia-myowavelettest </td><td·width="20%"·align="center"><a·accesskey="h"·href="index.html">Home</a></td><td·width="40%"·align="right"·valign="top"> Creation,·analysis,·and·filtering·of·triangular·3D·meshes</td></tr></table></div></body></html>
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5 Sysnopis:5 Sysnopis:
6 mia-wavelettrans·{-i·string}·{-o·string}·[·options·...]6 mia-wavelettrans·{-i·string}·{-o·string}·[·options·...]
7 Description:7 Description:
8 This·program·runs·the·a·column-wise·discret·wavelet·forward·transform·on·the8 This·program·runs·the·a·column-wise·discret·wavelet·forward·transform·on·the
9 data·given·by·an·input·text·file.9 data·given·by·an·input·text·file.
10 Options:10 Options:
11 File-IO11 File-IO
12 ··-i,·--in-file=(input,·required);·string12 ··-i,·--in-file=(required,·input);·string
13 ······input·data·set13 ······input·data·set
14 ··-o,·--out-file=(required,·output);·string14 ··-o,·--out-file=(required,·output);·string
15 ······output·data·set15 ······output·data·set
16 ··-s,·--save-wave=(output);·string16 ··-s,·--save-wave=(output);·string
17 ······base·name·of·the·output·files·that·will·store·the·wavelet·coefficients·as17 ······base·name·of·the·output·files·that·will·store·the·wavelet·coefficients·as
18 ······matrix18 ······matrix
19 Help·&·Info19 Help·&·Info
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mia-2dbinarycombine.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dbinarycombine·\-1·<file1>·\-2·<file2>·\-o·<out\-file>·[options]6 .B··mia\-2dbinarycombine·\-1·<file1>·\-2·<file2>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dbinarycombine8 .B·mia\-2dbinarycombine
9 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.9 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-1·\-\-file1=(required,·input);·io"12 .IP·"\-1·\-\-file1=(input,·required);·io"
13 input·mask·image·113 input·mask·image·1
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-2·\-\-file2=(required,·input);·io"15 .IP·"\-2·\-\-file2=(input,·required);·io"
16 input·mask·image·216 input·mask·image·2
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-o·\-\-out-file=(required,·output);·io"18 .IP·"\-o·\-\-out-file=(required,·output);·io"
19 output·mask·image19 output·mask·image
20 ·For·supported·file·types·see·PLUGINS:2dimage/io20 ·For·supported·file·types·see·PLUGINS:2dimage/io
21 .IP·"\-p·\-\-operation=nor"21 .IP·"\-p·\-\-operation=nor"
22 Operation·to·be·applied22 Operation·to·be·applied
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mia-2ddeform.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2ddeform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options]6 .B··mia\-2ddeform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2ddeform8 .B·mia\-2ddeform
9 This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.·Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation·formula·is·'x·->·x·-·v(x)'9 This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.·Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation·formula·is·'x·->·x·-·v(x)'
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image13 input·image
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 transformed··image16 transformed··image
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-t·\-\-transformation=(input,·required);·io"18 .IP·"\-t·\-\-transformation=(required,·input);·io"
19 transformation·vector·field19 transformation·vector·field
20 ·For·supported·file·types·see·PLUGINS:2dvf/io20 ·For·supported·file·types·see·PLUGINS:2dvf/io
21 .IP·"\-p·\-\-interpolator=bspline:d=3"21 .IP·"\-p·\-\-interpolator=bspline:d=3"
22 image·interpolator·kernel22 image·interpolator·kernel
23 ·For·supported·plugins·see·PLUGINS:1d/splinekernel23 ·For·supported·plugins·see·PLUGINS:1d/splinekernel
24 .RE24 .RE
25 .SS·Help·&·Info25 .SS·Help·&·Info
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./usr/share/man/man1/mia-2ddistance.1.gz
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mia-2ddistance.1
    
Offset 11, 15 lines modifiedOffset 11, 15 lines modified
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image13 input·image
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-d·\-\-distance-file=(required,·input);·io"15 .IP·"\-d·\-\-distance-file=(required,·input);·io"
16 distance·field·image·(floating·point)16 distance·field·image·(floating·point)
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-o·\-\-out-file=(output,·required);·string"18 .IP·"\-o·\-\-out-file=(required,·output);·string"
19 output·file,·'\-':·write·to·stdout19 output·file,·'\-':·write·to·stdout
  
20 .IP·"\-s·\-\-scale=1"20 .IP·"\-s·\-\-scale=1"
21 distance·scaling·factor21 distance·scaling·factor
  
22 .IP·"\-m·\-\-method=avg"22 .IP·"\-m·\-\-method=avg"
23 distance·measuring·method23 distance·measuring·method
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./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz
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mia-2dfluid-syn-registration.1
    
Offset 70, 18 lines modifiedOffset 70, 18 lines modified
70 .RS70 .RS
71 .IP·"\-i·\-\-in-image=(input,·required);·io"71 .IP·"\-i·\-\-in-image=(input,·required);·io"
72 test·image72 test·image
73 ·For·supported·file·types·see·PLUGINS:2dimage/io73 ·For·supported·file·types·see·PLUGINS:2dimage/io
74 .IP·"\-r·\-\-ref-image=(input,·required);·io"74 .IP·"\-r·\-\-ref-image=(input,·required);·io"
75 reference·image75 reference·image
76 ·For·supported·file·types·see·PLUGINS:2dimage/io76 ·For·supported·file·types·see·PLUGINS:2dimage/io
77 .IP·"\-o·\-\-transform=(output,·required);·io"77 .IP·"\-o·\-\-transform=(required,·output);·io"
78 output·transformation78 output·transformation
79 ·For·supported·file·types·see·PLUGINS:2dtransform/io79 ·For·supported·file·types·see·PLUGINS:2dtransform/io
80 .IP·"\-O·\-\-inverse-transform=(output,·required);·io"80 .IP·"\-O·\-\-inverse-transform=(required,·output);·io"
81 inverse·output·transformation81 inverse·output·transformation
82 ·For·supported·file·types·see·PLUGINS:2dtransform/io82 ·For·supported·file·types·see·PLUGINS:2dtransform/io
83 .RE83 .RE
84 .SS·Processing84 .SS·Processing
85 .RS85 .RS
86 .IP·"···\-\-threads=\-1"86 .IP·"···\-\-threads=\-1"
87 Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).87 Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).
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./usr/share/man/man1/mia-2dfluid.1.gz
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mia-2dfluid.1
    
Offset 14, 18 lines modifiedOffset 14, 18 lines modified
14 .UE14 .UE
15 .RE15 .RE
  
16 It·uses·SSD·as·the·sole·registration·criterion.16 It·uses·SSD·as·the·sole·registration·criterion.
17 .SH·OPTIONS17 .SH·OPTIONS
18 .SS·File-IO18 .SS·File-IO
19 .RS19 .RS
20 .IP·"\-i·\-\-in-image=(input,·required);·io"20 .IP·"\-i·\-\-in-image=(required,·input);·io"
21 input·(test)·image·to·be·registered21 input·(test)·image·to·be·registered
22 ·For·supported·file·types·see·PLUGINS:2dimage/io22 ·For·supported·file·types·see·PLUGINS:2dimage/io
23 .IP·"\-r·\-\-ref-image=(input,·required);·io"23 .IP·"\-r·\-\-ref-image=(required,·input);·io"
24 reference·image24 reference·image
25 ·For·supported·file·types·see·PLUGINS:2dimage/io25 ·For·supported·file·types·see·PLUGINS:2dimage/io
26 .IP·"\-o·\-\-out-transformation=(output);·io"26 .IP·"\-o·\-\-out-transformation=(output);·io"
27 output·transformation·comprising·the·registration27 output·transformation·comprising·the·registration
28 ·For·supported·file·types·see·PLUGINS:2dvf/io28 ·For·supported·file·types·see·PLUGINS:2dvf/io
29 .IP·"\-d·\-\-out-image=(output);·io"29 .IP·"\-d·\-\-out-image=(output);·io"
30 output·image·deformed·according·to·the·transformation30 output·image·deformed·according·to·the·transformation
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./usr/share/man/man1/mia-2dfuzzysegment.1.gz
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mia-2dfuzzysegment.1
    
Offset 6, 15 lines modifiedOffset 6, 15 lines modified
6 .B··mia\-2dfuzzysegment·\-i·<in\-file>·[options]6 .B··mia\-2dfuzzysegment·\-i·<in\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dfuzzysegment8 .B·mia\-2dfuzzysegment
9 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·fuzzy·segmentation·of·2D·image.·cf·D.L.·Pham·and·J.L.Prince,·"An·adaptive·fuzzy·C-means·algorithm·for·image·segmentation·in·the·presence·of·intensity·inhomogeneities",·Pat.·Rec.·Let.,·20:57-68,19999 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·fuzzy·segmentation·of·2D·image.·cf·D.L.·Pham·and·J.L.Prince,·"An·adaptive·fuzzy·C-means·algorithm·for·image·segmentation·in·the·presence·of·intensity·inhomogeneities",·Pat.·Rec.·Let.,·20:57-68,1999
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(required,·input);·io"13 .IP·"\-i·\-\-in-file=(input,·required);·io"
14 input·image(s)·to·be·segmenetd14 input·image(s)·to·be·segmenetd
15 ·For·supported·file·types·see·PLUGINS:2dimage/io15 ·For·supported·file·types·see·PLUGINS:2dimage/io
16 .IP·"\-c·\-\-cls-file=(output);·io"16 .IP·"\-c·\-\-cls-file=(output);·io"
17 output·class·probability·images·(floating·point·values·and·multi\-image)17 output·class·probability·images·(floating·point·values·and·multi\-image)
18 ·For·supported·file·types·see·PLUGINS:2dimage/io18 ·For·supported·file·types·see·PLUGINS:2dimage/io
19 .IP·"\-o·\-\-b0-file=(output);·io"19 .IP·"\-o·\-\-b0-file=(output);·io"
20 image·corrected·for·intensity·non\-uniformity20 image·corrected·for·intensity·non\-uniformity
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./usr/share/man/man1/mia-2dgroundtruthreg.1.gz
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mia-2dgroundtruthreg.1
    
Offset 15, 15 lines modifiedOffset 15, 15 lines modified
15 .RE15 .RE
  
16 ·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.16 ·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.
17 .SH·OPTIONS17 .SH·OPTIONS
18 .SS·18 .SS·
19 File-IO19 File-IO
20 .RS20 .RS
21 .IP·"\-i·\-\-in-file=(required,·input);·string"21 .IP·"\-i·\-\-in-file=(input,·required);·string"
22 input·perfusion·data·set22 input·perfusion·data·set
  
23 .IP·"\-o·\-\-out-file=(required,·output);·string"23 .IP·"\-o·\-\-out-file=(required,·output);·string"
24 output·perfusion·data·set24 output·perfusion·data·set
  
25 .IP·"\-r·\-\-registered=reg"25 .IP·"\-r·\-\-registered=reg"
26 file·name·base·for·registered·files26 file·name·base·for·registered·files
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./usr/share/man/man1/mia-2dimagecombiner.1.gz
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mia-2dimagecombiner.1
    
Offset 5, 18 lines modifiedOffset 5, 18 lines modified
5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dimagecombiner·\-1·<in\-file\-1>·\-2·<in\-file\-2>·\-o·<out\-file>·[options]6 .B··mia\-2dimagecombiner·\-1·<in\-file\-1>·\-2·<in\-file\-2>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dimagecombiner8 .B·mia\-2dimagecombiner
9 Combine·two·image·by·a·given·operation.9 Combine·two·image·by·a·given·operation.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-1·\-\-in-file-1=(input,·required);·io"12 .IP·"\-1·\-\-in-file-1=(required,·input);·io"
13 first·input·image·to·be·combined13 first·input·image·to·be·combined
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-2·\-\-in-file-2=(input,·required);·io"15 .IP·"\-2·\-\-in-file-2=(required,·input);·io"
16 second·input·image·to·be·combined16 second·input·image·to·be·combined
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-o·\-\-out-file=(required,·output);·io"18 .IP·"\-o·\-\-out-file=(required,·output);·io"
19 output·image(s)·that·have·been·filtered19 output·image(s)·that·have·been·filtered
20 ·For·supported·file·types·see·PLUGINS:2dimage/io20 ·For·supported·file·types·see·PLUGINS:2dimage/io
21 .IP·"\-p·\-\-operation=absdiff"21 .IP·"\-p·\-\-operation=absdiff"
22 operation·to·be·applied22 operation·to·be·applied
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./usr/share/man/man1/mia-2dimagefilter.1.gz
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mia-2dimagefilter.1
    
Offset 10, 15 lines modifiedOffset 10, 15 lines modified
10 ···'mia-plugin-help·filter/2dimage'10 ···'mia-plugin-help·filter/2dimage'
11 from·the·command·line11 from·the·command·line
12 .SH·OPTIONS12 .SH·OPTIONS
13 .RS13 .RS
14 .IP·"\-i·\-\-in-file=(input,·required);·io"14 .IP·"\-i·\-\-in-file=(input,·required);·io"
15 input·image(s)·to·be·filtered15 input·image(s)·to·be·filtered
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-o·\-\-out-file=(required,·output);·io"17 .IP·"\-o·\-\-out-file=(output,·required);·io"
18 output·image(s)·that·have·been·filtered18 output·image(s)·that·have·been·filtered
19 ·For·supported·file·types·see·PLUGINS:2dimage/io19 ·For·supported·file·types·see·PLUGINS:2dimage/io
20 .RE20 .RE
21 .SS·Help·&·Info21 .SS·Help·&·Info
22 .RS22 .RS
23 .IP·"\-V·\-\-verbose=warning"23 .IP·"\-V·\-\-verbose=warning"
24 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:24 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
Offset 826, 15 lines modifiedOffset 826, 15 lines modified
826 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.826 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.
  
827 .RE827 .RE
828 .RE828 .RE
829 .RS·14829 .RS·14
830 .I830 .I
831 varfile831 varfile
832 =(required,·output,·io)832 =(output,·required,·io)
833 .RS·2833 .RS·2
834 name·of·the·output·file·to·save·the·variation·image·too..834 name·of·the·output·file·to·save·the·variation·image·too..
835 For·supported·file·types·see·PLUGINS:2dimage/io835 For·supported·file·types·see·PLUGINS:2dimage/io
  
836 .RE836 .RE
837 .RE837 .RE
838 .RS·14838 .RS·14
Offset 862, 15 lines modifiedOffset 862, 15 lines modified
862 .TP·10862 .TP·10
863 .B·medianmad863 .B·medianmad
864 Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·864 Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
865 .P865 .P
866 .RS·14866 .RS·14
867 .I867 .I
868 madfile868 madfile
869 =(required,·output,·io)869 =(output,·required,·io)
870 .RS·2870 .RS·2
871 name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..871 name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
872 For·supported·file·types·see·PLUGINS:2dimage/io872 For·supported·file·types·see·PLUGINS:2dimage/io
  
873 .RE873 .RE
874 .RE874 .RE
875 .RS·14875 .RS·14
Offset 1181, 15 lines modifiedOffset 1181, 15 lines modified
1181 .TP·101181 .TP·10
1182 .B·tee1182 .B·tee
1183 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1183 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1184 .P1184 .P
1185 .RS·141185 .RS·14
1186 .I1186 .I
1187 file1187 file
1188 =(required,·output,·io)1188 =(output,·required,·io)
1189 .RS·21189 .RS·2
1190 name·of·the·output·file·to·save·the·image·too..1190 name·of·the·output·file·to·save·the·image·too..
1191 For·supported·file·types·see·PLUGINS:2dimage/io1191 For·supported·file·types·see·PLUGINS:2dimage/io
  
1192 .RE1192 .RE
1193 .RE1193 .RE
1194 .TP·101194 .TP·10
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./usr/share/man/man1/mia-2dimagefilterstack.1.gz
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mia-2dimagefilterstack.1
    
Offset 9, 15 lines modifiedOffset 9, 15 lines modified
9 This·program·runs·a·series·filters·on·a·series·of·consecutive·numbered·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.9 This·program·runs·a·series·filters·on·a·series·of·consecutive·numbered·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File·IO11 .SS·File·IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(required,·input);·io"13 .IP·"\-i·\-\-in-file=(required,·input);·io"
14 input·image(s)·to·be·filtered14 input·image(s)·to·be·filtered
15 ·For·supported·file·types·see·PLUGINS:2dimage/io15 ·For·supported·file·types·see·PLUGINS:2dimage/io
16 .IP·"\-o·\-\-out-file=(output,·required);·io"16 .IP·"\-o·\-\-out-file=(required,·output);·io"
17 output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option17 output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option
18 ·For·supported·file·types·see·PLUGINS:2dimage/io18 ·For·supported·file·types·see·PLUGINS:2dimage/io
19 .IP·"\-t·\-\-type="19 .IP·"\-t·\-\-type="
20 output·file·type,·if·not·given·the·input·type·is·used20 output·file·type,·if·not·given·the·input·type·is·used
  
21 .RS·1021 .RS·10
22 .I22 .I
Offset 866, 15 lines modifiedOffset 866, 15 lines modified
866 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.866 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.
  
