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| 2 | ·3547df93850adc74bec72c07bff214d9·3970592·libs·optional·libmia-2.4-4_2.4.7-7_armhf.deb | 2 | ·3547df93850adc74bec72c07bff214d9·3970592·libs·optional·libmia-2.4-4_2.4.7-7_armhf.deb |
| 3 | ·38c6aee8827e8529d802378c364adbc3·207292·libdevel·optional·libmia-2.4-dev_2.4.7-7_armhf.deb | 3 | ·38c6aee8827e8529d802378c364adbc3·207292·libdevel·optional·libmia-2.4-dev_2.4.7-7_armhf.deb |
| 4 | ·dc4b43f19afe1d1d3bb31bed2a1e2e9a·4755584·doc·optional·libmia-2.4-doc_2.4.7-7_all.deb | 4 | ·dc4b43f19afe1d1d3bb31bed2a1e2e9a·4755584·doc·optional·libmia-2.4-doc_2.4.7-7_all.deb |
| 5 | ·dcec706416c22847a9b49bd728ecb998·28924·science·optional·mia-doctools_2.4.7-7_all.deb | 5 | ·dcec706416c22847a9b49bd728ecb998·28924·science·optional·mia-doctools_2.4.7-7_all.deb |
| 6 | ·26a020df2207175dcb223a41c7a70f2e·31250232·debug·optional·mia-tools-dbgsym_2.4.7-7_armhf.deb | 6 | ·26a020df2207175dcb223a41c7a70f2e·31250232·debug·optional·mia-tools-dbgsym_2.4.7-7_armhf.deb |
| 7 | ·ae663eaad8b555094074390952faaf4f·99000·doc·optional·mia-tools-doc_2.4.7-7_all.deb | ||
| 8 | · | 7 | ·6f733997b452ba9ce1bb30102ca81bfc·98996·doc·optional·mia-tools-doc_2.4.7-7_all.deb |
| 8 | ·73171ee957bafa4b1c895049f9f7bad5·1695728·science·optional·mia-tools_2.4.7-7_armhf.deb | ||
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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">( | 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·->·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·->·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"> 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| 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 16, 19 lines modified | Offset 16, 19 lines modified | ||
| 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">( | 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">( | 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> |
| Offset 45, 15 lines modified | Offset 45, 15 lines modified | ||
| 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">( | 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·->·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·->·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 1, 4 lines modified | Offset 1, 4 lines modified | ||
| 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=( | 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·&·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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| 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=( | 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·&·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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| 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·->·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=( | 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·->·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·&·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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| 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=( | 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·&·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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| 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·transformation | 16 | ··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=( | 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·&·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·&·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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| 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=( | 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·&·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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| 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·&·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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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> 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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=( | 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;·uint</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-P,·--passes=4;·uint</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;·uint</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-P,·--passes=4;·uint</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;·uint</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;·uint</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·&·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;·uint</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;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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·run | 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·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=( | 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·&·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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| 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=( | 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·&·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;·uint</span></dt><dd><p>first·possible·number·of·file·number·range·to·be·filtered</p></dd><dt><span·class="term">-e,·--end=2147483647;·uint</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=( | 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·&·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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| 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=( | 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·&·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;·uint</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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| 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=( | 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;·uint</span></dt><dd><p>image·number·to·be·selected</p></dd></dl></div><h4><a·name="idp80"></a>Help·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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=(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·&·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> |
| Offset 1, 9 lines modified | Offset 1, 9 lines modified | ||
| 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=( | 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;·uint</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·&·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;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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;·uint</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-e,·--end=60;·uint</span></dt><dd><p>last·image·in·series</p></dd><dt><span·class="term">-C,·--components=0;·uint</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·&·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=( | 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·&·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;·uint</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;·uint</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;·uint</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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| 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=( | 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·&·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;·uint</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;·uint</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;·uint</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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| 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=( | 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·&·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;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-p,·--linear-passes=3;·uint</span></dt><dd><p>linear·registration·passes·(0·to·disable)</p></dd><dt><span·class="term">-P,·--nonlinear-passes=3;·uint</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> 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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=( | 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·&·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;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=5;·uint</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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| 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·computation | 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·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=( | 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;·uint</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;·uint</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;·uint</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;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·uint</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5152"></a>Help·&·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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·uint</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5152"></a>Help·&·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> |