867 .RE867 .RE
868 .RE868 .RE
869 .RS·14869 .RS·14
870 .I870 .I
871 varfile871 varfile
872 =(output,·required,·io)872 =(required,·output,·io)
873 .RS·2873 .RS·2
874 name·of·the·output·file·to·save·the·variation·image·too..874 name·of·the·output·file·to·save·the·variation·image·too..
875 For·supported·file·types·see·PLUGINS:2dimage/io875 For·supported·file·types·see·PLUGINS:2dimage/io
  
876 .RE876 .RE
877 .RE877 .RE
878 .RS·14878 .RS·14
Offset 902, 15 lines modifiedOffset 902, 15 lines modified
902 .TP·10902 .TP·10
903 .B·medianmad903 .B·medianmad
904 Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·904 Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
905 .P905 .P
906 .RS·14906 .RS·14
907 .I907 .I
908 madfile908 madfile
909 =(output,·required,·io)909 =(required,·output,·io)
910 .RS·2910 .RS·2
911 name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..911 name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
912 For·supported·file·types·see·PLUGINS:2dimage/io912 For·supported·file·types·see·PLUGINS:2dimage/io
  
913 .RE913 .RE
914 .RE914 .RE
915 .RS·14915 .RS·14
Offset 1221, 15 lines modifiedOffset 1221, 15 lines modified
1221 .TP·101221 .TP·10
1222 .B·tee1222 .B·tee
1223 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1223 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1224 .P1224 .P
1225 .RS·141225 .RS·14
1226 .I1226 .I
1227 file1227 file
1228 =(output,·required,·io)1228 =(required,·output,·io)
1229 .RS·21229 .RS·2
1230 name·of·the·output·file·to·save·the·image·too..1230 name·of·the·output·file·to·save·the·image·too..
1231 For·supported·file·types·see·PLUGINS:2dimage/io1231 For·supported·file·types·see·PLUGINS:2dimage/io
  
1232 .RE1232 .RE
1233 .RE1233 .RE
1234 .TP·101234 .TP·10
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./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz
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mia-2dimageseries-maximum-intensity-projection.1
    
Offset 5, 15 lines modifiedOffset 5, 15 lines modified
5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dimageseries\-maximum\-intensity\-projection·\-o·<out\-file>·[options]6 .B··mia\-2dimageseries\-maximum\-intensity\-projection·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dimageseries\-maximum\-intensity\-projection8 .B·mia\-2dimageseries\-maximum\-intensity\-projection
9 This·program·is·used·to·evaluate·the·per-pixel·maximum·intensity·of·an·image·series.9 This·program·is·used·to·evaluate·the·per-pixel·maximum·intensity·of·an·image·series.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-out-file=(output,·required);·io"12 .IP·"\-o·\-\-out-file=(required,·output);·io"
13 output·image13 output·image
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .RE15 .RE
16 .SS·Help·&·Info16 .SS·Help·&·Info
17 .RS17 .RS
18 .IP·"\-V·\-\-verbose=warning"18 .IP·"\-V·\-\-verbose=warning"
19 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:19 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz
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mia-2dimagestack-cmeans.1
    
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6 .B··mia\-2dimagestack\-cmeans·\-i·<in\-file>·\-o·<out\-probmap>·[options]6 .B··mia\-2dimagestack\-cmeans·\-i·<in\-file>·\-o·<out\-probmap>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dimagestack\-cmeans8 .B·mia\-2dimagestack\-cmeans
9 This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram·and·then·writes·the·probability·mapping·for·thr·original·intensity·values9 This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram·and·then·writes·the·probability·mapping·for·thr·original·intensity·values
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(required,·input);·io"13 .IP·"\-i·\-\-in-file=(input,·required);·io"
14 input·image(s)·to·be·filtered14 input·image(s)·to·be·filtered
15 ·For·supported·file·types·see·PLUGINS:2dimage/io15 ·For·supported·file·types·see·PLUGINS:2dimage/io
16 .IP·"\-o·\-\-out-probmap=(required,·output);·string"16 .IP·"\-o·\-\-out-probmap=(output,·required);·string"
17 Save·probability·map·to·this·file17 Save·probability·map·to·this·file
  
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
20 .RS20 .RS
21 .IP·"\-V·\-\-verbose=warning"21 .IP·"\-V·\-\-verbose=warning"
22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-2dimagestats.1.gz
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mia-2dimagestats.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dimagestats·\-i·<in\-file>·[options]6 .B··mia\-2dimagestats·\-i·<in\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dimagestats8 .B·mia\-2dimagestats
9 This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·and·Median·Average·Distance·of·the·intensity·values.·The·program·allows·one·to·set·a·lower·threshold·and·to·cut·off·a·percentage·of·the·high·intensity·pixels9 This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·and·Median·Average·Distance·of·the·intensity·values.·The·program·allows·one·to·set·a·lower·threshold·and·to·cut·off·a·percentage·of·the·high·intensity·pixels
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·image·to·be·analyzed13 input·image·to·be·analyzed
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-t·\-\-thresh=10"15 .IP·"\-t·\-\-thresh=10"
16 intensity·thresh·to·ignore16 intensity·thresh·to·ignore
  
17 .IP·"\-g·\-\-high-thresh=0.05"17 .IP·"\-g·\-\-high-thresh=0.05"
18 upper·histogram·percentage·to·ignore18 upper·histogram·percentage·to·ignore
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./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz
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mia-2dmany2one-nonrigid.1
    
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7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dmany2one\-nonrigid8 .B·mia\-2dmany2one\-nonrigid
9 This·program·registers·all·images·of·a·conscutively·numbered·set·of·images·to·one·common·user·defined·reference.9 This·program·registers·all·images·of·a·conscutively·numbered·set·of·images·to·one·common·user·defined·reference.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·11 .SS·
12 File-IO12 File-IO
13 .RS13 .RS
14 .IP·"\-i·\-\-in-file=(required,·input);·string"14 .IP·"\-i·\-\-in-file=(input,·required);·string"
15 input·perfusion·data·set15 input·perfusion·data·set
  
16 .IP·"\-o·\-\-out-file=(required,·output);·string"16 .IP·"\-o·\-\-out-file=(required,·output);·string"
17 file·name·for·registered·images,·numbering·and·pattern·are·deducted·from·the·input·data17 file·name·for·registered·images,·numbering·and·pattern·are·deducted·from·the·input·data
  
18 .RE18 .RE
19 .SS·19 .SS·
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./usr/share/man/man1/mia-2dmulti-force.1.gz
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mia-2dmulti-force.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dmulti\-force·\-o·<out\-file>·[options]·<PLUGINS:2dimage/fullcost>6 .B··mia\-2dmulti\-force·\-o·<out\-file>·[options]·<PLUGINS:2dimage/fullcost>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dmulti\-force8 .B·mia\-2dmulti\-force
9 This·program·evaluates·the·2D·image·cost·force·norm·image·of·a·given·cost·function·set.·The·input·images·must·be·of·the·same·dimensions·and·gray·scale·(whatever·bit-depth).9 This·program·evaluates·the·2D·image·cost·force·norm·image·of·a·given·cost·function·set.·The·input·images·must·be·of·the·same·dimensions·and·gray·scale·(whatever·bit-depth).
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-out-file=(required,·output);·io"12 .IP·"\-o·\-\-out-file=(output,·required);·io"
13 output·norm·image13 output·norm·image
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .RE15 .RE
16 .SS·Help·&·Info16 .SS·Help·&·Info
17 .RS17 .RS
18 .IP·"\-V·\-\-verbose=warning"18 .IP·"\-V·\-\-verbose=warning"
19 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:19 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz
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mia-2dmyocard-icaseries.1
    
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6 .B··mia\-2dmyocard\-icaseries·\-i·<in\-file>·[options]6 .B··mia\-2dmyocard\-icaseries·\-i·<in\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dmyocard\-icaseries8 .B·mia\-2dmyocard\-icaseries
9 This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this·program·is·essentially·the·same·without·the·registration·bits.9 This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this·program·is·essentially·the·same·without·the·registration·bits.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(input,·required);·string"13 .IP·"\-i·\-\-in-file=(required,·input);·string"
14 input·perfusion·data·set14 input·perfusion·data·set
  
15 .IP·"\-r·\-\-references=(output);·string"15 .IP·"\-r·\-\-references=(output);·string"
16 File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images.16 File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images.
  
17 .IP·"\-c·\-\-save-cropped=(output);·string"17 .IP·"\-c·\-\-save-cropped=(output);·string"
18 save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base18 save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base
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./usr/share/man/man1/mia-2dmyocard-segment.1.gz
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mia-2dmyocard-segment.1
    
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6 .B··mia\-2dmyocard\-segment·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dmyocard\-segment·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dmyocard\-segment8 .B·mia\-2dmyocard\-segment
9 This·program·is·work·in·progress9 This·program·is·work·in·progress
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(input,·required);·string"13 .IP·"\-i·\-\-in-file=(required,·input);·string"
14 input·perfusion·data·set14 input·perfusion·data·set
  
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 output·myocardial·mask16 output·myocardial·mask
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-f·\-\-save-features=(output);·string"18 .IP·"\-f·\-\-save-features=(output);·string"
19 save·ICA·features·to·files·with·this·name·base19 save·ICA·features·to·files·with·this·name·base
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./usr/share/man/man1/mia-2dmyoica-full.1.gz
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mia-2dmyoica-full.1
    
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14 .UE14 .UE
15 .RE15 .RE
  
16 ·The·software·may·first·run·a·linear·registration·and·then·a·non-linear·registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all·registrations·in·parallel.16 ·The·software·may·first·run·a·linear·registration·and·then·a·non-linear·registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all·registrations·in·parallel.
17 .SH·OPTIONS17 .SH·OPTIONS
18 .SS·File-IO18 .SS·File-IO
19 .RS19 .RS
20 .IP·"\-i·\-\-in-file=(input,·required);·string"20 .IP·"\-i·\-\-in-file=(required,·input);·string"
21 input·perfusion·data·set21 input·perfusion·data·set
  
22 .IP·"\-o·\-\-out-file=(required,·output);·string"22 .IP·"\-o·\-\-out-file=(required,·output);·string"
23 output·perfusion·data·set23 output·perfusion·data·set
  
24 .IP·"\-r·\-\-registered="24 .IP·"\-r·\-\-registered="
25 File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.25 File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.
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./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz
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mia-2dmyoica-nonrigid-parallel.1
    
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17 This·version·of·the·program·runs·all·registrations·in·parallel.17 This·version·of·the·program·runs·all·registrations·in·parallel.
18 .SH·OPTIONS18 .SH·OPTIONS
19 .SS·File-IO19 .SS·File-IO
20 .RS20 .RS
21 .IP·"\-i·\-\-in-file=(required,·input);·string"21 .IP·"\-i·\-\-in-file=(required,·input);·string"
22 input·perfusion·data·set22 input·perfusion·data·set
  
23 .IP·"\-o·\-\-out-file=(output,·required);·string"23 .IP·"\-o·\-\-out-file=(required,·output);·string"
24 output·perfusion·data·set24 output·perfusion·data·set
  
25 .IP·"\-r·\-\-registered=reg"25 .IP·"\-r·\-\-registered=reg"
26 File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.26 File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.
  
27 .IP·"···\-\-save-cropped=(output);·string"27 .IP·"···\-\-save-cropped=(output);·string"
28 save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base28 save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base
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./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz
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mia-2dmyoica-nonrigid.1
    
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13 Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.13 Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.
14 .UE14 .UE
15 .RE15 .RE
  
16 .SH·OPTIONS16 .SH·OPTIONS
17 .SS·File-IO17 .SS·File-IO
18 .RS18 .RS
19 .IP·"\-i·\-\-in-file=(required,·input);·string"19 .IP·"\-i·\-\-in-file=(input,·required);·string"
20 input·perfusion·data·set20 input·perfusion·data·set
  
21 .IP·"\-o·\-\-out-file=(output,·required);·string"21 .IP·"\-o·\-\-out-file=(required,·output);·string"
22 output·perfusion·data·set22 output·perfusion·data·set
  
23 .IP·"\-r·\-\-registered=reg"23 .IP·"\-r·\-\-registered=reg"
24 file·name·base·for·registered·fiels24 file·name·base·for·registered·fiels
  
25 .IP·"···\-\-save-cropped="25 .IP·"···\-\-save-cropped="
26 save·cropped·set·to·this·file26 save·cropped·set·to·this·file
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./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz
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mia-2dmyoperiodic-nonrigid.1
    
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17 .SH·OPTIONS17 .SH·OPTIONS
18 .SS·18 .SS·
19 File-IO19 File-IO
20 .RS20 .RS
21 .IP·"\-i·\-\-in-file=(required,·input);·string"21 .IP·"\-i·\-\-in-file=(required,·input);·string"
22 input·perfusion·data·set22 input·perfusion·data·set
  
23 .IP·"\-o·\-\-out-file=(required,·output);·string"23 .IP·"\-o·\-\-out-file=(output,·required);·string"
24 output·perfusion·data·set24 output·perfusion·data·set
  
25 .IP·"\-r·\-\-registered=reg"25 .IP·"\-r·\-\-registered=reg"
26 file·name·base·for·registered·fiels26 file·name·base·for·registered·fiels
  
27 .IP·"···\-\-save-references"27 .IP·"···\-\-save-references"
28 Save·synthetic·references·to·files·refXXXX.v28 Save·synthetic·references·to·files·refXXXX.v
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./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz
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mia-2dmyopgt-nonrigid.1
    
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15 .RE15 .RE
  
16 .·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.16 .·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.
17 .SH·OPTIONS17 .SH·OPTIONS
18 .SS·18 .SS·
19 File-IO19 File-IO
20 .RS20 .RS
21 .IP·"\-i·\-\-in-file=(input,·required);·string"21 .IP·"\-i·\-\-in-file=(required,·input);·string"
22 input·perfusion·data·set22 input·perfusion·data·set
  
23 .IP·"\-o·\-\-out-file=(output,·required);·string"23 .IP·"\-o·\-\-out-file=(output,·required);·string"
24 output·perfusion·data·set24 output·perfusion·data·set
  
25 .IP·"\-r·\-\-registered=reg"25 .IP·"\-r·\-\-registered=reg"
26 file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set26 file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set
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./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz
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mia-2dmyoserial-nonrigid.1
    
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14 .UE14 .UE
15 .RE15 .RE
  
16 .SH·OPTIONS16 .SH·OPTIONS
17 .SS·17 .SS·
18 File-IO18 File-IO
19 .RS19 .RS
20 .IP·"\-i·\-\-in-file=(required,·input);·string"20 .IP·"\-i·\-\-in-file=(input,·required);·string"
21 input·perfusion·data·set21 input·perfusion·data·set
  
22 .IP·"\-o·\-\-out-file=(output,·required);·string"22 .IP·"\-o·\-\-out-file=(output,·required);·string"
23 output·perfusion·data·set23 output·perfusion·data·set
  
24 .IP·"\-R·\-\-registered=reg"24 .IP·"\-R·\-\-registered=reg"
25 file·name·base·for·registered·fiels25 file·name·base·for·registered·fiels
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./usr/share/man/man1/mia-2dmyoseries-dice.1.gz
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mia-2dmyoseries-dice.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dmyoseries\-dice·\-i·<input>·[options]6 .B··mia\-2dmyoseries\-dice·\-i·<input>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dmyoseries\-dice8 .B·mia\-2dmyoseries\-dice
9 This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.9 This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-input=(input,·required);·string"12 .IP·"\-i·\-\-input=(required,·input);·string"
13 original·segmentation·set13 original·segmentation·set
  
14 .IP·"\-k·\-\-skip=2"14 .IP·"\-k·\-\-skip=2"
15 images·to·skip·atthe·bgin·of·the·series15 images·to·skip·atthe·bgin·of·the·series
  
16 .IP·"\-r·\-\-reference=20"16 .IP·"\-r·\-\-reference=20"
17 reference·image17 reference·image
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./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz
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mia-2dmyoset-all2one-nonrigid.1
    
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7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dmyoset\-all2one\-nonrigid8 .B·mia\-2dmyoset\-all2one\-nonrigid
9 This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an·image·set.·All·images·are·registered·to·one·user·defined·reference·image.9 This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an·image·set.·All·images·are·registered·to·one·user·defined·reference·image.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·11 .SS·
12 File-IO12 File-IO
13 .RS13 .RS
14 .IP·"\-i·\-\-in-file=(required,·input);·string"14 .IP·"\-i·\-\-in-file=(input,·required);·string"
15 input·perfusion·data·set15 input·perfusion·data·set
  
16 .IP·"\-o·\-\-out-file=(required,·output);·string"16 .IP·"\-o·\-\-out-file=(output,·required);·string"
17 output·perfusion·data·set17 output·perfusion·data·set
  
18 .IP·"···\-\-out-filebase=reg"18 .IP·"···\-\-out-filebase=reg"
19 file·name·basae·for·registered·files,·file·type·is·deducted·from·the·image·file·type·in·the·input·data·set.19 file·name·basae·for·registered·files,·file·type·is·deducted·from·the·image·file·type·in·the·input·data·set.
  