| Offset 1, 3 lines modified | Offset 1, 3 lines modified | ||
| 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=( | 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·&·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;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·uint</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> 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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=( | 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·&·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;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-p,·--linear-passes=3;·uint</span></dt><dd><p>linear·registration·passes·(0·to·disable)</p></dd><dt><span·class="term">-P,·--nonlinear-passes=3;·uint</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> 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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=( | 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·&·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;·uint</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;·uint</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;·uint</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;·uint</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;·uint</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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| 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=( | 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;·uint</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--max-candidates=20;·uint</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;·uint</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;·uint</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--max-candidates=20;·uint</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;·uint</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;·uint</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·&·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;·uint</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·&·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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| 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=( | 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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=4;·uint</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5869"></a>Help·&·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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=4;·uint</span></dt><dd><p>registration·passes</p></dd></dl></div><h4><a·name="idp5869"></a>Help·&·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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| 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=( | 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;·uint</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·&·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;·uint</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·&·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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| 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=( | 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;·uint</span></dt><dd><p>images·to·skip·atthe·begin·of·the·series</p></dd></dl></div><h4><a·name="idp6759"></a>Help·&·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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| 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=( | 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;·uint</span></dt><dd><p>reference·image</p></dd></dl></div><h4><a·name="idp6846"></a>Help·&·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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| 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=( | 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;·uint</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·&·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;·uint</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·&·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· 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| 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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| 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=( | 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·&·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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| 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>uint</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>uint</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=( | 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);·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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> 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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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·<·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·series | 4 | ···-3:·Middle·of·the·series |
| 5 | ···-2:·prefererred·reference | 5 | ···-2:·prefererred·reference |
| 6 | ···-1:·LV·peak | 6 | ···-1:·LV·peak |
| 7 | ···if·any·of·the·above·is·not·available·or·the·value·is·<·-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;·uint</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·&·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·<·-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;·uint</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·&·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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| 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=( | 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;·uint</span></dt><dd><p>skip·frames·at·the·beginning</p></dd></dl></div><h4><a·name="idp7321"></a>Help·&·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·"<20,30>"</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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| 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=( | 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·&·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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| 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=( | 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;·uint</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·uint</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;·uint</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·&·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·<128,64>·to·curve.txt.