20 .RE20 .RE
21 .SS·21 .SS·
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./usr/share/man/man1/mia-2dsegment-ahmed.1.gz
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mia-2dsegment-ahmed.1
    
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13 Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,13 Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,
14 .UE14 .UE
15 .RE15 .RE
  
16 ·changes·are:·p=2,·and·exp16 ·changes·are:·p=2,·and·exp
17 .SH·OPTIONS17 .SH·OPTIONS
18 .RS18 .RS
19 .IP·"\-i·\-\-in-file=(required,·input);·io"19 .IP·"\-i·\-\-in-file=(input,·required);·io"
20 image·to·be·segmented20 image·to·be·segmented
21 ·For·supported·file·types·see·PLUGINS:2dimage/io21 ·For·supported·file·types·see·PLUGINS:2dimage/io
22 .IP·"\-o·\-\-out-file=(required,·output);·io"22 .IP·"\-o·\-\-out-file=(required,·output);·io"
23 class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values23 class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values
24 ·For·supported·file·types·see·PLUGINS:2dimage/io24 ·For·supported·file·types·see·PLUGINS:2dimage/io
25 .IP·"\-a·\-\-no-of-classes=3"25 .IP·"\-a·\-\-no-of-classes=3"
26 number·of·classes26 number·of·classes
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./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz
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mia-2dsegment-per-pixel-kmeans.1
    
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6 .B··mia\-2dsegment\-per\-pixel\-kmeans·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dsegment\-per\-pixel\-kmeans·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dsegment\-per\-pixel\-kmeans8 .B·mia\-2dsegment\-per\-pixel\-kmeans
9 This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.9 This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(required,·input);·io"13 .IP·"\-i·\-\-in-file=(input,·required);·io"
14 image·to·be·segmented14 image·to·be·segmented
15 ·For·supported·file·types·see·PLUGINS:2dimage/io15 ·For·supported·file·types·see·PLUGINS:2dimage/io
16 .IP·"\-o·\-\-out-file=(required,·output);·io"16 .IP·"\-o·\-\-out-file=(required,·output);·io"
17 class·label·image·based·on·merging·local·labels17 class·label·image·based·on·merging·local·labels
18 ·For·supported·file·types·see·PLUGINS:2dimage/io18 ·For·supported·file·types·see·PLUGINS:2dimage/io
19 .RE19 .RE
20 .SS·Help·&·Info20 .SS·Help·&·Info
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./usr/share/man/man1/mia-2dsegseriesstats.1.gz
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mia-2dsegseriesstats.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dsegseriesstats·\-o·<original>·\-g·<registered>·[options]6 .B··mia\-2dsegseriesstats·\-o·<original>·\-g·<registered>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dsegseriesstats8 .B·mia\-2dsegseriesstats
9 This·program·is·used·evaluate·various·time-intensity·curves·over·a·series·of·images·given·by·a·segmentation·set.·Specifically,·the·program·is·taylored·to·evaluate·average·intensities·and·variations·of·sections·the·left·ventricle·myocardium.·The·segmentation·set·must·contain·the·segmentations·for·all·slices·that·will·be·accessed·during·evaluation.·9 This·program·is·used·evaluate·various·time-intensity·curves·over·a·series·of·images·given·by·a·segmentation·set.·Specifically,·the·program·is·taylored·to·evaluate·average·intensities·and·variations·of·sections·the·left·ventricle·myocardium.·The·segmentation·set·must·contain·the·segmentations·for·all·slices·that·will·be·accessed·during·evaluation.·
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-original=(required,·input);·string"12 .IP·"\-o·\-\-original=(input,·required);·string"
13 original·segmentation·set13 original·segmentation·set
  
14 .IP·"\-g·\-\-registered=(required,·input);·string"14 .IP·"\-g·\-\-registered=(input,·required);·string"
15 registered·segmentation·set15 registered·segmentation·set
  
16 .IP·"\-k·\-\-skip=2"16 .IP·"\-k·\-\-skip=2"
17 images·to·skip·at·the·begin·of·the·series,·if·(k·<·0)·use·RV·peak·of·the·registered·set·if·set17 images·to·skip·at·the·begin·of·the·series,·if·(k·<·0)·use·RV·peak·of·the·registered·set·if·set
  
18 .IP·"\-r·\-\-reference=\-1"18 .IP·"\-r·\-\-reference=\-1"
19 reference·frame·for·automatic·curve·extraction.·Negative·values·can·be·used·to·indicate·specific·values·(if·given·in·the·segmentation·set):19 reference·frame·for·automatic·curve·extraction.·Negative·values·can·be·used·to·indicate·specific·values·(if·given·in·the·segmentation·set):
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./usr/share/man/man1/mia-2dsegshift.1.gz
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mia-2dsegshift.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dsegshift·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dsegshift·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dsegshift8 .B·mia\-2dsegshift
9 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·equal·for·all·slices.·The·program·also·may·remove·images·from·the·begin·of·the·series.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·the·images·where·cropped.9 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·equal·for·all·slices.·The·program·also·may·remove·images·from·the·begin·of·the·series.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·the·images·where·cropped.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·segmentation·set13 input·segmentation·set
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(output,·required);·io"
16 input·segmentation·set16 input·segmentation·set
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-g·\-\-image-file=crop"18 .IP·"\-g·\-\-image-file=crop"
19 output·image·filename·base19 output·image·filename·base
  
20 .IP·"\-S·\-\-shift=[0,0]"20 .IP·"\-S·\-\-shift=[0,0]"
21 shift·of·segmentation21 shift·of·segmentation
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./usr/share/man/man1/mia-2dsegshiftperslice.1.gz
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mia-2dsegshiftperslice.1
    
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8 .B·mia\-2dsegshiftperslice8 .B·mia\-2dsegshiftperslice
9 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·given·on·a·per-slice·base.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·a·linear·registration·was·executed·that·only·applies·a·translation·and·does·not·correct·the·segmentation·automatically.·9 This·program·move·the·segmentation(s)·of·an·image·series·by·using·a·shift·that·is·given·on·a·per-slice·base.·The·program·can·be·used·to·correct·the·segmentation·of·the·images·if·a·linear·registration·was·executed·that·only·applies·a·translation·and·does·not·correct·the·segmentation·automatically.·
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(required,·input);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(output,·required);·string"14 .IP·"\-o·\-\-out-file=(required,·output);·string"
15 output·segmentation·set15 output·segmentation·set
  
16 .IP·"\-g·\-\-image-file=crop"16 .IP·"\-g·\-\-image-file=crop"
17 output·image·filename·base17 output·image·filename·base
  
18 .IP·"\-S·\-\-shift=(required);·string"18 .IP·"\-S·\-\-shift=(required);·string"
19 shift·of·segmentation·\-·base·name·19 shift·of·segmentation·\-·base·name·
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./usr/share/man/man1/mia-2dseries-sectionmask.1.gz
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mia-2dseries-sectionmask.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseries\-sectionmask·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dseries\-sectionmask·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseries\-sectionmask8 .B·mia\-2dseries\-sectionmask
9 Evaluate·the·masks·for·the·sections·of·a·segmented·frame.9 Evaluate·the·masks·for·the·sections·of·a·segmented·frame.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(required,·output);·io"14 .IP·"\-o·\-\-out-file=(output,·required);·io"
15 output·image·containing·the·mask15 output·image·containing·the·mask
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-f·\-\-frame=0"17 .IP·"\-f·\-\-frame=0"
18 Frame·number·for·which·to·extract·the·mask18 Frame·number·for·which·to·extract·the·mask
  
19 .RE19 .RE
20 .SS·Help·&·Info20 .SS·Help·&·Info
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./usr/share/man/man1/mia-2dseries-segdistance.1.gz
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mia-2dseries-segdistance.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseries\-segdistance·\-i·<in\-file>·[options]6 .B··mia\-2dseries\-segdistance·\-i·<in\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseries\-segdistance8 .B·mia\-2dseries\-segdistance
9 Get·the·mean·distance·of·a·segmentation·boundary·to·the·reference·boundary.9 Get·the·mean·distance·of·a·segmentation·boundary·to·the·reference·boundary.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-r·\-\-reference=20"14 .IP·"\-r·\-\-reference=20"
15 reference·frame15 reference·frame
  
16 .IP·"\-k·\-\-skip=0"16 .IP·"\-k·\-\-skip=0"
17 skip·images·at·the·beginning17 skip·images·at·the·beginning
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./usr/share/man/man1/mia-2dseries2dordermedian.1.gz
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mia-2dseries2dordermedian.1
    
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8 .B·mia\-2dseries2dordermedian8 .B·mia\-2dseries2dordermedian
9 This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the·gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In·addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given·pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving·additional·filters·as·free·parameters·(filter/2dimage).9 This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the·gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In·addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given·pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving·additional·filters·as·free·parameters·(filter/2dimage).
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(required,·output);·io"14 .IP·"\-o·\-\-out-file=(output,·required);·io"
15 output·image·name15 output·image·name
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-k·\-\-skip=0"17 .IP·"\-k·\-\-skip=0"
18 Skip·files·at·the·beginning18 Skip·files·at·the·beginning
  
19 .IP·"\-e·\-\-enlarge-boundary=5"19 .IP·"\-e·\-\-enlarge-boundary=5"
20 Enlarge·cropbox·by·number·of·pixels20 Enlarge·cropbox·by·number·of·pixels
Offset 842, 15 lines modifiedOffset 842, 15 lines modified
842 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.842 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.
  
843 .RE843 .RE
844 .RE844 .RE
845 .RS·14845 .RS·14
846 .I846 .I
847 varfile847 varfile
848 =(required,·output,·io)848 =(output,·required,·io)
849 .RS·2849 .RS·2
850 name·of·the·output·file·to·save·the·variation·image·too..850 name·of·the·output·file·to·save·the·variation·image·too..
851 For·supported·file·types·see·PLUGINS:2dimage/io851 For·supported·file·types·see·PLUGINS:2dimage/io
  
852 .RE852 .RE
853 .RE853 .RE
854 .RS·14854 .RS·14
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878 .TP·10878 .TP·10
879 .B·medianmad879 .B·medianmad
880 Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·880 Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
881 .P881 .P
882 .RS·14882 .RS·14
883 .I883 .I
884 madfile884 madfile
885 =(required,·output,·io)885 =(output,·required,·io)
886 .RS·2886 .RS·2
887 name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..887 name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
888 For·supported·file·types·see·PLUGINS:2dimage/io888 For·supported·file·types·see·PLUGINS:2dimage/io
  
889 .RE889 .RE
890 .RE890 .RE
891 .RS·14891 .RS·14
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1197 .TP·101197 .TP·10
1198 .B·tee1198 .B·tee
1199 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1199 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1200 .P1200 .P
1201 .RS·141201 .RS·14
1202 .I1202 .I
1203 file1203 file
1204 =(required,·output,·io)1204 =(output,·required,·io)
1205 .RS·21205 .RS·2
1206 name·of·the·output·file·to·save·the·image·too..1206 name·of·the·output·file·to·save·the·image·too..
1207 For·supported·file·types·see·PLUGINS:2dimage/io1207 For·supported·file·types·see·PLUGINS:2dimage/io
  
1208 .RE1208 .RE
1209 .RE1209 .RE
1210 .TP·101210 .TP·10
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./usr/share/man/man1/mia-2dseries2sets.1.gz
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mia-2dseries2sets.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseries2sets·\-o·<out\-directory>·[options]·<PLUGINS:2dimage/io>6 .B··mia\-2dseries2sets·\-o·<out\-directory>·[options]·<PLUGINS:2dimage/io>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseries2sets8 .B·mia\-2dseries2sets
9 This·program·takes·all·image·files·that·are·given·as·free·parameters·on·the·command·line·and·creates·segmentation·sets·based·on·information·found·in·the·images.·Used·information·is·the·z-location·of·the·slice·and·the·acquisition·number.·The·code·is·taylored·to·used·the·according·descriptors·defined·in·the·DICOM·standard.·All·images·with·the·same·slice·location·will·be·grouped·together·in·one·segmentation·set·and·ordered·according·to·their·acquisition·number.·Slice·locations·are·rounded·to·three·digits·accuracy·to·make·proper·comparison·of·floating·point·values·feasible.9 This·program·takes·all·image·files·that·are·given·as·free·parameters·on·the·command·line·and·creates·segmentation·sets·based·on·information·found·in·the·images.·Used·information·is·the·z-location·of·the·slice·and·the·acquisition·number.·The·code·is·taylored·to·used·the·according·descriptors·defined·in·the·DICOM·standard.·All·images·with·the·same·slice·location·will·be·grouped·together·in·one·segmentation·set·and·ordered·according·to·their·acquisition·number.·Slice·locations·are·rounded·to·three·digits·accuracy·to·make·proper·comparison·of·floating·point·values·feasible.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-out-directory=(required,·output);·string"12 .IP·"\-o·\-\-out-directory=(output,·required);·string"
13 output·directory·(needs·to·exist·and·be·writable)13 output·directory·(needs·to·exist·and·be·writable)
  
14 .IP·"···\-\-no-copy"14 .IP·"···\-\-no-copy"
15 don't·copy·image·files·to·output·directory15 don't·copy·image·files·to·output·directory
  
16 .RE16 .RE
17 .SS·Help·&·Info17 .SS·Help·&·Info
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./usr/share/man/man1/mia-2dseriescorr.1.gz
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mia-2dseriescorr.1
    
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8 .B·mia\-2dseriescorr8 .B·mia\-2dseriescorr
9 Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent·the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as·average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be·of·the·same·pixel·type·and·size.9 Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent·the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as·average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be·of·the·same·pixel·type·and·size.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-base=(required,·input);·io"12 .IP·"\-i·\-\-in-base=(required,·input);·io"
13 input·file·name·base13 input·file·name·base
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-o·\-\-outname=(output,·required);·io"15 .IP·"\-o·\-\-outname=(required,·output);·io"
16 output·file·name·to·save·the·avarage·per\-pixel·correlation16 output·file·name·to·save·the·avarage·per\-pixel·correlation
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-z·\-\-horizontal=(output);·io"18 .IP·"\-z·\-\-horizontal=(output);·io"
19 horiZontal·correlation·output·file·name19 horiZontal·correlation·output·file·name
20 ·For·supported·file·types·see·PLUGINS:2dimage/io20 ·For·supported·file·types·see·PLUGINS:2dimage/io
21 .IP·"\-t·\-\-vertical=(output);·io"21 .IP·"\-t·\-\-vertical=(output);·io"
22 verTical··correlation·output·file·name22 verTical··correlation·output·file·name
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./usr/share/man/man1/mia-2dseriesgradMAD.1.gz
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mia-2dseriesgradMAD.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseriesgradMAD·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter>6 .B··mia\-2dseriesgradMAD·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseriesgradMAD8 .B·mia\-2dseriesgradMAD
9 Given·a·set·of·images·of·temporal·sucession,·evaluates·the·pixel-wise·temporal·gradient·and·then·its·median·average·distance·(MAD)·and·stores·the·result·in·an·image.·Spacial·pre-filtering·may·be·applied·as·given·additional·plugin(s)·(filter/2dimage).9 Given·a·set·of·images·of·temporal·sucession,·evaluates·the·pixel-wise·temporal·gradient·and·then·its·median·average·distance·(MAD)·and·stores·the·result·in·an·image.·Spacial·pre-filtering·may·be·applied·as·given·additional·plugin(s)·(filter/2dimage).
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(output,·required);·io"14 .IP·"\-o·\-\-out-file=(required,·output);·io"
15 output·file·name15 output·file·name
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-k·\-\-skip=0"17 .IP·"\-k·\-\-skip=0"
18 Skip·files·at·the·beginning18 Skip·files·at·the·beginning
  
19 .IP·"\-e·\-\-enlarge-boundary=5"19 .IP·"\-e·\-\-enlarge-boundary=5"
20 Enlarge·cropbox·by·number·of·pixels20 Enlarge·cropbox·by·number·of·pixels
Offset 355, 15 lines modifiedOffset 355, 15 lines modified
355 .TP·10355 .TP·10
356 .B·combiner356 .B·combiner
357 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·357 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
358 .P358 .P
359 .RS·14359 .RS·14
360 .I360 .I
361 image361 image
362 =(required,·input,·io)362 =(input,·required,·io)
363 .RS·2363 .RS·2
364 second·image·that·is·needed·in·the·combiner.364 second·image·that·is·needed·in·the·combiner.
365 For·supported·file·types·see·PLUGINS:2dimage/io365 For·supported·file·types·see·PLUGINS:2dimage/io
  
366 .RE366 .RE
367 .RE367 .RE
368 .RS·14368 .RS·14
Offset 699, 15 lines modifiedOffset 699, 15 lines modified
699 .TP·10699 .TP·10
700 .B·labelmap700 .B·labelmap
701 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·701 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
702 .P702 .P
703 .RS·14703 .RS·14
704 .I704 .I
705 map705 map
706 =(required,·input,·string)706 =(input,·required,·string)
707 .RS·2707 .RS·2
708 Label·mapping·file.708 Label·mapping·file.
  
709 .RE709 .RE
710 .RE710 .RE
711 .TP·10711 .TP·10
712 .B·labelscale712 .B·labelscale
Offset 725, 15 lines modifiedOffset 725, 15 lines modified
725 .TP·10725 .TP·10
726 .B·load726 .B·load
727 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·727 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
728 .P728 .P
729 .RS·14729 .RS·14
730 .I730 .I
731 file731 file
732 =(required,·input,·io)732 =(input,·required,·io)
733 .RS·2733 .RS·2
734 name·of·the·input·file·to·load·from..734 name·of·the·input·file·to·load·from..
735 For·supported·file·types·see·PLUGINS:2dimage/io735 For·supported·file·types·see·PLUGINS:2dimage/io
  
736 .RE736 .RE
737 .RE737 .RE
738 .TP·10738 .TP·10
Offset 764, 15 lines modifiedOffset 764, 15 lines modified
764 .RE764 .RE
  
765 .RE765 .RE
766 .RE766 .RE
767 .RS·14767 .RS·14
768 .I768 .I
769 input769 input
770 =(required,·input,·io)770 =(input,·required,·io)
771 .RS·2771 .RS·2
772 second·input·image·file·name.772 second·input·image·file·name.
773 For·supported·file·types·see·PLUGINS:2dimage/io773 For·supported·file·types·see·PLUGINS:2dimage/io
  
774 .RE774 .RE
775 .RE775 .RE
776 .RS·14776 .RS·14
Offset 787, 25 lines modifiedOffset 787, 25 lines modified
787 .TP·10787 .TP·10
788 .B·maxflow788 .B·maxflow
789 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·789 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·
790 .P790 .P
791 .RS·14791 .RS·14
792 .I792 .I
793 sink-flow793 sink-flow
794 =(required,·input,·io)794 =(input,·required,·io)
795 .RS·2795 .RS·2
796 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.796 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.
797 For·supported·file·types·see·PLUGINS:2dimage/io797 For·supported·file·types·see·PLUGINS:2dimage/io
  
798 .RE798 .RE
799 .RE799 .RE
800 .RS·14800 .RS·14
801 .I801 .I
802 source-flow802 source-flow
803 =(required,·input,·io)803 =(input,·required,·io)
804 .RS·2804 .RS·2
805 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.805 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.
806 For·supported·file·types·see·PLUGINS:2dimage/io806 For·supported·file·types·see·PLUGINS:2dimage/io
  
807 .RE807 .RE
808 .RE808 .RE
809 .TP·10809 .TP·10
Offset 833, 15 lines modifiedOffset 833, 15 lines modified
833 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.833 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.
  