</p><pre·class="screen">mia-2dseries2dordermedian·-i·segment.set·-o·gradmedian.exr·-g·1·--itc-file·curve.txt·--itc-loc·"<128,64>"</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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| 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=( | 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;·uint</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd><dt><span·class="term">-e,·--end=60;·uint</span></dt><dd><p>last·image·in·series</p></dd></dl></div><h4><a·name="idp7987"></a>Help·&·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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| 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=( | 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;·uint</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·uint</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·&·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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| 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=( | 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;·uint</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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;·uint</span></dt><dd><p>skip·images·at·beginning·of·series</p></dd></dl></div><h4><a·name="idp7506"></a>Help·&·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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| 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=( | 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;·uint</span></dt><dd><p>Frame·number·for·which·to·extract·the·mask</p></dd></dl></div><h4><a·name="idp7596"></a>Help·&·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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| 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=( | 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;·uint</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·&·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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| 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=( | 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;·uint</span></dt><dd><p>Skip·files·at·the·beginning</p></dd><dt><span·class="term">-e,·--enlarge-boundary=5;·uint</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;·uint</span></dt><dd><p>gauss·filter·width·for·moothing·the·gradient</p></dd></dl></div><h4><a·name="idp8380"></a>Help·&·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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| 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=( | 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;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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=( | 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·&·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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| 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·format | 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·format |
| 4 | ···id;time;x;y;z;reserved | 4 | ···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=( | 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·&·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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 14 | ········end_range·<-·2·+·as.numeric(line[2]) | 14 | ········end_range·<-·2·+·as.numeric(line[2]) |
| 15 | ········s·<-·as.numeric(line[3:end_range]) | 15 | ········s·<-·as.numeric(line[3:end_range]) |
| 16 | ········result·<-·sprintf("%d·%8.4f·%8.4f·%8.4f·%8.4f\n" | 16 | ········result·<-·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=( | 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·&·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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| 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·transformation | 16 | ··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=( | 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·&·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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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·&·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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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;·uint</span></dt><dd><p>start·slice·number</p></dd><dt><span·class="term">-n,·--number=1;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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=( | 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;·uint</span></dt><dd><p>image·number·to·be·selected</p></dd></dl></div><h4><a·name="idp550"></a>Help·&·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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| 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=( | 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·&·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;·uint·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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=(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·&·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> |
| Offset 1, 9 lines modified | Offset 1, 9 lines modified | ||
| 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=( | 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;·uint</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·&·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;·uint</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·&·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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| 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=( | 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·&·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·<10,23,21>·and·use·the·18n·neighbourhood.</p><pre·class="screen">mia-3dmaskseeded·-i·image.v·-o·masked.v·-s·'<10,23,21>'·-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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| 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=( | 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·&·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;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>multi-resolution·levels</p></dd><dt><span·class="term">-P,·--passes=3;·uint</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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| 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·&·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=( | 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·&·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;·uint</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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| 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=( | 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·&·Preprocessing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·uint</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--preskip=20;·uint</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;·uint</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;·uint</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;·uint</span></dt><dd><p>Maximum·delta·between·two·elements·of·the·prealigned·subset</p></dd></dl></div><h4><a·name="idp13220"></a> | 5 | Preconditions·&·Preprocessing</h4><div·class="variablelist"><dl·class="variablelist·compact"><dt><span·class="term">-k,·--skip=0;·uint</span></dt><dd><p>Skip·images·at·the·begin·of·the·series</p></dd><dt><span·class="term">--preskip=20;·uint</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;·uint</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;·uint</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;·uint</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;·uint</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·&·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;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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·<=·0.5:·create·segmentation·based·on·highest·class·probability,·labels·start·at·0.·For·values·>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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| 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=( | 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;·uint</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·&·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;·uint</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·&·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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| 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=( | 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·&·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·<12,13,14>·and·<222,113,214></p><pre·class="screen">mia-3dseries-track-intensity·-i·images0000.v·-o·curves.txt·'<12,13,14>'·'<222,113,214>'</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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| 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·format | 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·format |
| 4 | ···id;time;x;y;z;reserved | 4 | ···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=( | 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·&·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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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=( | 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·&·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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| 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.·<FIXME:·Reference></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=( | 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.·<FIXME:·Reference></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·&·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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| 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=( | 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·&·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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| 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·run | 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·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=( | 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·&·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·<0,0,0>·-·<128,128,128>·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=[<0,0,0>],box-end=[<128,128,128>]</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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| 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=( | 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·&·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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| 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=( | 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;·uint</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·&·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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| 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=( | 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·&·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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| 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=( | 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·<FX,FY></p></dd><dt><span·class="term">-s,·--size=(required);·2dbounds</span></dt><dd><p>size·of·input·<NX,NY></p></dd><dt><span·class="term">-k,·--skip=0;·uint</span></dt><dd><p>skip·number·of·bytes·from·beginning·of·file</p></dd></dl></div><h4><a·name="idp699"></a>Help·&·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·<10,20>·of·short·integer·data·with·a·pixel·size·of·<1.2,·2.3>·to·a·PNG·file·image.png</p><pre·class="screen">mia-raw2image·-i·data.raw·-o·image.png·-s·'<10,20>'·-k·'<1.2,2.3>'·-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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| 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=( | 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·<FX,FY,FZ></p></dd><dt><span·class="term">-k,·--skip=0;·uint</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·<NX,NY,NZ></p></dd></dl></div><h4><a·name="idp848"></a>Help·&·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·<1.2,·2.3,·3.4>·to·an·Analyze·file·image.hdr</p><pre·class="screen">mia-raw2volume·-i·data.raw·-o·image.hdr·-s·"<10,20,30>"·-k·"<1.2,2.3,3.4>"·-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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| 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=( | 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·&·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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| 149 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/man/man1/ | 149 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/man/man1/ |
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| 168 | -rw-r--r--···0·root·········(0)·root·········(0)·····5276·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimageregistration.1.gz | 168 | -rw-r--r--···0·root·········(0)·root·········(0)·····5276·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimageregistration.1.gz |
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| 170 | -rw-r--r--···0·root·········(0)·root·········(0)·····142 | 170 | -rw-r--r--···0·root·········(0)·root·········(0)·····1428·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz |
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| 179 | -rw-r--r--···0·root·········(0)·root·········(0)·····2193·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmyocard-ica.1.gz | 179 | -rw-r--r--···0·root·········(0)·root·········(0)·····2193·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmyocard-ica.1.gz |
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| 212 | -rw-r--r--···0·root·········(0)·root·········(0)·····172 | 212 | -rw-r--r--···0·root·········(0)·root·········(0)·····1723·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dseriesgradvariation.1.gz |
| 213 | -rw-r--r--···0·root·········(0)·root·········(0)······992·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dserieshausdorff.1.gz | 213 | -rw-r--r--···0·root·········(0)·root·········(0)······992·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dserieshausdorff.1.gz |
| 214 | -rw-r--r--···0·root·········(0)·root·········(0)·····634 | 214 | -rw-r--r--···0·root·········(0)·root·········(0)·····6348·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz |
| 215 | -rw-r--r--···0·root·········(0)·root·········(0)·····1570·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dseriestovolume.1.gz | 215 | -rw-r--r--···0·root·········(0)·root·········(0)·····1570·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dseriestovolume.1.gz |
| 216 | -rw-r--r--···0·root·········(0)·root·········(0)·····21 | 216 | -rw-r--r--···0·root·········(0)·root·········(0)·····2127·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz |
| 217 | -rw-r--r--···0·root·········(0)·root·········(0)·····6956·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dstackfilter.1.gz | 217 | -rw-r--r--···0·root·········(0)·root·········(0)·····6956·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dstackfilter.1.gz |
| 218 | -rw-r--r--···0·root·········(0)·root·········(0)·····1878·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dto3dimage.1.gz | 218 | -rw-r--r--···0·root·········(0)·root·········(0)·····1878·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dto3dimage.1.gz |
| 219 | -rw-r--r--···0·root·········(0)·root·········(0)·····1888·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dto3dimageb.1.gz | 219 | -rw-r--r--···0·root·········(0)·root·········(0)·····1888·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dto3dimageb.1.gz |
| 220 | -rw-r--r--···0·root·········(0)·root·········(0)·····136 | 220 | -rw-r--r--···0·root·········(0)·root·········(0)·····1365·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz |
| 221 | -rw-r--r--···0·root·········(0)·root·········(0)·····167 | 221 | -rw-r--r--···0·root·········(0)·root·········(0)·····1677·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dtransform.1.gz |