834 .RE834 .RE
835 .RE835 .RE
836 .RS·14836 .RS·14
837 .I837 .I
838 varfile838 varfile
839 =(output,·required,·io)839 =(required,·output,·io)
840 .RS·2840 .RS·2
841 name·of·the·output·file·to·save·the·variation·image·too..841 name·of·the·output·file·to·save·the·variation·image·too..
842 For·supported·file·types·see·PLUGINS:2dimage/io842 For·supported·file·types·see·PLUGINS:2dimage/io
  
843 .RE843 .RE
844 .RE844 .RE
845 .RS·14845 .RS·14
Offset 869, 15 lines modifiedOffset 869, 15 lines modified
869 .TP·10869 .TP·10
870 .B·medianmad870 .B·medianmad
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./usr/share/man/man1/mia-2dseriesgradvariation.1.gz
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mia-2dseriesgradvariation.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseriesgradvariation·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dseriesgradvariation·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseriesgradvariation8 .B·mia\-2dseriesgradvariation
9 Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·gradient·variation·of·the·pixel-wise·time-intensity·curves·of·this·series.·If·the·input·image·set·provides·a·segmentation,·then·this·segmentation·can·be·used·to·create·a·bounding·box·and·restrict·evaluation·to·this·box.·9 Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·gradient·variation·of·the·pixel-wise·time-intensity·curves·of·this·series.·If·the·input·image·set·provides·a·segmentation,·then·this·segmentation·can·be·used·to·create·a·bounding·box·and·restrict·evaluation·to·this·box.·
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·string"12 .IP·"\-i·\-\-in-file=(required,·input);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(output,·required);·io"14 .IP·"\-o·\-\-out-file=(required,·output);·io"
15 output·file·name15 output·file·name
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-k·\-\-skip=0"17 .IP·"\-k·\-\-skip=0"
18 Skip·files·at·the·beginning18 Skip·files·at·the·beginning
  
19 .IP·"\-e·\-\-enlarge-boundary=5"19 .IP·"\-e·\-\-enlarge-boundary=5"
20 Enlarge·cropbox·by·number·of·pixels20 Enlarge·cropbox·by·number·of·pixels
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./usr/share/man/man1/mia-2dserieshausdorff.1.gz
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mia-2dserieshausdorff.1
    
Offset 5, 18 lines modifiedOffset 5, 18 lines modified
5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dserieshausdorff·\-i·<in\-file>·\-r·<ref\-file>·[options]6 .B··mia\-2dserieshausdorff·\-i·<in\-file>·\-r·<ref\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dserieshausdorff8 .B·mia\-2dserieshausdorff
9 Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given·reference·segmentation·set.9 Get·the·per-slice·Hausdorff·distance·of·a·segmentation·with·respect·to·a·given·reference·segmentation·set.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-r·\-\-ref-file=(required,·input);·string"14 .IP·"\-r·\-\-ref-file=(input,·required);·string"
15 reference·segmentation·set15 reference·segmentation·set
  
16 .IP·"\-k·\-\-skip=0"16 .IP·"\-k·\-\-skip=0"
17 skip·images·at·the·beginning17 skip·images·at·the·beginning
  
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
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./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz
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mia-2dseriessmoothgradMAD.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseriessmoothgradMAD·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter>6 .B··mia\-2dseriessmoothgradMAD·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseriessmoothgradMAD8 .B·mia\-2dseriessmoothgradMAD
9 Given·a·set·of·images·of·temporal·sucession,·evaluate·the·temporal·pixel-wise·gaussian·and·evaluate·pixel-wise·its·MAD.A·spacial·pre-filtering·may·be·applied·by·specifying·additional·plugins·(filter/2dimage)9 Given·a·set·of·images·of·temporal·sucession,·evaluate·the·temporal·pixel-wise·gaussian·and·evaluate·pixel-wise·its·MAD.A·spacial·pre-filtering·may·be·applied·by·specifying·additional·plugins·(filter/2dimage)
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(required,·output);·io"14 .IP·"\-o·\-\-out-file=(output,·required);·io"
15 output·file·name15 output·file·name
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-k·\-\-skip=0"17 .IP·"\-k·\-\-skip=0"
18 Skip·files·at·the·beginning18 Skip·files·at·the·beginning
  
19 .IP·"\-e·\-\-enlarge-boundary=5"19 .IP·"\-e·\-\-enlarge-boundary=5"
20 Enlarge·cropbox·by·number·of·pixels20 Enlarge·cropbox·by·number·of·pixels
Offset 358, 15 lines modifiedOffset 358, 15 lines modified
358 .TP·10358 .TP·10
359 .B·combiner359 .B·combiner
360 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·360 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
361 .P361 .P
362 .RS·14362 .RS·14
363 .I363 .I
364 image364 image
365 =(required,·input,·io)365 =(input,·required,·io)
366 .RS·2366 .RS·2
367 second·image·that·is·needed·in·the·combiner.367 second·image·that·is·needed·in·the·combiner.
368 For·supported·file·types·see·PLUGINS:2dimage/io368 For·supported·file·types·see·PLUGINS:2dimage/io
  
369 .RE369 .RE
370 .RE370 .RE
371 .RS·14371 .RS·14
Offset 702, 15 lines modifiedOffset 702, 15 lines modified
702 .TP·10702 .TP·10
703 .B·labelmap703 .B·labelmap
704 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·704 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
705 .P705 .P
706 .RS·14706 .RS·14
707 .I707 .I
708 map708 map
709 =(required,·input,·string)709 =(input,·required,·string)
710 .RS·2710 .RS·2
711 Label·mapping·file.711 Label·mapping·file.
  
712 .RE712 .RE
713 .RE713 .RE
714 .TP·10714 .TP·10
715 .B·labelscale715 .B·labelscale
Offset 728, 15 lines modifiedOffset 728, 15 lines modified
728 .TP·10728 .TP·10
729 .B·load729 .B·load
730 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·730 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
731 .P731 .P
732 .RS·14732 .RS·14
733 .I733 .I
734 file734 file
735 =(required,·input,·io)735 =(input,·required,·io)
736 .RS·2736 .RS·2
737 name·of·the·input·file·to·load·from..737 name·of·the·input·file·to·load·from..
738 For·supported·file·types·see·PLUGINS:2dimage/io738 For·supported·file·types·see·PLUGINS:2dimage/io
  
739 .RE739 .RE
740 .RE740 .RE
741 .TP·10741 .TP·10
Offset 767, 15 lines modifiedOffset 767, 15 lines modified
767 .RE767 .RE
  
768 .RE768 .RE
769 .RE769 .RE
770 .RS·14770 .RS·14
771 .I771 .I
772 input772 input
773 =(required,·input,·io)773 =(input,·required,·io)
774 .RS·2774 .RS·2
775 second·input·image·file·name.775 second·input·image·file·name.
776 For·supported·file·types·see·PLUGINS:2dimage/io776 For·supported·file·types·see·PLUGINS:2dimage/io
  
777 .RE777 .RE
778 .RE778 .RE
779 .RS·14779 .RS·14
Offset 790, 25 lines modifiedOffset 790, 25 lines modified
790 .TP·10790 .TP·10
791 .B·maxflow791 .B·maxflow
792 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·792 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·
793 .P793 .P
794 .RS·14794 .RS·14
795 .I795 .I
796 sink-flow796 sink-flow
797 =(required,·input,·io)797 =(input,·required,·io)
798 .RS·2798 .RS·2
799 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.799 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.
800 For·supported·file·types·see·PLUGINS:2dimage/io800 For·supported·file·types·see·PLUGINS:2dimage/io
  
801 .RE801 .RE
802 .RE802 .RE
803 .RS·14803 .RS·14
804 .I804 .I
805 source-flow805 source-flow
806 =(required,·input,·io)806 =(input,·required,·io)
807 .RS·2807 .RS·2
808 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.808 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.
809 For·supported·file·types·see·PLUGINS:2dimage/io809 For·supported·file·types·see·PLUGINS:2dimage/io
  
810 .RE810 .RE
811 .RE811 .RE
812 .TP·10812 .TP·10
Offset 836, 15 lines modifiedOffset 836, 15 lines modified
836 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.836 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.
  
837 .RE837 .RE
838 .RE838 .RE
839 .RS·14839 .RS·14
840 .I840 .I
841 varfile841 varfile
842 =(required,·output,·io)842 =(output,·required,·io)
843 .RS·2843 .RS·2
844 name·of·the·output·file·to·save·the·variation·image·too..844 name·of·the·output·file·to·save·the·variation·image·too..
845 For·supported·file·types·see·PLUGINS:2dimage/io845 For·supported·file·types·see·PLUGINS:2dimage/io
  
846 .RE846 .RE
847 .RE847 .RE
848 .RS·14848 .RS·14
Offset 872, 15 lines modifiedOffset 872, 15 lines modified
872 .TP·10872 .TP·10
873 .B·medianmad873 .B·medianmad
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./usr/share/man/man1/mia-2dseriestovolume.1.gz
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mia-2dseriestovolume.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dseriestovolume·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dseriestovolume·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dseriestovolume8 .B·mia\-2dseriestovolume
9 Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.9 Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·segmentation·set13 input·segmentation·set
  
14 .IP·"\-o·\-\-out-file=(required,·output);·io"14 .IP·"\-o·\-\-out-file=(output,·required);·io"
15 output·3D·image·15 output·3D·image·
16 ·For·supported·file·types·see·PLUGINS:3dimage/io16 ·For·supported·file·types·see·PLUGINS:3dimage/io
17 .IP·"\-k·\-\-skip=0"17 .IP·"\-k·\-\-skip=0"
18 number·of·frames·to·skip·at·the·beginning·of·the·series.18 number·of·frames·to·skip·at·the·beginning·of·the·series.
  
19 .RE19 .RE
20 .SS·Help·&·Info20 .SS·Help·&·Info
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./usr/share/man/man1/mia-2dstackfilter.1.gz
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mia-2dstackfilter.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dstackfilter·\-i·<in\-file>·\-o·<out\-file>·\-t·<type>·[options]·<PLUGINS:2dstack/filter>6 .B··mia\-2dstackfilter·\-i·<in\-file>·\-o·<out\-file>·\-t·<type>·[options]·<PLUGINS:2dstack/filter>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dstackfilter8 .B·mia\-2dstackfilter
9 This·program·is·used·to·filter·and·convert·a·series·of·2D·gray·scale·images·in·a·3D·fashion·by·running·filters·(filter/2dimage)·as·given·on·the·command·line.9 This·program·is·used·to·filter·and·convert·a·series·of·2D·gray·scale·images·in·a·3D·fashion·by·running·filters·(filter/2dimage)·as·given·on·the·command·line.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·image(s)·to·be·filtered13 input·image(s)·to·be·filtered
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-o·\-\-out-file=(output,·required);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 output·file·name·base,·the·actual·names·is·created·by·adding·the·file·number·based·on·output·order·and·the·extension·bysed·on·the·'type'·parameter16 output·file·name·base,·the·actual·names·is·created·by·adding·the·file·number·based·on·output·order·and·the·extension·bysed·on·the·'type'·parameter
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-t·\-\-type=(required);·set"18 .IP·"\-t·\-\-type=(required);·set"
19 output·file·type19 output·file·type
  
20 .RS·1020 .RS·10
21 .I21 .I
Offset 378, 15 lines modifiedOffset 378, 15 lines modified
378 .TP·10378 .TP·10
379 .B·combiner379 .B·combiner
380 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·380 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
381 .P381 .P
382 .RS·14382 .RS·14
383 .I383 .I
384 image384 image
385 =(required,·input,·io)385 =(input,·required,·io)
386 .RS·2386 .RS·2
387 second·image·that·is·needed·in·the·combiner.387 second·image·that·is·needed·in·the·combiner.
388 For·supported·file·types·see·PLUGINS:2dimage/io388 For·supported·file·types·see·PLUGINS:2dimage/io
  
389 .RE389 .RE
390 .RE390 .RE
391 .RS·14391 .RS·14
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722 .TP·10722 .TP·10
723 .B·labelmap723 .B·labelmap
724 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·724 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
725 .P725 .P
726 .RS·14726 .RS·14
727 .I727 .I
728 map728 map
729 =(required,·input,·string)729 =(input,·required,·string)
730 .RS·2730 .RS·2
731 Label·mapping·file.731 Label·mapping·file.
  
732 .RE732 .RE
733 .RE733 .RE
734 .TP·10734 .TP·10
735 .B·labelscale735 .B·labelscale
Offset 748, 15 lines modifiedOffset 748, 15 lines modified
748 .TP·10748 .TP·10
749 .B·load749 .B·load
750 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·750 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
751 .P751 .P
752 .RS·14752 .RS·14
753 .I753 .I
754 file754 file
755 =(required,·input,·io)755 =(input,·required,·io)
756 .RS·2756 .RS·2
757 name·of·the·input·file·to·load·from..757 name·of·the·input·file·to·load·from..
758 For·supported·file·types·see·PLUGINS:2dimage/io758 For·supported·file·types·see·PLUGINS:2dimage/io
  
759 .RE759 .RE
760 .RE760 .RE
761 .TP·10761 .TP·10
Offset 787, 15 lines modifiedOffset 787, 15 lines modified
787 .RE787 .RE
  
788 .RE788 .RE
789 .RE789 .RE
790 .RS·14790 .RS·14
791 .I791 .I
792 input792 input
793 =(required,·input,·io)793 =(input,·required,·io)
794 .RS·2794 .RS·2
795 second·input·image·file·name.795 second·input·image·file·name.
796 For·supported·file·types·see·PLUGINS:2dimage/io796 For·supported·file·types·see·PLUGINS:2dimage/io
  
797 .RE797 .RE
798 .RE798 .RE
799 .RS·14799 .RS·14
Offset 810, 25 lines modifiedOffset 810, 25 lines modified
810 .TP·10810 .TP·10
811 .B·maxflow811 .B·maxflow
812 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·812 This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·
813 .P813 .P
814 .RS·14814 .RS·14
815 .I815 .I
816 sink-flow816 sink-flow
817 =(required,·input,·io)817 =(input,·required,·io)
818 .RS·2818 .RS·2
819 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.819 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.
820 For·supported·file·types·see·PLUGINS:2dimage/io820 For·supported·file·types·see·PLUGINS:2dimage/io
  
821 .RE821 .RE
822 .RE822 .RE
823 .RS·14823 .RS·14
824 .I824 .I
825 source-flow825 source-flow
826 =(required,·input,·io)826 =(input,·required,·io)
827 .RS·2827 .RS·2
828 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.828 Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.
829 For·supported·file·types·see·PLUGINS:2dimage/io829 For·supported·file·types·see·PLUGINS:2dimage/io
  
830 .RE830 .RE
831 .RE831 .RE
832 .TP·10832 .TP·10
Offset 856, 15 lines modifiedOffset 856, 15 lines modified
856 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.856 Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.
  