| 222 | -rw-r--r--···0·root·········(0)·root·········(0)·····1118·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz | 222 | -rw-r--r--···0·root·········(0)·root·········(0)·····1118·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz |
| 223 | -rw-r--r--···0·root·········(0)·root·········(0)·····1630·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dbinarycombine.1.gz | 223 | -rw-r--r--···0·root·········(0)·root·········(0)·····1630·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dbinarycombine.1.gz |
| 224 | -rw-r--r--···0·root·········(0)·root·········(0)·····1882·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dbrainextractT1.1.gz | 224 | -rw-r--r--···0·root·········(0)·root·········(0)·····1882·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dbrainextractT1.1.gz |
| 225 | -rw-r--r--···0·root·········(0)·root·········(0)·····17 | 225 | -rw-r--r--···0·root·········(0)·root·········(0)·····1739·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcombine-imageseries.1.gz |
| 226 | -rw-r--r--···0·root·········(0)·root·········(0)·····1655·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz | 226 | -rw-r--r--···0·root·········(0)·root·········(0)·····1655·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz |
| 227 | -rw-r--r--···0·root·········(0)·root·········(0)·····3430·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz | 227 | -rw-r--r--···0·root·········(0)·root·········(0)·····3430·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz |
| 228 | -rw-r--r--···0·root·········(0)·root·········(0)·····6732·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcost.1.gz | 228 | -rw-r--r--···0·root·········(0)·root·········(0)·····6732·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcost.1.gz |
| 229 | -rw-r--r--···0·root·········(0)·root·········(0)·····1646·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcrispsegment.1.gz | 229 | -rw-r--r--···0·root·········(0)·root·········(0)·····1646·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dcrispsegment.1.gz |
| 230 | -rw-r--r--···0·root·········(0)·root·········(0)·····186 | 230 | -rw-r--r--···0·root·········(0)·root·········(0)·····1866·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3ddeform.1.gz |
| 231 | -rw-r--r--···0·root·········(0)·root·········(0)·····201 | 231 | -rw-r--r--···0·root·········(0)·root·········(0)·····2012·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3ddistance-stats.1.gz |
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| 236 | -rw-r--r--···0·root·········(0)·root·········(0)·····2319·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dfluid.1.gz | 236 | -rw-r--r--···0·root·········(0)·root·········(0)·····2319·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dfluid.1.gz |
| 237 | -rw-r--r--···0·root·········(0)·root·········(0)·····236 | 237 | -rw-r--r--···0·root·········(0)·root·········(0)·····2369·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dforce.1.gz |
| 238 | -rw-r--r--···0·root·········(0)·root·········(0)·····170 | 238 | -rw-r--r--···0·root·········(0)·root·········(0)·····1706·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dfuzzysegment.1.gz |
| 239 | -rw-r--r--···0·root·········(0)·root·········(0)·····1469·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dgetsize.1.gz | 239 | -rw-r--r--···0·root·········(0)·root·········(0)·····1469·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dgetsize.1.gz |
| 240 | -rw-r--r--···0·root·········(0)·root·········(0)·····2199·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dgetslice.1.gz | 240 | -rw-r--r--···0·root·········(0)·root·········(0)·····2199·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dgetslice.1.gz |
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| 242 | -rw-r--r--···0·root·········(0)·root·········(0)·····16 | 242 | -rw-r--r--···0·root·········(0)·root·········(0)·····1658·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dimagecombine.1.gz |
| 243 | -rw-r--r--···0·root·········(0)·root·········(0)·····190 | 243 | -rw-r--r--···0·root·········(0)·root·········(0)·····1907·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dimagecreator.1.gz |
| 244 | -rw-r--r--···0·root·········(0)·root·········(0)·····5698·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dimagefilter.1.gz | 244 | -rw-r--r--···0·root·········(0)·root·········(0)·····5698·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dimagefilter.1.gz |
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| 246 | -rw-r--r--···0·root·········(0)·root·········(0)·····1543·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dimageselect.1.gz | 246 | -rw-r--r--···0·root·········(0)·root·········(0)·····1543·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dimageselect.1.gz |
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| 249 | -rw-r--r--···0·root·········(0)·root·········(0)·····1263·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3disosurface-from-stack.1.gz | 249 | -rw-r--r--···0·root·········(0)·root·········(0)·····1263·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3disosurface-from-stack.1.gz |
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| 251 | -rw-r--r--···0·root·········(0)·root·········(0)·····1140·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dlandmarks-distances.1.gz | 251 | -rw-r--r--···0·root·········(0)·root·········(0)·····1140·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-3dlandmarks-distances.1.gz |
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| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2davgmasked·\-i·<in\-files>·\-m·<mask\-file>·[options] | 6 | .B··mia\-2davgmasked·\-i·<in\-files>·\-m·<mask\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2davgmasked | 8 | .B·mia\-2davgmasked |
| 9 | 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. | 9 | 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. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-files=( | 12 | .IP·"\-i·\-\-in-files=(input,·required);·io" |
| 13 | input·image(s) | 13 | input·image(s) |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-m·\-\-mask-file=( | 15 | .IP·"\-m·\-\-mask-file=(input,·required);·io" |
| 16 | mask·image,·must·be·of·type·byte | 16 | mask·image,·must·be·of·type·byte |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| 20 | .RS | 20 | .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: |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dbinarycombine | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-1·\-\-file1=( | 12 | .IP·"\-1·\-\-file1=(input,·required);·io" |
| 13 | input·mask·image·1 | 13 | input·mask·image·1 |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-2·\-\-file2=( | 15 | .IP·"\-2·\-\-file2=(input,·required);·io" |
| 16 | input·mask·image·2 | 16 | input·mask·image·2 |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-o·\-\-out-file=(output,·required);·io" | 18 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 19 | output·mask·image | 19 | output·mask·image |
| 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 21 | .IP·"\-p·\-\-operation=nor" | 21 | .IP·"\-p·\-\-operation=nor" |
| 22 | Operation·to·be·applied | 22 | Operation·to·be·applied |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2ddeform | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 16 | transformed··image | 16 | transformed··image |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-t·\-\-transformation=( | 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" |
| 19 | transformation·vector·field | 19 | transformation·vector·field |
| 20 | ·For·supported·file·types·see·PLUGINS:2dvf/io | 20 | ·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·kernel | 22 | image·interpolator·kernel |
| 23 | ·For·supported·plugins·see·PLUGINS:1d/splinekernel | 23 | ·For·supported·plugins·see·PLUGINS:1d/splinekernel |
| 24 | .RE | 24 | .RE |
| 25 | .SS·Help·&·Info | 25 | .SS·Help·&·Info |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2ddistance·\-i·<in\-file>·\-d·<distance\-file>·\-o·<out\-file>·[options] | 6 | .B··mia\-2ddistance·\-i·<in\-file>·\-d·<distance\-file>·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2ddistance | 8 | .B·mia\-2ddistance |
| 9 | 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. | 9 | 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. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-d·\-\-distance-file=( | 15 | .IP·"\-d·\-\-distance-file=(input,·required);·io" |
| 16 | distance·field·image·(floating·point) | 16 | distance·field·image·(floating·point) |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-o·\-\-out-file=( | 18 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 19 | output·file,·'\-':·write·to·stdout | 19 | output·file,·'\-':·write·to·stdout |
| 20 | .IP·"\-s·\-\-scale=1" | 20 | .IP·"\-s·\-\-scale=1" |
| 21 | distance·scaling·factor | 21 | distance·scaling·factor |
| 22 | .IP·"\-m·\-\-method=avg" | 22 | .IP·"\-m·\-\-method=avg" |
| 23 | distance·measuring·method | 23 | distance·measuring·method |
| Offset 70, 18 lines modified | Offset 70, 18 lines modified | ||
| 70 | .RS | 70 | .RS |
| 71 | .IP·"\-i·\-\-in-image=(input,·required);·io" | 71 | .IP·"\-i·\-\-in-image=(input,·required);·io" |
| 72 | test·image | 72 | test·image |
| 73 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 73 | ·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·image | 75 | reference·image |
| 76 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 76 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 77 | .IP·"\-o·\-\-transform=( | 77 | .IP·"\-o·\-\-transform=(output,·required);·io" |
| 78 | output·transformation | 78 | output·transformation |
| 79 | ·For·supported·file·types·see·PLUGINS:2dtransform/io | 79 | ·For·supported·file·types·see·PLUGINS:2dtransform/io |
| 80 | .IP·"\-O·\-\-inverse-transform=( | 80 | .IP·"\-O·\-\-inverse-transform=(output,·required);·io" |
| 81 | inverse·output·transformation | 81 | inverse·output·transformation |
| 82 | ·For·supported·file·types·see·PLUGINS:2dtransform/io | 82 | ·For·supported·file·types·see·PLUGINS:2dtransform/io |
| 83 | .RE | 83 | .RE |
| 84 | .SS·Processing | 84 | .SS·Processing |
| 85 | .RS | 85 | .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). |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dforce·\-i·<src\-file>·\-r·<ref\-file>·\-o·<out\-file>·\-c·<cost>·[options] | 6 | .B··mia\-2dforce·\-i·<src\-file>·\-r·<ref\-file>·\-o·<out\-file>·\-c·<cost>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dforce | 8 | .B·mia\-2dforce |
| 9 | This·image·evaluate·the·force·field·between·two·images·based·on·a·given·cost·function. | 9 | This·image·evaluate·the·force·field·between·two·images·based·on·a·given·cost·function. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-src-file=( | 12 | .IP·"\-i·\-\-src-file=(required,·input);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-r·\-\-ref-file=( | 15 | .IP·"\-r·\-\-ref-file=(required,·input);·io" |
| 16 | reference·image | 16 | reference·image |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-o·\-\-out-file=( | 18 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 19 | output·force·norm·image | 19 | output·force·norm·image |
| 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 21 | .IP·"\-c·\-\-cost=(required);·string" | 21 | .IP·"\-c·\-\-cost=(required);·string" |
| 22 | cost·function·to·use | 22 | cost·function·to·use |
| 23 | .RE | 23 | .RE |
| 24 | .SS·Help·&·Info | 24 | .SS·Help·&·Info |
| Offset 6, 15 lines modified | Offset 6, 15 lines modified | ||
| 6 | .B··mia\-2dfuzzysegment·\-i·<in\-file>·[options] | 6 | .B··mia\-2dfuzzysegment·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dfuzzysegment | 8 | .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.,·20:57-68,1999 | 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.,·20:57-68,1999 |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(input,·required);·io" |
| 14 | input·image(s)·to·be·segmenetd | 14 | input·image(s)·to·be·segmenetd |
| 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 15 | ·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/io | 18 | ·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\-uniformity | 20 | image·corrected·for·intensity·non\-uniformity |
| Offset 15, 18 lines modified | Offset 15, 18 lines modified | ||
| 15 | .RE | 15 | .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·OPTIONS | 17 | .SH·OPTIONS |
| 18 | .SS· | 18 | .SS· |
| 19 | File-IO | 19 | File-IO |
| 20 | .RS | 20 | .RS |
| 21 | .IP·"\-i·\-\-in-file=( | 21 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 22 | input·perfusion·data·set | 22 | input·perfusion·data·set |
| 23 | .IP·"\-o·\-\-out-file=( | 23 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 24 | output·perfusion·data·set | 24 | output·perfusion·data·set |
| 25 | .IP·"\-r·\-\-registered=reg" | 25 | .IP·"\-r·\-\-registered=reg" |
| 26 | file·name·base·for·registered·files | 26 | file·name·base·for·registered·files |
| 27 | .RE | 27 | .RE |
| 28 | .SS· | 28 | .SS· |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dimagecombiner | 8 | .B·mia\-2dimagecombiner |
| 9 | Combine·two·image·by·a·given·operation. | 9 | Combine·two·image·by·a·given·operation. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-1·\-\-in-file-1=( | 12 | .IP·"\-1·\-\-in-file-1=(required,·input);·io" |
| 13 | first·input·image·to·be·combined | 13 | first·input·image·to·be·combined |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-2·\-\-in-file-2=( | 15 | .IP·"\-2·\-\-in-file-2=(required,·input);·io" |
| 16 | second·input·image·to·be·combined | 16 | second·input·image·to·be·combined |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-o·\-\-out-file=( | 18 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 19 | output·image(s)·that·have·been·filtered | 19 | output·image(s)·that·have·been·filtered |
| 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 21 | .IP·"\-p·\-\-operation=absdiff" | 21 | .IP·"\-p·\-\-operation=absdiff" |
| 22 | operation·to·be·applied | 22 | operation·to·be·applied |
| 23 | ·For·supported·plugins·see·PLUGINS:2dimage/combiner | 23 | ·For·supported·plugins·see·PLUGINS:2dimage/combiner |
| 24 | .RE | 24 | .RE |
| 25 | .SS·Help·&·Info | 25 | .SS·Help·&·Info |
| Offset 10, 15 lines modified | Offset 10, 15 lines modified | ||
| 10 | ···'mia-plugin-help·filter/2dimage' | 10 | ···'mia-plugin-help·filter/2dimage' |
| 11 | from·the·command·line | 11 | from·the·command·line |
| 12 | .SH·OPTIONS | 12 | .SH·OPTIONS |
| 13 | .RS | 13 | .RS |
| 14 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 14 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 15 | input·image(s)·to·be·filtered | 15 | input·image(s)·to·be·filtered |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 17 | .IP·"\-o·\-\-out-file=( | 17 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 18 | output·image(s)·that·have·been·filtered | 18 | output·image(s)·that·have·been·filtered |
| 19 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 19 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 20 | .RE | 20 | .RE |
| 21 | .SS·Help·&·Info | 21 | .SS·Help·&·Info |
| 22 | .RS | 22 | .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 6, 18 lines modified | Offset 6, 18 lines modified | ||
| 6 | .B··mia\-2dimagefilterstack·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter> | 6 | .B··mia\-2dimagefilterstack·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter> |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dimagefilterstack | 8 | .B·mia\-2dimagefilterstack |
| 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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File·IO | 11 | .SS·File·IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(input,·required);·io" |
| 14 | input·image(s)·to·be·filtered | 14 | input·image(s)·to·be·filtered |
| 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 16 | .IP·"\-o·\-\-out-file=( | 16 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 17 | output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option | 17 | output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option |
| 18 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 18 | ·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·used | 20 | output·file·type,·if·not·given·the·input·type·is·used |
| 21 | .RS·10 | 21 | .RS·10 |
| 22 | .I | 22 | .I |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dimagefullstats·\-i·<in\-file>·[options] | 6 | .B··mia\-2dimagefullstats·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dimagefullstats | 8 | .B·mia\-2dimagefullstats |