857 .RE857 .RE
858 .RE858 .RE
859 .RS·14859 .RS·14
860 .I860 .I
861 varfile861 varfile
862 =(output,·required,·io)862 =(required,·output,·io)
863 .RS·2863 .RS·2
864 name·of·the·output·file·to·save·the·variation·image·too..864 name·of·the·output·file·to·save·the·variation·image·too..
865 For·supported·file·types·see·PLUGINS:2dimage/io865 For·supported·file·types·see·PLUGINS:2dimage/io
  
866 .RE866 .RE
867 .RE867 .RE
868 .RS·14868 .RS·14
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892 .TP·10892 .TP·10
893 .B·medianmad893 .B·medianmad
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./usr/share/man/man1/mia-2dto3dimage.1.gz
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mia-2dto3dimage.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dto3dimage·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dto3dimage·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dto3dimage8 .B·mia\-2dto3dimage
9 This·program·is·used·to·combine·a·series·of·2D·images·of·equal·size·and·type·images·following·a·certain·numbering·scheme·to·a·3D·image.9 This·program·is·used·to·combine·a·series·of·2D·images·of·equal·size·and·type·images·following·a·certain·numbering·scheme·to·a·3D·image.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image(s)·to·be·combined13 input·image(s)·to·be·combined
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-o·\-\-out-file=(output,·required);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 output·file·name16 output·file·name
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
20 .RS20 .RS
21 .IP·"\-V·\-\-verbose=warning"21 .IP·"\-V·\-\-verbose=warning"
22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-2dto3dimageb.1.gz
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mia-2dto3dimageb.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dto3dimageb·\-o·<out\-file>·[options]·<PLUGINS:2dimage/io>6 .B··mia\-2dto3dimageb·\-o·<out\-file>·[options]·<PLUGINS:2dimage/io>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dto3dimageb8 .B·mia\-2dto3dimageb
9 This·program·is·used·to·convert·a·series·2D·images·into·a·3D·image.·The·2D·images·are·read·as·additional·command·line·parameters·and·the·slice·ordering·corresponds·to·the·ordering·of·the·file·names·on·the·commend·line.9 This·program·is·used·to·convert·a·series·2D·images·into·a·3D·image.·The·2D·images·are·read·as·additional·command·line·parameters·and·the·slice·ordering·corresponds·to·the·ordering·of·the·file·names·on·the·commend·line.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-out-file=(required,·output);·io"12 .IP·"\-o·\-\-out-file=(output,·required);·io"
13 output·file·name13 output·file·name
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .RE15 .RE
16 .SS·Help·&·Info16 .SS·Help·&·Info
17 .RS17 .RS
18 .IP·"\-V·\-\-verbose=warning"18 .IP·"\-V·\-\-verbose=warning"
19 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:19 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz
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mia-2dtrackpixelmovement.1
    
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13 .SH·OPTIONS13 .SH·OPTIONS
14 .SS·14 .SS·
15 File-IO15 File-IO
16 .RS16 .RS
17 .IP·"\-i·\-\-in-file=(required,·input);·string"17 .IP·"\-i·\-\-in-file=(required,·input);·string"
18 input·point·set18 input·point·set
  
19 .IP·"\-o·\-\-out-file=(required,·output);·string"19 .IP·"\-o·\-\-out-file=(output,·required);·string"
20 output·point·set20 output·point·set
  
21 .IP·"\-t·\-\-transformation=(required,·input);·io"21 .IP·"\-t·\-\-transformation=(required,·input);·io"
22 transformation·describing·the·monitored·change22 transformation·describing·the·monitored·change
23 ·For·supported·file·types·see·PLUGINS:2dtransform/io23 ·For·supported·file·types·see·PLUGINS:2dtransform/io
24 .RE24 .RE
25 .SS·25 .SS·
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./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz
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mia-2dtransformation-to-strain.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-2dtransformation\-to\-strain·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-2dtransformation\-to\-strain·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-2dtransformation\-to\-strain8 .B·mia\-2dtransformation\-to\-strain
9 Evaluate·the·Green·strain·tensor·corresponding·to·a·given·2D·transformation·for·each·grid·point.9 Evaluate·the·Green·strain·tensor·corresponding·to·a·given·2D·transformation·for·each·grid·point.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·transformation13 input·transformation
14 ·For·supported·file·types·see·PLUGINS:2dtransform/io14 ·For·supported·file·types·see·PLUGINS:2dtransform/io
15 .IP·"\-o·\-\-out-file=(required,·output);·string"15 .IP·"\-o·\-\-out-file=(output,·required);·string"
16 output·Green's·strain·tensor16 output·Green's·strain·tensor
  
17 .RE17 .RE
18 .SS·Help·&·Info18 .SS·Help·&·Info
19 .RS19 .RS
20 .IP·"\-V·\-\-verbose=warning"20 .IP·"\-V·\-\-verbose=warning"
21 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:21 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dbinarycombine.1.gz
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mia-3dbinarycombine.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dbinarycombine·\-1·<file1>·\-2·<file2>·\-o·<out\-file>·[options]6 .B··mia\-3dbinarycombine·\-1·<file1>·\-2·<file2>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dbinarycombine8 .B·mia\-3dbinarycombine
9 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.9 This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-1·\-\-file1=(required,·input);·io"12 .IP·"\-1·\-\-file1=(input,·required);·io"
13 input·mask·image·113 input·mask·image·1
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-2·\-\-file2=(required,·input);·io"15 .IP·"\-2·\-\-file2=(input,·required);·io"
16 input·mask·image·216 input·mask·image·2
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-p·\-\-operation=nor"18 .IP·"\-p·\-\-operation=nor"
19 Operation·to·be·applied19 Operation·to·be·applied
  
20 .RS·1020 .RS·10
21 .I21 .I
Offset 44, 15 lines modifiedOffset 44, 15 lines modified
44 \(hy·logocal·xor44 \(hy·logocal·xor
45 .RE45 .RE
46 .RS·1046 .RS·10
47 .I47 .I
48 nxor48 nxor
49 \(hy·logocal·nxor49 \(hy·logocal·nxor
50 .RE50 .RE
51 .IP·"\-o·\-\-out-file=(required,·output);·io"51 .IP·"\-o·\-\-out-file=(output,·required);·io"
52 output·mask·image52 output·mask·image
53 ·For·supported·file·types·see·PLUGINS:3dimage/io53 ·For·supported·file·types·see·PLUGINS:3dimage/io
54 .RE54 .RE
55 .SS·Help·&·Info55 .SS·Help·&·Info
56 .RS56 .RS
57 .IP·"\-V·\-\-verbose=warning"57 .IP·"\-V·\-\-verbose=warning"
58 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:58 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dbrainextractT1.1.gz
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mia-3dbrainextractT1.1
    
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8 .B·mia\-3dbrainextractT18 .B·mia\-3dbrainextractT1
9 This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter·segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to·obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the·brain·from·the·B0·field·corrected·images.9 This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter·segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to·obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the·brain·from·the·B0·field·corrected·images.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·image(s)·to·be·segmented13 input·image(s)·to·be·segmented
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(output,·required);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 brain·mask16 brain·mask
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-n·\-\-no-of-classes=3"18 .IP·"\-n·\-\-no-of-classes=3"
19 number·of·classes19 number·of·classes
  
20 .IP·"\-w·\-\-wm-class=2"20 .IP·"\-w·\-\-wm-class=2"
21 index·of·white·matter21 index·of·white·matter
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./usr/share/man/man1/mia-3dcombine-imageseries.1.gz
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mia-3dcombine-imageseries.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dcombine\-imageseries·\-o·<out\-file>·[options]·<PLUGINS:3dimage/io>6 .B··mia\-3dcombine\-imageseries·\-o·<out\-file>·[options]·<PLUGINS:3dimage/io>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dcombine\-imageseries8 .B·mia\-3dcombine\-imageseries
9 This·programs·takes·various·input·images·of·the·same·dimensions·and·creates·a·combined·output·images·that·uses·the·define·operation·for·the·combination.9 This·programs·takes·various·input·images·of·the·same·dimensions·and·creates·a·combined·output·images·that·uses·the·define·operation·for·the·combination.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-out-file=(output,·required);·io"12 .IP·"\-o·\-\-out-file=(required,·output);·io"
13 output·file·that·contains·the·combined·image.13 output·file·that·contains·the·combined·image.
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-p·\-\-operation=mean"15 .IP·"\-p·\-\-operation=mean"
16 Operation·to·be·applied·when·combining·the·images16 Operation·to·be·applied·when·combining·the·images
  
17 .RS·1017 .RS·10
18 .I18 .I
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./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz
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mia-3dcombine-mr-segmentations.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dcombine\-mr\-segmentations·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:3dimage/io>6 .B··mia\-3dcombine\-mr\-segmentations·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:3dimage/io>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dcombine\-mr\-segmentations8 .B·mia\-3dcombine\-mr\-segmentations
9 This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue·probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are·translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel·is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.9 This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue·probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are·translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel·is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·probability·images.·The·number·of·mask·images·must·correspond·to·the·number·of·probability·images·given·here.13 input·probability·images.·The·number·of·mask·images·must·correspond·to·the·number·of·probability·images·given·here.
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(output,·required);·io"
16 output·image·that·contains·the·labeling.16 output·image·that·contains·the·labeling.
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
20 .RS20 .RS
21 .IP·"\-V·\-\-verbose=warning"21 .IP·"\-V·\-\-verbose=warning"
22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz
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mia-3dcost-translatedgrad.1
    
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11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·image·13 input·image·
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-r·\-\-ref-file=(input,·required);·io"15 .IP·"\-r·\-\-ref-file=(input,·required);·io"
16 reference·image·16 reference·image·
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-o·\-\-out-file=(output,·required);·io"18 .IP·"\-o·\-\-out-file=(required,·output);·io"
19 output·vector·field·19 output·vector·field·
20 ·For·supported·file·types·see·PLUGINS:3dtransform/io20 ·For·supported·file·types·see·PLUGINS:3dtransform/io
21 .IP·"\-g·\-\-gradimg-file=(output);·io"21 .IP·"\-g·\-\-gradimg-file=(output);·io"
22 norm·image·of·the·spline·transformed·gradient22 norm·image·of·the·spline·transformed·gradient
23 ·For·supported·file·types·see·PLUGINS:3dimage/io23 ·For·supported·file·types·see·PLUGINS:3dimage/io
24 .IP·"\-C·\-\-cost-gradimg-file=(output);·io"24 .IP·"\-C·\-\-cost-gradimg-file=(output);·io"
25 norm·image·of·the·cost·gradient25 norm·image·of·the·cost·gradient
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./usr/share/man/man1/mia-3dcost.1.gz
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mia-3dcost.1
    
Offset 403, 15 lines modifiedOffset 403, 15 lines modified
403 .TP·10403 .TP·10
404 .B·combiner404 .B·combiner
405 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·405 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
406 .P406 .P
407 .RS·14407 .RS·14
408 .I408 .I
409 image409 image
410 =(required,·input,·io)410 =(input,·required,·io)
411 .RS·2411 .RS·2
412 second·image·that·is·needed·in·the·combiner.412 second·image·that·is·needed·in·the·combiner.
413 For·supported·file·types·see·PLUGINS:3dimage/io413 For·supported·file·types·see·PLUGINS:3dimage/io
  
414 .RE414 .RE
415 .RE415 .RE
416 .RS·14416 .RS·14
Offset 717, 15 lines modifiedOffset 717, 15 lines modified
717 lower·threshold·for·mask·growing.717 lower·threshold·for·mask·growing.
  
718 .RE718 .RE
719 .RE719 .RE
720 .RS·14720 .RS·14
721 .I721 .I
722 ref722 ref
723 =(required,·input,·io)723 =(input,·required,·io)
724 .RS·2724 .RS·2
725 reference·image·for·mask·region·growing.725 reference·image·for·mask·region·growing.
726 For·supported·file·types·see·PLUGINS:3dimage/io726 For·supported·file·types·see·PLUGINS:3dimage/io
  
727 .RE727 .RE
728 .RE728 .RE
729 .RS·14729 .RS·14
Offset 798, 15 lines modifiedOffset 798, 15 lines modified
798 .TP·10798 .TP·10
799 .B·labelmap799 .B·labelmap
800 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·800 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
801 .P801 .P
802 .RS·14802 .RS·14
803 .I803 .I
804 map804 map
805 =(required,·input,·string)805 =(input,·required,·string)
806 .RS·2806 .RS·2
807 Label·mapping·file.807 Label·mapping·file.
  
808 .RE808 .RE
809 .RE809 .RE
810 .TP·10810 .TP·10
811 .B·labelscale811 .B·labelscale
Offset 824, 15 lines modifiedOffset 824, 15 lines modified
824 .TP·10824 .TP·10
825 .B·load825 .B·load
826 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·826 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
827 .P827 .P
828 .RS·14828 .RS·14
829 .I829 .I
830 file830 file
831 =(required,·input,·io)831 =(input,·required,·io)
832 .RS·2832 .RS·2
833 name·of·the·input·file·to·load·from..833 name·of·the·input·file·to·load·from..
834 For·supported·file·types·see·PLUGINS:3dimage/io834 For·supported·file·types·see·PLUGINS:3dimage/io
  
835 .RE835 .RE
836 .RE836 .RE
837 .TP·10837 .TP·10
Offset 851, 15 lines modifiedOffset 851, 15 lines modified
851 .TP·10851 .TP·10
852 .B·mask852 .B·mask
853 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·853 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·
854 .P854 .P
855 .RS·14855 .RS·14
856 .I856 .I
857 input857 input
858 =(required,·input,·io)858 =(input,·required,·io)
859 .RS·2859 .RS·2
860 second·input·image·file·name.860 second·input·image·file·name.
861 For·supported·file·types·see·PLUGINS:3dimage/io861 For·supported·file·types·see·PLUGINS:3dimage/io
  
862 .RE862 .RE
863 .RE863 .RE
864 .TP·10864 .TP·10
Offset 1241, 15 lines modifiedOffset 1241, 15 lines modified
1241 For·supported·plug-ins·see·PLUGINS:3dimage/shape1241 For·supported·plug-ins·see·PLUGINS:3dimage/shape
  
1242 .RE1242 .RE
1243 .RE1243 .RE
1244 .RS·141244 .RS·14
1245 .I1245 .I
1246 seed1246 seed
1247 =(required,·input,·string)1247 =(input,·required,·string)
1248 .RS·21248 .RS·2
1249 seed·input·image·containing·the·lables·for·the·initial·regions.1249 seed·input·image·containing·the·lables·for·the·initial·regions.
  
1250 .RE1250 .RE
1251 .RE1251 .RE
1252 .TP·101252 .TP·10
1253 .B·tee1253 .B·tee
Offset 1275, 15 lines modifiedOffset 1275, 15 lines modified
1275 .TP·101275 .TP·10
1276 .B·transform1276 .B·transform
1277 Transform·the·input·image·with·the·given·transformation.,·supported·parameters·are:·1277 Transform·the·input·image·with·the·given·transformation.,·supported·parameters·are:·
1278 .P1278 .P
1279 .RS·141279 .RS·14
1280 .I1280 .I
1281 file1281 file
1282 =(required,·input,·io)1282 =(input,·required,·io)
1283 .RS·21283 .RS·2
1284 Name·of·the·file·containing·the·transformation..1284 Name·of·the·file·containing·the·transformation..
1285 For·supported·file·types·see·PLUGINS:3dtransform/io1285 For·supported·file·types·see·PLUGINS:3dtransform/io
  
1286 .RE1286 .RE
1287 .RE1287 .RE
1288 .RS·141288 .RS·14
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./usr/share/man/man1/mia-3dcrispsegment.1.gz
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mia-3dcrispsegment.1
    
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8 .B·mia\-3dcrispsegment8 .B·mia\-3dcrispsegment
9 This·program·creates·a·label·image·from·a·fuzzy·segmentation.·or·each·pixel·the·label·is·set·to·the·class·with·the·higest·probability·plus·a·given·offset9 This·program·creates·a·label·image·from·a·fuzzy·segmentation.·or·each·pixel·the·label·is·set·to·the·class·with·the·higest·probability·plus·a·given·offset
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·class·file,·should·contain·multiple·images·with·tissue·class·probabilities13 input·class·file,·should·contain·multiple·images·with·tissue·class·probabilities
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(output,·required);·io"
16 output·class·label·image16 output·class·label·image
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-l·\-\-label-offset=1"18 .IP·"\-l·\-\-label-offset=1"
19 label·offset19 label·offset
  
20 .RE20 .RE
21 .SS·Help·&·Info21 .SS·Help·&·Info
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./usr/share/man/man1/mia-3ddeform.1.gz
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mia-3ddeform.1
    
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8 .B·mia\-3ddeform8 .B·mia\-3ddeform
9 Transform·a·3D·image·by·applying·a·given·3D·transformation·that·is·defined·by·a·3D·vector·field·v·according·to·x:=x-v(x)9 Transform·a·3D·image·by·applying·a·given·3D·transformation·that·is·defined·by·a·3D·vector·field·v·according·to·x:=x-v(x)
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-image=(input,·required);·io"12 .IP·"\-i·\-\-in-image=(input,·required);·io"
13 input·image13 input·image
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-image=(output,·required);·io"15 .IP·"\-o·\-\-out-image=(required,·output);·io"
16 transformed·image16 transformed·image
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-t·\-\-transformation=(input,·required);·io"18 .IP·"\-t·\-\-transformation=(input,·required);·io"
19 transformation·vector·field19 transformation·vector·field
20 ·For·supported·file·types·see·PLUGINS:3dvf/io20 ·For·supported·file·types·see·PLUGINS:3dvf/io
21 .IP·"\-p·\-\-interpolator=bspline:d=3"21 .IP·"\-p·\-\-interpolator=bspline:d=3"
22 image·interpolator·kernel22 image·interpolator·kernel
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./usr/share/man/man1/mia-3ddistance-stats.1.gz
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mia-3ddistance-stats.1
    
Offset 24, 24 lines modifiedOffset 24, 24 lines modified
24 ········cat(result)24 ········cat(result)
25 ····}25 ····}
  
  
26 .SH·OPTIONS26 .SH·OPTIONS
27 .SS·File-IO27 .SS·File-IO
28 .RS28 .RS
29 .IP·"\-i·\-\-in-labels=(input,·required);·io"29 .IP·"\-i·\-\-in-labels=(required,·input);·io"
30 input·label·image30 input·label·image
31 ·For·supported·file·types·see·PLUGINS:3dimage/io31 ·For·supported·file·types·see·PLUGINS:3dimage/io
32 .IP·"\-r·\-\-ref-labels=(input,·required);·io"32 .IP·"\-r·\-\-ref-labels=(required,·input);·io"
33 reference·label·image33 reference·label·image
34 ·For·supported·file·types·see·PLUGINS:3dimage/io34 ·For·supported·file·types·see·PLUGINS:3dimage/io
35 .IP·"\-l·\-\-label-map=(input);·string"35 .IP·"\-l·\-\-label-map=(input);·string"
36 optional·mapping·of·label·numbers36 optional·mapping·of·label·numbers
  
37 .IP·"\-o·\-\-out-file=(output,·required);·string"37 .IP·"\-o·\-\-out-file=(required,·output);·string"
38 output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.38 output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.
  