| 9 | This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·Min·and·Max·of·the·intensity·values. | 9 | This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·Min·and·Max·of·the·intensity·values. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .RE | 15 | .RE |
| 16 | .SS·Help·&·Info | 16 | .SS·Help·&·Info |
| 17 | .RS | 17 | .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: |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-2dimageselect | 8 | .B·mia\-2dimageselect |
| 9 | This·program·is·used·to·select·one·2D·images·from·a·multi-image·file. | 9 | This·program·is·used·to·select·one·2D·images·from·a·multi-image·file. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(input,·required);·io" | 12 | .IP·"\-i·\-\-in-file=(input,·required);·io" |
| 13 | input·images | 13 | input·images |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 16 | output·image | 16 | output·image |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-n·\-\-number=0" | 18 | .IP·"\-n·\-\-number=0" |
| 19 | image·number·to·be·selected | 19 | image·number·to·be·selected |
| 20 | .RE | 20 | .RE |
| 21 | .SS·Help·&·Info | 21 | .SS·Help·&·Info |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dimageseries\-maximum\-intensity\-projection | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-file=( | 12 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 13 | output·image | 13 | output·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .RE | 15 | .RE |
| 16 | .SS·Help·&·Info | 16 | .SS·Help·&·Info |
| 17 | .RS | 17 | .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: |
| Offset 6, 15 lines modified | Offset 6, 15 lines modified | ||
| 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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dimagestack\-cmeans | 8 | .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·values | 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·values |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 14 | input·image(s)·to·be·filtered | 14 | input·image(s)·to·be·filtered |
| 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 16 | .IP·"\-o·\-\-out-probmap=(required,·output);·string" | 16 | .IP·"\-o·\-\-out-probmap=(required,·output);·string" |
| 17 | Save·probability·map·to·this·file | 17 | Save·probability·map·to·this·file |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dimagestats·\-i·<in\-file>·[options] | 6 | .B··mia\-2dimagestats·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dimagestats | 8 | .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·pixels | 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·pixels |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image·to·be·analyzed | 13 | input·image·to·be·analyzed |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-t·\-\-thresh=10" | 15 | .IP·"\-t·\-\-thresh=10" |
| 16 | intensity·thresh·to·ignore | 16 | intensity·thresh·to·ignore |
| 17 | .IP·"\-g·\-\-high-thresh=0.05" | 17 | .IP·"\-g·\-\-high-thresh=0.05" |
| 18 | upper·histogram·percentage·to·ignore | 18 | upper·histogram·percentage·to·ignore |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dlerp·\-1·<first>·\-2·<second>·\-o·<out\-file>·\-p·<positions>·[options] | 6 | .B··mia\-2dlerp·\-1·<first>·\-2·<second>·\-o·<out\-file>·\-p·<positions>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dlerp | 8 | .B·mia\-2dlerp |
| 9 | Merge·two·images·by·pixel-wise·linearly·combining·their·intensities. | 9 | Merge·two·images·by·pixel-wise·linearly·combining·their·intensities. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-1·\-\-first=( | 12 | .IP·"\-1·\-\-first=(input,·required);·io" |
| 13 | first·input·image· | 13 | first·input·image· |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-2·\-\-second=( | 15 | .IP·"\-2·\-\-second=(input,·required);·io" |
| 16 | second·input·image· | 16 | second·input·image· |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-o·\-\-out-file=(output,·required);·io" | 18 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 19 | output·vector·field | 19 | output·vector·field |
| 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 20 | ·For·supported·file·types·see·PLUGINS:2dimage/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) |
| Offset 7, 15 lines modified | Offset 7, 15 lines modified | ||
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmany2one\-nonrigid | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS· | 11 | .SS· |
| 12 | File-IO | 12 | File-IO |
| 13 | .RS | 13 | .RS |
| 14 | .IP·"\-i·\-\-in-file=( | 14 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 15 | input·perfusion·data·set | 15 | 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·data | 17 | file·name·for·registered·images,·numbering·and·pattern·are·deducted·from·the·input·data |
| 18 | .RE | 18 | .RE |
| 19 | .SS· | 19 | .SS· |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmulti\-force | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-file=( | 12 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 13 | output·norm·image | 13 | output·norm·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .RE | 15 | .RE |
| 16 | .SS·Help·&·Info | 16 | .SS·Help·&·Info |
| 17 | .RS | 17 | .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: |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dmultiimageto3d·\-i·<in\-file>·\-o·<out\-file>·[options] | 6 | .B··mia\-2dmultiimageto3d·\-i·<in\-file>·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmultiimageto3d | 8 | .B·mia\-2dmultiimageto3d |
| 9 | This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image. | 9 | This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·images | 13 | input·images |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" | 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 16 | output·image | 16 | output·image |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dmultiimagevar·\-o·<out\-file>·[options]·<PLUGINS:2dimage/io> | 6 | .B··mia\-2dmultiimagevar·\-o·<out\-file>·[options]·<PLUGINS:2dimage/io> |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmultiimagevar | 8 | .B·mia\-2dmultiimagevar |
| 9 | This·program·evaluates·the·pixel-wise·accumulated·intensity·variation·of·a·set·of·image·given·on·the·command·line.·If·the·input·image·files·contain·more·then·one·image·all·images·are·used.·All·images·must·be·of·the·same·size. | 9 | This·program·evaluates·the·pixel-wise·accumulated·intensity·variation·of·a·set·of·image·given·on·the·command·line.·If·the·input·image·files·contain·more·then·one·image·all·images·are·used.·All·images·must·be·of·the·same·size. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-file=( | 12 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 13 | output·image· | 13 | output·image· |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .RE | 15 | .RE |
| 16 | .SS·Help·&·Info | 16 | .SS·Help·&·Info |
| 17 | .RS | 17 | .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: |
| Offset 6, 15 lines modified | Offset 6, 15 lines modified | ||
| 6 | .B··mia\-2dmyocard\-ica·\-i·<in\-base>·[options] | 6 | .B··mia\-2dmyocard\-ica·\-i·<in\-base>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmyocard\-ica | 8 | .B·mia\-2dmyocard\-ica |
| 9 | 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. | 9 | 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. |
| 10 | This·program·is·essentially·used·to·test·different·options·on·how·to·run·the·ICA·forreference·image·creation. | 10 | This·program·is·essentially·used·to·test·different·options·on·how·to·run·the·ICA·forreference·image·creation. |
| 11 | .SH·OPTIONS | 11 | .SH·OPTIONS |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-base=( | 13 | .IP·"\-i·\-\-in-base=(input,·required);·io" |
| 14 | input·file·name·ofolloing·pattern·nameXXXX.ext·X=numbers | 14 | input·file·name·ofolloing·pattern·nameXXXX.ext·X=numbers |
| 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 16 | .IP·"···\-\-coefs=" | 16 | .IP·"···\-\-coefs=" |
| 17 | output·mixing·coefficients·to·this·file | 17 | output·mixing·coefficients·to·this·file |
| 18 | .IP·"\-o·\-\-out-base=(output);·string" | 18 | .IP·"\-o·\-\-out-base=(output);·string" |
| 19 | output·file·name·base | 19 | output·file·name·base |