39 .RE39 .RE
40 .SS·Help·&·Info40 .SS·Help·&·Info
41 .RS41 .RS
42 .IP·"\-V·\-\-verbose=warning"42 .IP·"\-V·\-\-verbose=warning"
43 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:43 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3deval-transformquantity.1.gz
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mia-3deval-transformquantity.1
    
Offset 27, 18 lines modifiedOffset 27, 18 lines modified
27 .SH·OPTIONS27 .SH·OPTIONS
28 .SS·28 .SS·
29 File-IO29 File-IO
30 .RS30 .RS
31 .IP·"\-i·\-\-in-file=(input);·string"31 .IP·"\-i·\-\-in-file=(input);·string"
32 input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.32 input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.
  
33 .IP·"\-o·\-\-out-file=(required,·output);·string"33 .IP·"\-o·\-\-out-file=(output,·required);·string"
34 output·strains·file,·for·a·format·description·see·above.34 output·strains·file,·for·a·format·description·see·above.
  
35 .IP·"\-t·\-\-transformation=(required,·input);·io"35 .IP·"\-t·\-\-transformation=(input,·required);·io"
36 transformation·of·which·the·quantity·will·be·evaluated.36 transformation·of·which·the·quantity·will·be·evaluated.
37 ·For·supported·file·types·see·PLUGINS:3dtransform/io37 ·For·supported·file·types·see·PLUGINS:3dtransform/io
38 .RE38 .RE
39 .SS·39 .SS·
40 Parameters40 Parameters
41 .RS41 .RS
42 .IP·"\-q·\-\-quantity=strain"42 .IP·"\-q·\-\-quantity=strain"
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./usr/share/man/man1/mia-3dfield2norm.1.gz
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mia-3dfield2norm.1
    
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8 .B·mia\-3dfield2norm8 .B·mia\-3dfield2norm
9 This·program·converts·a·3d·vector·field·to·an·image·of·its·voxel-wise·norm.9 This·program·converts·a·3d·vector·field·to·an·image·of·its·voxel-wise·norm.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-vectorfield=(input,·required);·io"12 .IP·"\-i·\-\-in-vectorfield=(input,·required);·io"
13 input·vector·field13 input·vector·field
14 ·For·supported·file·types·see·PLUGINS:3dvf/io14 ·For·supported·file·types·see·PLUGINS:3dvf/io
15 .IP·"\-o·\-\-out-image=(output,·required);·io"15 .IP·"\-o·\-\-out-image=(required,·output);·io"
16 output·image·comprising·the·per·voxel·norm·of·each·image16 output·image·comprising·the·per·voxel·norm·of·each·image
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
20 .RS20 .RS
21 .IP·"\-V·\-\-verbose=warning"21 .IP·"\-V·\-\-verbose=warning"
22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz
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mia-3dfluid-syn-registration.1
    
Offset 64, 24 lines modifiedOffset 64, 24 lines modified
  
64 .IP·"···\-\-version"64 .IP·"···\-\-version"
65 print·the·version·number·and·exit65 print·the·version·number·and·exit
  
66 .RE66 .RE
67 .SS·IO67 .SS·IO
68 .RS68 .RS
69 .IP·"\-i·\-\-in-image=(required,·input);·io"69 .IP·"\-i·\-\-in-image=(input,·required);·io"
70 test·image70 test·image
71 ·For·supported·file·types·see·PLUGINS:3dimage/io71 ·For·supported·file·types·see·PLUGINS:3dimage/io
72 .IP·"\-r·\-\-ref-image=(required,·input);·io"72 .IP·"\-r·\-\-ref-image=(input,·required);·io"
73 reference·image73 reference·image
74 ·For·supported·file·types·see·PLUGINS:3dimage/io74 ·For·supported·file·types·see·PLUGINS:3dimage/io
75 .IP·"\-o·\-\-transform=(output,·required);·io"75 .IP·"\-o·\-\-transform=(required,·output);·io"
76 output·transformation76 output·transformation
77 ·For·supported·file·types·see·PLUGINS:3dtransform/io77 ·For·supported·file·types·see·PLUGINS:3dtransform/io
78 .IP·"\-O·\-\-inverse-transform=(output,·required);·io"78 .IP·"\-O·\-\-inverse-transform=(required,·output);·io"
79 inverse·output·transformation79 inverse·output·transformation
80 ·For·supported·file·types·see·PLUGINS:3dtransform/io80 ·For·supported·file·types·see·PLUGINS:3dtransform/io
81 .RE81 .RE
82 .SS·Processing82 .SS·Processing
83 .RS83 .RS
84 .IP·"···\-\-threads=\-1"84 .IP·"···\-\-threads=\-1"
85 Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).85 Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).
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./usr/share/man/man1/mia-3dforce.1.gz
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mia-3dforce.1
    
Offset 11, 15 lines modifiedOffset 11, 15 lines modified
11 .RS11 .RS
12 .IP·"\-i·\-\-src-file=(input,·required);·io"12 .IP·"\-i·\-\-src-file=(input,·required);·io"
13 input·image13 input·image
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-r·\-\-ref-file=(input,·required);·io"15 .IP·"\-r·\-\-ref-file=(input,·required);·io"
16 output·force·norm·image16 output·force·norm·image
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-o·\-\-out-file=(required,·output);·io"18 .IP·"\-o·\-\-out-file=(output,·required);·io"
19 reference·image19 reference·image
20 ·For·supported·file·types·see·PLUGINS:3dimage/io20 ·For·supported·file·types·see·PLUGINS:3dimage/io
21 .IP·"\-c·\-\-cost=ssd"21 .IP·"\-c·\-\-cost=ssd"
22 cost·function·to·use22 cost·function·to·use
23 ·For·supported·plugins·see·PLUGINS:3dimage/cost23 ·For·supported·plugins·see·PLUGINS:3dimage/cost
24 .RE24 .RE
25 .SS·Help·&·Info25 .SS·Help·&·Info
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./usr/share/man/man1/mia-3dfuzzysegment.1.gz
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mia-3dfuzzysegment.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dfuzzysegment·\-i·<in\-file>·[options]6 .B··mia\-3dfuzzysegment·\-i·<in\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dfuzzysegment8 .B·mia\-3dfuzzysegment
9 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image9 This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image(s)·to·be·segmenetd13 input·image(s)·to·be·segmenetd
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-c·\-\-cls-file=(output);·io"15 .IP·"\-c·\-\-cls-file=(output);·io"
16 output·class·probability·images.·Note,·the·used·file·format·must·support·multible·images·(best·is·to·use·vista)16 output·class·probability·images.·Note,·the·used·file·format·must·support·multible·images·(best·is·to·use·vista)
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-o·\-\-b0-file=(output);·io"18 .IP·"\-o·\-\-b0-file=(output);·io"
19 image·corrected·for·intensity·non\-uniformity19 image·corrected·for·intensity·non\-uniformity
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./usr/share/man/man1/mia-3dimageaddattributes.1.gz
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mia-3dimageaddattributes.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dimageaddattributes·\-i·<in\-file>·\-o·<out\-file>·\-a·<attr>·[options]6 .B··mia\-3dimageaddattributes·\-i·<in\-file>·\-o·<out\-file>·\-a·<attr>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dimageaddattributes8 .B·mia\-3dimageaddattributes
9 This·program·appends·all·the·meta-data·attributes·found·in·a·2D·input·image·to·a·3D·image·(if·the·output·format·supports·such·attributes).·Attributes·that·are·already·present·in·the·3D·image·are·not·overwritten.9 This·program·appends·all·the·meta-data·attributes·found·in·a·2D·input·image·to·a·3D·image·(if·the·output·format·supports·such·attributes).·Attributes·that·are·already·present·in·the·3D·image·are·not·overwritten.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image(s)·to·be·filtered13 input·image(s)·to·be·filtered
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(output,·required);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 output·image(s)·with·the·added·attributes16 output·image(s)·with·the·added·attributes
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-a·\-\-attr=(input,·required);·io"18 .IP·"\-a·\-\-attr=(required,·input);·io"
19 2D·image·providing·the·attributes19 2D·image·providing·the·attributes
20 ·For·supported·file·types·see·PLUGINS:2dimage/io20 ·For·supported·file·types·see·PLUGINS:2dimage/io
21 .RE21 .RE
22 .SS·Help·&·Info22 .SS·Help·&·Info
23 .RS23 .RS
24 .IP·"\-V·\-\-verbose=warning"24 .IP·"\-V·\-\-verbose=warning"
25 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:25 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dimagefilterstack.1.gz
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mia-3dimagefilterstack.1
    
Offset 5, 18 lines modifiedOffset 5, 18 lines modified
5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dimagefilterstack·\-i·<in\-file>·\-o·<out\-file>·\-t·<type>·[options]·<PLUGINS:3dimage/filter>6 .B··mia\-3dimagefilterstack·\-i·<in\-file>·\-o·<out\-file>·\-t·<type>·[options]·<PLUGINS:3dimage/filter>
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dimagefilterstack8 .B·mia\-3dimagefilterstack
9 This·program·is·used·to·filter·and·convert·a·consecutive·numbered·series·gray·of·scale·images.·File·names·must·follow·the·pattern·'dataXXXX.v'·(X·being·digits),·i.e.·the·numbering·comes·right·before·the·dot.·9 This·program·is·used·to·filter·and·convert·a·consecutive·numbered·series·gray·of·scale·images.·File·names·must·follow·the·pattern·'dataXXXX.v'·(X·being·digits),·i.e.·the·numbering·comes·right·before·the·dot.·
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·image(s)·to·be·filtered13 input·image(s)·to·be·filtered
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(output,·required);·io"
16 output·file·name·base,·numbers·are·added·accorfing·to·the·input·file·pattern,·and·the·file··extension·is·added·according·to·the·'type'·option.16 output·file·name·base,·numbers·are·added·accorfing·to·the·input·file·pattern,·and·the·file··extension·is·added·according·to·the·'type'·option.
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-t·\-\-type=(required);·set"18 .IP·"\-t·\-\-type=(required);·set"
19 output·file·type19 output·file·type
  
20 .RS·1020 .RS·10
21 .I21 .I
Offset 283, 15 lines modifiedOffset 283, 15 lines modified
283 .TP·10283 .TP·10
284 .B·combiner284 .B·combiner
285 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·285 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
286 .P286 .P
287 .RS·14287 .RS·14
288 .I288 .I
289 image289 image
290 =(required,·input,·io)290 =(input,·required,·io)
291 .RS·2291 .RS·2
292 second·image·that·is·needed·in·the·combiner.292 second·image·that·is·needed·in·the·combiner.
293 For·supported·file·types·see·PLUGINS:3dimage/io293 For·supported·file·types·see·PLUGINS:3dimage/io
  
294 .RE294 .RE
295 .RE295 .RE
296 .RS·14296 .RS·14
Offset 597, 15 lines modifiedOffset 597, 15 lines modified
597 lower·threshold·for·mask·growing.597 lower·threshold·for·mask·growing.
  
598 .RE598 .RE
599 .RE599 .RE
600 .RS·14600 .RS·14
601 .I601 .I
602 ref602 ref
603 =(required,·input,·io)603 =(input,·required,·io)
604 .RS·2604 .RS·2
605 reference·image·for·mask·region·growing.605 reference·image·for·mask·region·growing.
606 For·supported·file·types·see·PLUGINS:3dimage/io606 For·supported·file·types·see·PLUGINS:3dimage/io
  
607 .RE607 .RE
608 .RE608 .RE
609 .RS·14609 .RS·14
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678 .TP·10678 .TP·10
679 .B·labelmap679 .B·labelmap
680 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·680 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
681 .P681 .P
682 .RS·14682 .RS·14
683 .I683 .I
684 map684 map
685 =(required,·input,·string)685 =(input,·required,·string)
686 .RS·2686 .RS·2
687 Label·mapping·file.687 Label·mapping·file.
  
688 .RE688 .RE
689 .RE689 .RE
690 .TP·10690 .TP·10
691 .B·labelscale691 .B·labelscale
Offset 704, 15 lines modifiedOffset 704, 15 lines modified
704 .TP·10704 .TP·10
705 .B·load705 .B·load
706 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·706 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
707 .P707 .P
708 .RS·14708 .RS·14
709 .I709 .I
710 file710 file
711 =(required,·input,·io)711 =(input,·required,·io)
712 .RS·2712 .RS·2
713 name·of·the·input·file·to·load·from..713 name·of·the·input·file·to·load·from..
714 For·supported·file·types·see·PLUGINS:3dimage/io714 For·supported·file·types·see·PLUGINS:3dimage/io
  
715 .RE715 .RE
716 .RE716 .RE
717 .TP·10717 .TP·10
Offset 731, 15 lines modifiedOffset 731, 15 lines modified
731 .TP·10731 .TP·10
732 .B·mask732 .B·mask
733 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·733 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·
734 .P734 .P
735 .RS·14735 .RS·14
736 .I736 .I
737 input737 input
738 =(required,·input,·io)738 =(input,·required,·io)
739 .RS·2739 .RS·2
740 second·input·image·file·name.740 second·input·image·file·name.
741 For·supported·file·types·see·PLUGINS:3dimage/io741 For·supported·file·types·see·PLUGINS:3dimage/io
  
742 .RE742 .RE
743 .RE743 .RE
744 .TP·10744 .TP·10
Offset 1121, 28 lines modifiedOffset 1121, 28 lines modified
1121 For·supported·plug-ins·see·PLUGINS:3dimage/shape1121 For·supported·plug-ins·see·PLUGINS:3dimage/shape
  
1122 .RE1122 .RE
1123 .RE1123 .RE
1124 .RS·141124 .RS·14
1125 .I1125 .I
1126 seed1126 seed
1127 =(required,·input,·string)1127 =(input,·required,·string)
1128 .RS·21128 .RS·2
1129 seed·input·image·containing·the·lables·for·the·initial·regions.1129 seed·input·image·containing·the·lables·for·the·initial·regions.
  
1130 .RE1130 .RE
1131 .RE1131 .RE
1132 .TP·101132 .TP·10
1133 .B·tee1133 .B·tee
1134 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1134 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1135 .P1135 .P
1136 .RS·141136 .RS·14
1137 .I1137 .I
1138 file1138 file
1139 =(required,·output,·io)1139 =(output,·required,·io)
1140 .RS·21140 .RS·2
1141 name·of·the·output·file·to·save·the·image·too..1141 name·of·the·output·file·to·save·the·image·too..
1142 For·supported·file·types·see·PLUGINS:3dimage/io1142 For·supported·file·types·see·PLUGINS:3dimage/io
  
1143 .RE1143 .RE
1144 .RE1144 .RE
1145 .TP·101145 .TP·10
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./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz
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mia-3dimagestatistics-in-mask.1
    
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6 .B··mia\-3dimagestatistics\-in\-mask·\-i·<image>·\-m·<mask>·[options]6 .B··mia\-3dimagestatistics\-in\-mask·\-i·<image>·\-m·<mask>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dimagestatistics\-in\-mask8 .B·mia\-3dimagestatistics\-in\-mask
9 This·program·evaluates·the·statistics·of·an·image·within·a·masked·region·of·the·image.·Possible·outputs·are·a·summary·statistics·and·a·histogram·of·the·values.9 This·program·evaluates·the·statistics·of·an·image·within·a·masked·region·of·the·image.·Possible·outputs·are·a·summary·statistics·and·a·histogram·of·the·values.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-image=(required,·input);·io"13 .IP·"\-i·\-\-image=(input,·required);·io"
14 input·image·to·be·analyzed14 input·image·to·be·analyzed
15 ·For·supported·file·types·see·PLUGINS:3dimage/io15 ·For·supported·file·types·see·PLUGINS:3dimage/io
16 .IP·"\-m·\-\-mask=(required,·input);·io"16 .IP·"\-m·\-\-mask=(input,·required);·io"
17 mask·image·to·use·to·restrict·the·analysis17 mask·image·to·use·to·restrict·the·analysis
18 ·For·supported·file·types·see·PLUGINS:3dimage/io18 ·For·supported·file·types·see·PLUGINS:3dimage/io
19 .IP·"\-s·\-\-summary=(output);·string"19 .IP·"\-s·\-\-summary=(output);·string"
20 File·to·write·the·summary·statistics·to·as·plain·text.20 File·to·write·the·summary·statistics·to·as·plain·text.
  
21 .IP·"\-H·\-\-histogram=(output);·string"21 .IP·"\-H·\-\-histogram=(output);·string"
22 File·to·write·the·histogram·to22 File·to·write·the·histogram·to
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./usr/share/man/man1/mia-3disosurface-from-stack.1.gz
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mia-3disosurface-from-stack.1
    
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6 .B··mia\-3disosurface\-from\-stack·\-i·<in\-image>·\-o·<out\-mesh>·[options]6 .B··mia\-3disosurface\-from\-stack·\-i·<in\-image>·\-o·<out\-mesh>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3disosurface\-from\-stack8 .B·mia\-3disosurface\-from\-stack
9 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·given·as·slices.9 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·given·as·slices.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-image=(required,·input);·string"13 .IP·"\-i·\-\-in-image=(input,·required);·string"
14 input·image·filename·pattern14 input·image·filename·pattern
  
15 .IP·"\-o·\-\-out-mesh=(required,·output);·string"15 .IP·"\-o·\-\-out-mesh=(required,·output);·string"
16 output·mesh16 output·mesh
  
17 .RE17 .RE
18 .SS·Help·&·Info18 .SS·Help·&·Info
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./usr/share/man/man1/mia-3disosurface-from-volume.1.gz
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mia-3disosurface-from-volume.1
    
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6 .B··mia\-3disosurface\-from\-volume·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-3disosurface\-from\-volume·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3disosurface\-from\-volume8 .B·mia\-3disosurface\-from\-volume
9 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·by·using·marching·thetrahedra.9 This·program·is·used·to·extract·an·iso-surface·from·the·input·gray·scale·image·by·using·marching·thetrahedra.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File-IO11 .SS·File-IO
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(input,·required);·io"13 .IP·"\-i·\-\-in-file=(required,·input);·io"
14 input·image14 input·image
15 ·For·supported·file·types·see·PLUGINS:3dimage/io15 ·For·supported·file·types·see·PLUGINS:3dimage/io
16 .IP·"\-o·\-\-out-file=(output,·required);·io"16 .IP·"\-o·\-\-out-file=(required,·output);·io"
17 output·mesh17 output·mesh
18 ·For·supported·file·types·see·PLUGINS:mesh/io18 ·For·supported·file·types·see·PLUGINS:mesh/io
19 .RE19 .RE
20 .SS·Help·&·Info20 .SS·Help·&·Info
21 .RS21 .RS
22 .IP·"\-V·\-\-verbose=warning"22 .IP·"\-V·\-\-verbose=warning"
23 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:23 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dlandmarks-distances.1.gz
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mia-3dlandmarks-distances.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dlandmarks\-distances·\-i·<in\-file\-1>·\-o·<in\-file\-2>·[options]6 .B··mia\-3dlandmarks\-distances·\-i·<in\-file\-1>·\-o·<in\-file\-2>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dlandmarks\-distances8 .B·mia\-3dlandmarks\-distances
9 Evaluate·Euclidian·distances·between·the·corresponding·landmarks·in·two·landmark·sets.·The·programs·prints·out·only·values·for·landmarks·that·are·available·and·have·location·values·in·both·sets·9 Evaluate·Euclidian·distances·between·the·corresponding·landmarks·in·two·landmark·sets.·The·programs·prints·out·only·values·for·landmarks·that·are·available·and·have·location·values·in·both·sets·
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file-1=(required,·input);·io"12 .IP·"\-i·\-\-in-file-1=(input,·required);·io"
13 input·landmark·set·113 input·landmark·set·1
14 ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io14 ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io
15 .IP·"\-o·\-\-in-file-2=(required,·input);·io"15 .IP·"\-o·\-\-in-file-2=(input,·required);·io"
16 input·landmark·set·216 input·landmark·set·2
17 ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io17 ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
20 .RS20 .RS
21 .IP·"\-V·\-\-verbose=warning"21 .IP·"\-V·\-\-verbose=warning"
22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dlerp.1.gz
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mia-3dlerp.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dlerp·\-1·<first>·\-2·<second>·\-o·<out\-file>·\-p·<positions>·[options]6 .B··mia\-3dlerp·\-1·<first>·\-2·<second>·\-o·<out\-file>·\-p·<positions>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dlerp8 .B·mia\-3dlerp
9 merge·two·images·by·linear·combination.9 merge·two·images·by·linear·combination.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-1·\-\-first=(required,·input);·io"12 .IP·"\-1·\-\-first=(input,·required);·io"
13 first·input·image·13 first·input·image·
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-2·\-\-second=(required,·input);·io"15 .IP·"\-2·\-\-second=(input,·required);·io"
16 second·input·image·16 second·input·image·
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-o·\-\-out-file=(output,·required);·io"18 .IP·"\-o·\-\-out-file=(required,·output);·io"
19 linearly·interpolated·image19 linearly·interpolated·image
20 ·For·supported·file·types·see·PLUGINS:3dimage/io20 ·For·supported·file·types·see·PLUGINS:3dimage/io
21 .IP·"\-p·\-\-positions=(required);·vfloat"21 .IP·"\-p·\-\-positions=(required);·vfloat"
22 image·series·positions·(first,·target,·second)22 image·series·positions·(first,·target,·second)
  
23 .RE23 .RE
24 .SS·Help·&·Info24 .SS·Help·&·Info
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./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz
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mia-3dmany2one-nonrigid.1
    
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7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dmany2one\-nonrigid8 .B·mia\-3dmany2one\-nonrigid
9 This·program·runs·the·non-rigid·registration·of·an·image·series·by·registereing·all·images·to·a·user-selected·reference.9 This·program·runs·the·non-rigid·registration·of·an·image·series·by·registereing·all·images·to·a·user-selected·reference.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·11 .SS·
12 File-IO12 File-IO
13 .RS13 .RS
14 .IP·"\-i·\-\-in-file=(input,·required);·io"14 .IP·"\-i·\-\-in-file=(required,·input);·io"
15 input·perfusion·data·set15 input·perfusion·data·set
16 ·For·supported·file·types·see·PLUGINS:3dimage/io16 ·For·supported·file·types·see·PLUGINS:3dimage/io
17 .IP·"\-o·\-\-out-file=(output);·io"17 .IP·"\-o·\-\-out-file=(output);·io"
18 file·name·for·registered·files18 file·name·for·registered·files
19 ·For·supported·file·types·see·PLUGINS:3dimage/io19 ·For·supported·file·types·see·PLUGINS:3dimage/io
20 .RE20 .RE
21 .SS·21 .SS·
Offset 429, 15 lines modifiedOffset 429, 15 lines modified
429 .TP·10429 .TP·10
430 .B·combiner430 .B·combiner
431 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·431 Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
432 .P432 .P
433 .RS·14433 .RS·14
434 .I434 .I
435 image435 image
436 =(input,·required,·io)436 =(required,·input,·io)
437 .RS·2437 .RS·2
438 second·image·that·is·needed·in·the·combiner.438 second·image·that·is·needed·in·the·combiner.
439 For·supported·file·types·see·PLUGINS:3dimage/io439 For·supported·file·types·see·PLUGINS:3dimage/io
  
440 .RE440 .RE
441 .RE441 .RE
442 .RS·14442 .RS·14
Offset 743, 15 lines modifiedOffset 743, 15 lines modified
743 lower·threshold·for·mask·growing.743 lower·threshold·for·mask·growing.
  
744 .RE744 .RE
745 .RE745 .RE
746 .RS·14746 .RS·14
747 .I747 .I
748 ref748 ref
749 =(input,·required,·io)749 =(required,·input,·io)
750 .RS·2750 .RS·2
751 reference·image·for·mask·region·growing.751 reference·image·for·mask·region·growing.
752 For·supported·file·types·see·PLUGINS:3dimage/io752 For·supported·file·types·see·PLUGINS:3dimage/io
  
753 .RE753 .RE
754 .RE754 .RE
755 .RS·14755 .RS·14
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824 .TP·10824 .TP·10
825 .B·labelmap825 .B·labelmap
826 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·826 Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
827 .P827 .P
828 .RS·14828 .RS·14
829 .I829 .I
830 map830 map
831 =(input,·required,·string)831 =(required,·input,·string)
832 .RS·2832 .RS·2
833 Label·mapping·file.833 Label·mapping·file.
  
834 .RE834 .RE
835 .RE835 .RE
836 .TP·10836 .TP·10
837 .B·labelscale837 .B·labelscale
Offset 850, 15 lines modifiedOffset 850, 15 lines modified
850 .TP·10850 .TP·10
851 .B·load851 .B·load
852 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·852 Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
853 .P853 .P
854 .RS·14854 .RS·14
855 .I855 .I
856 file856 file
857 =(input,·required,·io)857 =(required,·input,·io)
858 .RS·2858 .RS·2
859 name·of·the·input·file·to·load·from..859 name·of·the·input·file·to·load·from..
860 For·supported·file·types·see·PLUGINS:3dimage/io860 For·supported·file·types·see·PLUGINS:3dimage/io
  
861 .RE861 .RE
862 .RE862 .RE
863 .TP·10863 .TP·10
Offset 877, 15 lines modifiedOffset 877, 15 lines modified
877 .TP·10877 .TP·10
878 .B·mask878 .B·mask
879 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·879 Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·
880 .P880 .P
881 .RS·14881 .RS·14
882 .I882 .I
883 input883 input
884 =(input,·required,·io)884 =(required,·input,·io)
885 .RS·2885 .RS·2
886 second·input·image·file·name.886 second·input·image·file·name.
887 For·supported·file·types·see·PLUGINS:3dimage/io887 For·supported·file·types·see·PLUGINS:3dimage/io
  
888 .RE888 .RE
889 .RE889 .RE
890 .TP·10890 .TP·10
Offset 1267, 28 lines modifiedOffset 1267, 28 lines modified
1267 For·supported·plug-ins·see·PLUGINS:3dimage/shape1267 For·supported·plug-ins·see·PLUGINS:3dimage/shape
  
1268 .RE1268 .RE
1269 .RE1269 .RE
1270 .RS·141270 .RS·14
1271 .I1271 .I
1272 seed1272 seed
1273 =(input,·required,·string)1273 =(required,·input,·string)
1274 .RS·21274 .RS·2
1275 seed·input·image·containing·the·lables·for·the·initial·regions.1275 seed·input·image·containing·the·lables·for·the·initial·regions.
  
1276 .RE1276 .RE
1277 .RE1277 .RE
1278 .TP·101278 .TP·10
1279 .B·tee1279 .B·tee
1280 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1280 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1281 .P1281 .P
1282 .RS·141282 .RS·14
1283 .I1283 .I
1284 file1284 file
1285 =(output,·required,·io)1285 =(required,·output,·io)
1286 .RS·21286 .RS·2
1287 name·of·the·output·file·to·save·the·image·too..1287 name·of·the·output·file·to·save·the·image·too..
1288 For·supported·file·types·see·PLUGINS:3dimage/io1288 For·supported·file·types·see·PLUGINS:3dimage/io
  
1289 .RE1289 .RE
1290 .RE1290 .RE
1291 .TP·101291 .TP·10
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1301 .TP·101301 .TP·10
1302 .B·transform1302 .B·transform
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./usr/share/man/man1/mia-3dmaskseeded.1.gz
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mia-3dmaskseeded.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dmaskseeded·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-3dmaskseeded·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dmaskseeded8 .B·mia\-3dmaskseeded
9 3D·image·segmentation·based·on·region·growing·from·a·seed·point.·Neighboring·points·are·added,·either·when·their·intensity·is·equal·or·higher·than·that·of·the·seed·point,·or·of·the·intensity·is·lower·or·equal·then·that·of·the·neighoring·point.·After·region·growing·is·finished,·this·mask·is·used·to·zero·out·the·region·in·the·original·image·yielding·the·resulting·image.·9 3D·image·segmentation·based·on·region·growing·from·a·seed·point.·Neighboring·points·are·added,·either·when·their·intensity·is·equal·or·higher·than·that·of·the·seed·point,·or·of·the·intensity·is·lower·or·equal·then·that·of·the·neighoring·point.·After·region·growing·is·finished,·this·mask·is·used·to·zero·out·the·region·in·the·original·image·yielding·the·resulting·image.·
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image(s)·to·be·filtered13 input·image(s)·to·be·filtered
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(output,·required);·io"
16 output·image(s)·that·have·been·filtered16 output·image(s)·that·have·been·filtered
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-s·\-\-seed=[0,0,0]"18 .IP·"\-s·\-\-seed=[0,0,0]"
19 seed·point19 seed·point
  
20 .IP·"\-n·\-\-neighborhood=6n"20 .IP·"\-n·\-\-neighborhood=6n"
21 neighborhood·shape21 neighborhood·shape
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./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz
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mia-3dpropose-boundingbox.1
    
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1122 .TP·101122 .TP·10
1123 .B·tee1123 .B·tee
1124 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1124 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1125 .P1125 .P
1126 .RS·141126 .RS·14
1127 .I1127 .I
1128 file1128 file
1129 =(output,·required,·io)1129 =(required,·output,·io)
1130 .RS·21130 .RS·2
1131 name·of·the·output·file·to·save·the·image·too..1131 name·of·the·output·file·to·save·the·image·too..
1132 For·supported·file·types·see·PLUGINS:3dimage/io1132 For·supported·file·types·see·PLUGINS:3dimage/io
  
1133 .RE1133 .RE
1134 .RE1134 .RE
1135 .TP·101135 .TP·10
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./usr/share/man/man1/mia-3drigidreg.1.gz
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mia-3drigidreg.1
    
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12 .RS12 .RS
13 .IP·"\-i·\-\-in-image=(required,·input);·io"13 .IP·"\-i·\-\-in-image=(required,·input);·io"
14 test·image14 test·image
15 ·For·supported·file·types·see·PLUGINS:3dimage/io15 ·For·supported·file·types·see·PLUGINS:3dimage/io
16 .IP·"\-r·\-\-ref-image=(required,·input);·io"16 .IP·"\-r·\-\-ref-image=(required,·input);·io"
17 reference·image17 reference·image
18 ·For·supported·file·types·see·PLUGINS:3dimage/io18 ·For·supported·file·types·see·PLUGINS:3dimage/io
19 .IP·"\-o·\-\-out-image=(required,·output);·io"19 .IP·"\-o·\-\-out-image=(output,·required);·io"
20 registered·output·image20 registered·output·image
21 ·For·supported·file·types·see·PLUGINS:3dimage/io21 ·For·supported·file·types·see·PLUGINS:3dimage/io
22 .IP·"\-t·\-\-transformation=(output);·io"22 .IP·"\-t·\-\-transformation=(output);·io"
23 transformation·output·file·name23 transformation·output·file·name
24 ·For·supported·file·types·see·PLUGINS:3dtransform/io24 ·For·supported·file·types·see·PLUGINS:3dtransform/io
25 .IP·"\-c·\-\-cost=ssd"25 .IP·"\-c·\-\-cost=ssd"
26 cost·function26 cost·function
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./usr/share/man/man1/mia-3dsegment-ahmed.1.gz
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mia-3dsegment-ahmed.1
    
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14 .UE14 .UE
15 .RE15 .RE
  
16 ·changes·are:·p=2,·and·exp16 ·changes·are:·p=2,·and·exp
17 .SH·OPTIONS17 .SH·OPTIONS
18 .SS·File-IO18 .SS·File-IO
19 .RS19 .RS
20 .IP·"\-i·\-\-in-file=(required,·input);·io"20 .IP·"\-i·\-\-in-file=(input,·required);·io"
21 image·to·be·segmented21 image·to·be·segmented
22 ·For·supported·file·types·see·PLUGINS:3dimage/io22 ·For·supported·file·types·see·PLUGINS:3dimage/io
23 .IP·"\-c·\-\-class-file=(output,·required);·io"23 .IP·"\-c·\-\-class-file=(output,·required);·io"
24 class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values24 class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values
25 ·For·supported·file·types·see·PLUGINS:3dimage/io25 ·For·supported·file·types·see·PLUGINS:3dimage/io
26 .IP·"\-b·\-\-out-file=(output);·io"26 .IP·"\-b·\-\-out-file=(output);·io"
27 Bias·corrected·image·will·be·of·the·same·type·like·the·input·image.·If·this·parameter·is·not·given,·then·the·bias·correction·will·not·be·applied.27 Bias·corrected·image·will·be·of·the·same·type·like·the·input·image.·If·this·parameter·is·not·given,·then·the·bias·correction·will·not·be·applied.
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./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz
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mia-3dtrackpixelmovement.1
    
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10 ···id;time;x;y;z;reserved10 ···id;time;x;y;z;reserved
  
11 The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and·the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.11 The·fields·'time',·'x',·'y',·and·'z'·are·updated,·and·the·fields·'id'·and·'reserved'·are·preserved,·empty·lines·are·ignored.
12 .SH·OPTIONS12 .SH·OPTIONS
13 .SS·13 .SS·
14 File-IO14 File-IO
15 .RS15 .RS
16 .IP·"\-i·\-\-in-file=(required,·input);·string"16 .IP·"\-i·\-\-in-file=(input,·required);·string"
17 input·point·set17 input·point·set
  
18 .IP·"\-o·\-\-out-file=(output,·required);·string"18 .IP·"\-o·\-\-out-file=(output,·required);·string"
19 output·point·set19 output·point·set
  
20 .IP·"\-t·\-\-transformation=(required,·input);·io"20 .IP·"\-t·\-\-transformation=(input,·required);·io"
21 transformation·describing·the·monitored·change21 transformation·describing·the·monitored·change
22 ·For·supported·file·types·see·PLUGINS:3dtransform/io22 ·For·supported·file·types·see·PLUGINS:3dtransform/io
23 .RE23 .RE
24 .SS·24 .SS·
25 Parameters25 Parameters
26 .RS26 .RS
27 .IP·"\-T·\-\-time-step=1"27 .IP·"\-T·\-\-time-step=1"
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./usr/share/man/man1/mia-3dtransform.1.gz
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mia-3dtransform.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dtransform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options]6 .B··mia\-3dtransform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dtransform8 .B·mia\-3dtransform
9 Transform·a·3D·image·by·applying·a·given·3D·transformation.9 Transform·a·3D·image·by·applying·a·given·3D·transformation.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image13 input·image
14 ·For·supported·file·types·see·PLUGINS:3dimage/io14 ·For·supported·file·types·see·PLUGINS:3dimage/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 transformed·image16 transformed·image
17 ·For·supported·file·types·see·PLUGINS:3dimage/io17 ·For·supported·file·types·see·PLUGINS:3dimage/io
18 .IP·"\-t·\-\-transformation=(input,·required);·io"18 .IP·"\-t·\-\-transformation=(required,·input);·io"
19 transformation·file19 transformation·file
20 ·For·supported·file·types·see·PLUGINS:3dtransform/io20 ·For·supported·file·types·see·PLUGINS:3dtransform/io
21 .IP·"\-p·\-\-interpolator="21 .IP·"\-p·\-\-interpolator="
22 override·the·interpolator·provided·by·the·transformation22 override·the·interpolator·provided·by·the·transformation
  
23 .IP·"\-b·\-\-boundary=mirror"23 .IP·"\-b·\-\-boundary=mirror"
24 override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·also·overridden.24 override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·also·overridden.
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./usr/share/man/man1/mia-3dtransform2vf.1.gz
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mia-3dtransform2vf.1
    
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8 .B·mia\-3dtransform2vf8 .B·mia\-3dtransform2vf
9 Create·a·3D·vector·field·from·a·given·transformation.·The·output·vector·field·will·have·the·dimesions·as·given·in·the·transformation·description.9 Create·a·3D·vector·field·from·a·given·transformation.·The·output·vector·field·will·have·the·dimesions·as·given·in·the·transformation·description.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·transformation·13 input·transformation·
14 ·For·supported·file·types·see·PLUGINS:3dtransform/io14 ·For·supported·file·types·see·PLUGINS:3dtransform/io
15 .IP·"\-o·\-\-out-file=(output,·required);·io"15 .IP·"\-o·\-\-out-file=(required,·output);·io"
16 output·vector·field·16 output·vector·field·
17 ·For·supported·file·types·see·PLUGINS:3dvf/io17 ·For·supported·file·types·see·PLUGINS:3dvf/io
18 .RE18 .RE
19 .SS·Help·&·Info19 .SS·Help·&·Info
20 .RS20 .RS
21 .IP·"\-V·\-\-verbose=warning"21 .IP·"\-V·\-\-verbose=warning"
22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:22 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz
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mia-3dvectorfieldcreate.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dvectorfieldcreate·\-o·<out\-file>·[options]6 .B··mia\-3dvectorfieldcreate·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dvectorfieldcreate8 .B·mia\-3dvectorfieldcreate
9 This·program·is·used·to·create·a·file·containing·a·3D·vector·field.9 This·program·is·used·to·create·a·file·containing·a·3D·vector·field.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-o·\-\-out-file=(required,·output);·io"12 .IP·"\-o·\-\-out-file=(output,·required);·io"
13 output·file·for·the·vector·field13 output·file·for·the·vector·field
14 ·For·supported·file·types·see·PLUGINS:3dvf/io14 ·For·supported·file·types·see·PLUGINS:3dvf/io
15 .IP·"\-s·\-\-size=[64,64,64]"15 .IP·"\-s·\-\-size=[64,64,64]"
16 size·of·the·vector·field16 size·of·the·vector·field
  
17 .IP·"\-y·\-\-ftype=0"17 .IP·"\-y·\-\-ftype=0"
18 vector·field·type18 vector·field·type
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./usr/share/man/man1/mia-3dvf2transform.1.gz
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mia-3dvf2transform.1
    
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8 .B·mia\-3dvf2transform8 .B·mia\-3dvf2transform
9 Creates·a·3D·transformation·from·a·vector·field.·The·input·vector·field·is·simply·encapsulated·into·the·transformation·file·format.·The·boundary·conditions·and·the·image·interpolator·kernel·can·be·set·at·the·command·line.9 Creates·a·3D·transformation·from·a·vector·field.·The·input·vector·field·is·simply·encapsulated·into·the·transformation·file·format.·The·boundary·conditions·and·the·image·interpolator·kernel·can·be·set·at·the·command·line.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(input,·required);·io"
13 input·transformation·13 input·transformation·
14 ·For·supported·file·types·see·PLUGINS:3dvf/io14 ·For·supported·file·types·see·PLUGINS:3dvf/io
15 .IP·"\-o·\-\-out-file=(required,·output);·io"15 .IP·"\-o·\-\-out-file=(output,·required);·io"
16 output·vector·field·16 output·vector·field·
17 ·For·supported·file·types·see·PLUGINS:3dtransform/io17 ·For·supported·file·types·see·PLUGINS:3dtransform/io
18 .IP·"\-k·\-\-imgkernel=bspline:d=3"18 .IP·"\-k·\-\-imgkernel=bspline:d=3"
19 image·interpolator·kernel·which·is·used·when·the·transformation·is·applied·to·an·image19 image·interpolator·kernel·which·is·used·when·the·transformation·is·applied·to·an·image
20 ·For·supported·plugins·see·PLUGINS:1d/splinekernel20 ·For·supported·plugins·see·PLUGINS:1d/splinekernel
21 .IP·"\-b·\-\-imgboundary=mirror"21 .IP·"\-b·\-\-imgboundary=mirror"
22 Boundary·condition·applied·when·the·transformation·is·used·to·transform·an·image22 Boundary·condition·applied·when·the·transformation·is·used·to·transform·an·image
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./usr/share/man/man1/mia-3dvfcompare.1.gz
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mia-3dvfcompare.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-3dvfcompare·\-1·<in\-file\-1>·\-2·<in\-file\-2>·[options]6 .B··mia\-3dvfcompare·\-1·<in\-file\-1>·\-2·<in\-file\-2>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-3dvfcompare8 .B·mia\-3dvfcompare
9 Compare·two·vector·fields·and·print·the·out·the·difference·norm·per·pixel·to·cout·it·it·is·larger·than·delta.9 Compare·two·vector·fields·and·print·the·out·the·difference·norm·per·pixel·to·cout·it·it·is·larger·than·delta.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-1·\-\-in-file-1=(input,·required);·io"12 .IP·"\-1·\-\-in-file-1=(required,·input);·io"
13 input·vector·field·113 input·vector·field·1
14 ·For·supported·file·types·see·PLUGINS:3dvf/io14 ·For·supported·file·types·see·PLUGINS:3dvf/io
15 .IP·"\-2·\-\-in-file-2=(input,·required);·io"15 .IP·"\-2·\-\-in-file-2=(required,·input);·io"
16 input·vector·field·216 input·vector·field·2
17 ·For·supported·file·types·see·PLUGINS:3dvf/io17 ·For·supported·file·types·see·PLUGINS:3dvf/io
18 .IP·"\-d·\-\-delta=0"18 .IP·"\-d·\-\-delta=0"
19 Maximum·difference·between·vector·to·be·ignored19 Maximum·difference·between·vector·to·be·ignored
  
20 .RE20 .RE
21 .SS·Help·&·Info21 .SS·Help·&·Info
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./usr/share/man/man1/mia-labelsort.1.gz
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mia-labelsort.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-labelsort·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-labelsort·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-labelsort8 .B·mia\-labelsort
9 This·program·is·used·create·a·mapping·based·on·a·histogram·that·puts·the·intensities·with·high·values·at·the·beginning·of·the·histogram.·The·main·use·case·will·be·to·sort·labels·of·connected·components·in·out-of-core·image·processing.9 This·program·is·used·create·a·mapping·based·on·a·histogram·that·puts·the·intensities·with·high·values·at·the·beginning·of·the·histogram.·The·main·use·case·will·be·to·sort·labels·of·connected·components·in·out-of-core·image·processing.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·file·name·containing·the·histogram13 input·file·name·containing·the·histogram
  
14 .IP·"\-o·\-\-out-file=(required,·output);·string"14 .IP·"\-o·\-\-out-file=(output,·required);·string"
15 output·file·name·to·store·probabilities15 output·file·name·to·store·probabilities
  
16 .RE16 .RE
17 .SS·Help·&·Info17 .SS·Help·&·Info
18 .RS18 .RS
19 .IP·"\-V·\-\-verbose=warning"19 .IP·"\-V·\-\-verbose=warning"
20 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:20 verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:
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./usr/share/man/man1/mia-mesh-deformable-model.1.gz
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mia-mesh-deformable-model.1
    
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9 This·program·runs·a·deformable·model·to·adapt·a·mesh·to·an·iso-value·within·a·given·image.·<FIXME:·Reference>9 This·program·runs·a·deformable·model·to·adapt·a·mesh·to·an·iso-value·within·a·given·image.·<FIXME:·Reference>
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File·I/O11 .SS·File·I/O
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(input,·required);·io"13 .IP·"\-i·\-\-in-file=(input,·required);·io"
14 input·mesh·to·be·adapted14 input·mesh·to·be·adapted
15 ·For·supported·file·types·see·PLUGINS:mesh/io15 ·For·supported·file·types·see·PLUGINS:mesh/io
16 .IP·"\-o·\-\-out-file=(output,·required);·io"16 .IP·"\-o·\-\-out-file=(required,·output);·io"
17 output·mesh·that·has·been·deformed17 output·mesh·that·has·been·deformed
18 ·For·supported·file·types·see·PLUGINS:mesh/io18 ·For·supported·file·types·see·PLUGINS:mesh/io
19 .IP·"\-r·\-\-ref-file=(input,·required);·io"19 .IP·"\-r·\-\-ref-file=(input,·required);·io"
20 reference·image20 reference·image
21 ·For·supported·file·types·see·PLUGINS:3dimage/io21 ·For·supported·file·types·see·PLUGINS:3dimage/io
22 .RE22 .RE
23 .SS·Help·&·Info23 .SS·Help·&·Info
Offset 1152, 15 lines modifiedOffset 1152, 15 lines modified
1152 .TP·101152 .TP·10
1153 .B·tee1153 .B·tee
1154 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·1154 Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1155 .P1155 .P
1156 .RS·141156 .RS·14
1157 .I1157 .I
1158 file1158 file
1159 =(output,·required,·io)1159 =(required,·output,·io)
1160 .RS·21160 .RS·2
1161 name·of·the·output·file·to·save·the·image·too..1161 name·of·the·output·file·to·save·the·image·too..
1162 For·supported·file·types·see·PLUGINS:3dimage/io1162 For·supported·file·types·see·PLUGINS:3dimage/io
  
1163 .RE1163 .RE
1164 .RE1164 .RE
1165 .TP·101165 .TP·10
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./usr/share/man/man1/mia-mesh-to-maskimage.1.gz
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mia-mesh-to-maskimage.1
    
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6 .B··mia\-mesh\-to\-maskimage·\-i·<in\-file>·\-o·<out\-file>·[options]6 .B··mia\-mesh\-to\-maskimage·\-i·<in\-file>·\-o·<out\-file>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-mesh\-to\-maskimage8 .B·mia\-mesh\-to\-maskimage
9 This·program·converts·a·3D·mesh·into·a·binary·mask·comprising·the·mesh·surface.·The·output·image·size·is·either·given·on·the·command·line·or·deducted·from·the·mesh·dimensions.9 This·program·converts·a·3D·mesh·into·a·binary·mask·comprising·the·mesh·surface.·The·output·image·size·is·either·given·on·the·command·line·or·deducted·from·the·mesh·dimensions.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .SS·File·I/O11 .SS·File·I/O
12 .RS12 .RS
13 .IP·"\-i·\-\-in-file=(required,·input);·io"13 .IP·"\-i·\-\-in-file=(input,·required);·io"
14 input·mesh·to·be·adapted14 input·mesh·to·be·adapted
15 ·For·supported·file·types·see·PLUGINS:mesh/io15 ·For·supported·file·types·see·PLUGINS:mesh/io
16 .IP·"\-o·\-\-out-file=(required,·output);·io"16 .IP·"\-o·\-\-out-file=(required,·output);·io"
17 output·image·containing·the·binary·mask17 output·image·containing·the·binary·mask
18 ·For·supported·file·types·see·PLUGINS:3dimage/io18 ·For·supported·file·types·see·PLUGINS:3dimage/io
19 .RE19 .RE
20 .SS·Help·&·Info20 .SS·Help·&·Info
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./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz
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mia-meshdistance-to-stackmask.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-meshdistance\-to\-stackmask·\-i·<in\-mesh>·\-r·<ref\-mask>·\-o·<out\-mesh>·[options]6 .B··mia\-meshdistance\-to\-stackmask·\-i·<in\-mesh>·\-r·<ref\-mask>·\-o·<out\-mesh>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-meshdistance\-to\-stackmask8 .B·mia\-meshdistance\-to\-stackmask
9 This·program·takes·a·binary·masks·and·a·triangular·mesh·as·input·and·evaluates·the·distance·of·the·mesh·vertices·to·the·binary·maskand·stores·the·result·in·a·new·mesh.9 This·program·takes·a·binary·masks·and·a·triangular·mesh·as·input·and·evaluates·the·distance·of·the·mesh·vertices·to·the·binary·maskand·stores·the·result·in·a·new·mesh.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-mesh=(required,·input);·io"12 .IP·"\-i·\-\-in-mesh=(input,·required);·io"
13 input·mesh13 input·mesh
14 ·For·supported·file·types·see·PLUGINS:mesh/io14 ·For·supported·file·types·see·PLUGINS:mesh/io
15 .IP·"\-r·\-\-ref-mask=(required,·input);·io"15 .IP·"\-r·\-\-ref-mask=(input,·required);·io"
16 reference·binary·mask16 reference·binary·mask
17 ·For·supported·file·types·see·PLUGINS:2dimage/io17 ·For·supported·file·types·see·PLUGINS:2dimage/io
18 .IP·"\-o·\-\-out-mesh=(required,·output);·io"18 .IP·"\-o·\-\-out-mesh=(required,·output);·io"
19 output·mesh19 output·mesh
20 ·For·supported·file·types·see·PLUGINS:mesh/io20 ·For·supported·file·types·see·PLUGINS:mesh/io
21 .RE21 .RE
22 .SS·Help·&·Info22 .SS·Help·&·Info
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./usr/share/man/man1/mia-meshfilter.1.gz
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mia-meshfilter.1
    
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7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-meshfilter8 .B·mia\-meshfilter
9 This·program·runs·a·series·filters·on·a·given·input·mesh.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run9 This·program·runs·a·series·filters·on·a·given·input·mesh.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run
10 ···'mia-plugin-help·mesh/filter'10 ···'mia-plugin-help·mesh/filter'
11 from·the·command·line11 from·the·command·line
12 .SH·OPTIONS12 .SH·OPTIONS
13 .RS13 .RS
14 .IP·"\-i·\-\-in-file=(required,·input);·io"14 .IP·"\-i·\-\-in-file=(input,·required);·io"
15 input·mesh·to·be·filtered15 input·mesh·to·be·filtered
16 ·For·supported·file·types·see·PLUGINS:mesh/io16 ·For·supported·file·types·see·PLUGINS:mesh/io
17 .IP·"\-o·\-\-out-file=(required,·output);·io"17 .IP·"\-o·\-\-out-file=(required,·output);·io"
18 output·mesh·that·have·been·filtered18 output·mesh·that·have·been·filtered
19 ·For·supported·file·types·see·PLUGINS:mesh/io19 ·For·supported·file·types·see·PLUGINS:mesh/io
20 .RE20 .RE
21 .SS·Help·&·Info21 .SS·Help·&·Info
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./usr/share/man/man1/mia-multihist.1.gz
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mia-multihist.1
    
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5 .SH·SYNOPSIS5 .SH·SYNOPSIS
6 .B··mia\-multihist·\-i·<in\-file>·\-o·<out\-histogram>·[options]6 .B··mia\-multihist·\-i·<in\-file>·\-o·<out\-histogram>·[options]
7 .SH·DESCRIPTION7 .SH·DESCRIPTION
8 .B·mia\-multihist8 .B·mia\-multihist
9 This·program·evaluates·the·histogram·over·a·series·of·2D·images9 This·program·evaluates·the·histogram·over·a·series·of·2D·images
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·io"12 .IP·"\-i·\-\-in-file=(required,·input);·io"
13 input·image(s)·to·be·filtered13 input·image(s)·to·be·filtered
14 ·For·supported·file·types·see·PLUGINS:2dimage/io14 ·For·supported·file·types·see·PLUGINS:2dimage/io
15 .IP·"\-o·\-\-out-histogram=(output,·required);·string"15 .IP·"\-o·\-\-out-histogram=(output,·required);·string"
16 output·file·name16 output·file·name
  
17 .IP·"···\-\-min=0"17 .IP·"···\-\-min=0"
18 minimum·of·histogram·range18 minimum·of·histogram·range
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./usr/share/man/man1/mia-raw2image.1.gz
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mia-raw2image.1
    
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8 .B·mia\-raw2image8 .B·mia\-raw2image
9 This·program·is·used·to·convert·raw·data·to·a·2D·file·format.9 This·program·is·used·to·convert·raw·data·to·a·2D·file·format.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(required,·input);·string"12 .IP·"\-i·\-\-in-file=(required,·input);·string"
13 input·file·name13 input·file·name
  
14 .IP·"\-o·\-\-out-file=(output,·required);·io"14 .IP·"\-o·\-\-out-file=(required,·output);·io"
15 output·file·name15 output·file·name
16 ·For·supported·file·types·see·PLUGINS:2dimage/io16 ·For·supported·file·types·see·PLUGINS:2dimage/io
17 .IP·"\-r·\-\-repn=ubyte"17 .IP·"\-r·\-\-repn=ubyte"
18 input·pixel·type·18 input·pixel·type·
  
19 .RS·1019 .RS·10
20 .I20 .I
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./usr/share/man/man1/mia-raw2volume.1.gz
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mia-raw2volume.1
    
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8 .B·mia\-raw2volume8 .B·mia\-raw2volume
9 This·program·is·used·to·convert·raw·data·into·3D·images·with·apropriate·metadata.9 This·program·is·used·to·convert·raw·data·into·3D·images·with·apropriate·metadata.
10 .SH·OPTIONS10 .SH·OPTIONS
11 .RS11 .RS
12 .IP·"\-i·\-\-in-file=(input,·required);·string"12 .IP·"\-i·\-\-in-file=(input,·required);·string"
13 input·file·name13 input·file·name
  
14 .IP·"\-o·\-\-out-file=(output,·required);·io"14 .IP·"\-o·\-\-out-file=(required,·output);·io"
15 output·file·name15 output·file·name
16 ·For·supported·file·types·see·PLUGINS:3dimage/io16 ·For·supported·file·types·see·PLUGINS:3dimage/io
17 .IP·"\-r·\-\-repn=ubyte"17 .IP·"\-r·\-\-repn=ubyte"
18 input·pixel·type·18 input·pixel·type·
  
19 .RS·1019 .RS·10
20 .I20 .I
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