| Offset 9, 15 lines modified | Offset 9, 15 lines modified | ||
| 9 | This·program·is·work·in·progress | 9 | This·program·is·work·in·progress |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=(input,·required);·string" | 13 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 14 | input·perfusion·data·set | 14 | input·perfusion·data·set |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 16 | output·myocardial·mask | 16 | output·myocardial·mask |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·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·base | 19 | save·ICA·features·to·files·with·this·name·base |
| 20 | .RE | 20 | .RE |
| 21 | .SS·Help·&·Info | 21 | .SS·Help·&·Info |
| Offset 14, 18 lines modified | Offset 14, 18 lines modified | ||
| 14 | .UE | 14 | .UE |
| 15 | .RE | 15 | .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·OPTIONS | 17 | .SH·OPTIONS |
| 18 | .SS·File-IO | 18 | .SS·File-IO |
| 19 | .RS | 19 | .RS |
| 20 | .IP·"\-i·\-\-in-file=( | 20 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 21 | input·perfusion·data·set | 21 | input·perfusion·data·set |
| 22 | .IP·"\-o·\-\-out-file=( | 22 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 23 | output·perfusion·data·set | 23 | 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. |
| 26 | .IP·"···\-\-save-cropped=(output);·string" | 26 | .IP·"···\-\-save-cropped=(output);·string" |
| 27 | save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base | 27 | save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base |
| Offset 14, 18 lines modified | Offset 14, 18 lines modified | ||
| 14 | .UE | 14 | .UE |
| 15 | .RE | 15 | .RE |
| 16 | This·version·of·the·program·runs·all·registrations·in·parallel. | 16 | This·version·of·the·program·runs·all·registrations·in·parallel. |
| 17 | .SH·OPTIONS | 17 | .SH·OPTIONS |
| 18 | .SS·File-IO | 18 | .SS·File-IO |
| 19 | .RS | 19 | .RS |
| 20 | .IP·"\-i·\-\-in-file=( | 20 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 21 | input·perfusion·data·set | 21 | input·perfusion·data·set |
| 22 | .IP·"\-o·\-\-out-file=( | 22 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 23 | output·perfusion·data·set | 23 | output·perfusion·data·set |
| 24 | .IP·"\-r·\-\-registered=reg" | 24 | .IP·"\-r·\-\-registered=reg" |
| 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. |
| 26 | .IP·"···\-\-save-cropped=(output);·string" | 26 | .IP·"···\-\-save-cropped=(output);·string" |
| 27 | save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base | 27 | save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base |
| Offset 13, 15 lines modified | Offset 13, 15 lines modified | ||
| 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 | .UE | 14 | .UE |
| 15 | .RE | 15 | .RE |
| 16 | .SH·OPTIONS | 16 | .SH·OPTIONS |
| 17 | .SS·File-IO | 17 | .SS·File-IO |
| 18 | .RS | 18 | .RS |
| 19 | .IP·"\-i·\-\-in-file=( | 19 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 20 | input·perfusion·data·set | 20 | input·perfusion·data·set |
| 21 | .IP·"\-o·\-\-out-file=(required,·output);·string" | 21 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 22 | output·perfusion·data·set | 22 | output·perfusion·data·set |
| 23 | .IP·"\-r·\-\-registered=reg" | 23 | .IP·"\-r·\-\-registered=reg" |
| 24 | file·name·base·for·registered·fiels | 24 | file·name·base·for·registered·fiels |
| Offset 11, 15 lines modified | Offset 11, 15 lines modified | ||
| 11 | .SH·OPTIONS | 11 | .SH·OPTIONS |
| 12 | .SS· | 12 | .SS· |
| 13 | File-IO | 13 | File-IO |
| 14 | .RS | 14 | .RS |
| 15 | .IP·"\-i·\-\-in-file=(required,·input);·string" | 15 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 16 | input·perfusion·data·set | 16 | input·perfusion·data·set |
| 17 | .IP·"\-o·\-\-out-file=( | 17 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 18 | output·perfusion·data·set | 18 | output·perfusion·data·set |
| 19 | .IP·"\-r·\-\-registered=reg" | 19 | .IP·"\-r·\-\-registered=reg" |
| 20 | file·name·base·for·registered·fiels | 20 | file·name·base·for·registered·fiels |
| 21 | .IP·"···\-\-save-cropped=" | 21 | .IP·"···\-\-save-cropped=" |
| 22 | save·cropped·set·to·this·file | 22 | save·cropped·set·to·this·file |
| Offset 43, 18 lines modified | Offset 43, 18 lines modified | ||
| 43 | .IP·"\-T·\-\-rho-thresh=0.85" | 43 | .IP·"\-T·\-\-rho-thresh=0.85" |
| 44 | correlation·threshold·for·neighborhood·analysis | 44 | correlation·threshold·for·neighborhood·analysis |
| 45 | .RE | 45 | .RE |
| 46 | .SS·File-IO | 46 | .SS·File-IO |
| 47 | .RS | 47 | .RS |
| 48 | .IP·"\-i·\-\-in-file=( | 48 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 49 | input·perfusion·data·set | 49 | input·perfusion·data·set |
| 50 | .IP·"\-o·\-\-out-file=( | 50 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 51 | output·perfusion·data·set | 51 | output·perfusion·data·set |
| 52 | .IP·"\-r·\-\-registered=" | 52 | .IP·"\-r·\-\-registered=" |
| 53 | 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. | 53 | 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. |
| 54 | .IP·"···\-\-save-cropped=(output);·string" | 54 | .IP·"···\-\-save-cropped=(output);·string" |
| 55 | save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base | 55 | save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base |
| Offset 14, 18 lines modified | Offset 14, 18 lines modified | ||
| 14 | .UE | 14 | .UE |
| 15 | .RE | 15 | .RE |
| 16 | .SH·OPTIONS | 16 | .SH·OPTIONS |
| 17 | .SS· | 17 | .SS· |
| 18 | File-IO | 18 | File-IO |
| 19 | .RS | 19 | .RS |
| 20 | .IP·"\-i·\-\-in-file=( | 20 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 21 | input·perfusion·data·set | 21 | input·perfusion·data·set |
| 22 | .IP·"\-o·\-\-out-file=( | 22 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 23 | output·perfusion·data·set | 23 | output·perfusion·data·set |
| 24 | .IP·"\-r·\-\-registered=reg" | 24 | .IP·"\-r·\-\-registered=reg" |
| 25 | file·name·base·for·registered·fiels | 25 | file·name·base·for·registered·fiels |
| 26 | .IP·"···\-\-save-references" | 26 | .IP·"···\-\-save-references" |
| 27 | Save·synthetic·references·to·files·refXXXX.v | 27 | Save·synthetic·references·to·files·refXXXX.v |
| Offset 14, 18 lines modified | Offset 14, 18 lines modified | ||
| 14 | .UE | 14 | .UE |
| 15 | .RE | 15 | .RE |
| 16 | .SH·OPTIONS | 16 | .SH·OPTIONS |
| 17 | .SS· | 17 | .SS· |
| 18 | File-IO | 18 | File-IO |
| 19 | .RS | 19 | .RS |
| 20 | .IP·"\-i·\-\-in-file=( | 20 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 21 | input·perfusion·data·set | 21 | input·perfusion·data·set |
| 22 | .IP·"\-o·\-\-out-file=( | 22 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 23 | output·perfusion·data·set | 23 | output·perfusion·data·set |
| 24 | .IP·"\-R·\-\-registered=reg" | 24 | .IP·"\-R·\-\-registered=reg" |
| 25 | file·name·base·for·registered·fiels | 25 | file·name·base·for·registered·fiels |
| 26 | .RE | 26 | .RE |
| 27 | .SS· | 27 | .SS· |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dmyoseries\-compdice·\-1·<first>·\-2·<second>·[options] | 6 | .B··mia\-2dmyoseries\-compdice·\-1·<first>·\-2·<second>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmyoseries\-compdice | 8 | .B·mia\-2dmyoseries\-compdice |
| 9 | This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·two·image·series | 9 | This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·two·image·series |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-1·\-\-first=( | 12 | .IP·"\-1·\-\-first=(required,·input);·string" |
| 13 | first·segmentation·set | 13 | first·segmentation·set |
| 14 | .IP·"\-2·\-\-second=( | 14 | .IP·"\-2·\-\-second=(required,·input);·string" |
| 15 | second·segmentation·set | 15 | second·segmentation·set |
| 16 | .IP·"\-k·\-\-skip=2" | 16 | .IP·"\-k·\-\-skip=2" |
| 17 | images·to·skip·atthe·begin·of·the·series | 17 | images·to·skip·atthe·begin·of·the·series |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dmyoseries\-dice·\-i·<input>·[options] | 6 | .B··mia\-2dmyoseries\-dice·\-i·<input>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmyoseries\-dice | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-input=( | 12 | .IP·"\-i·\-\-input=(required,·input);·string" |
| 13 | original·segmentation·set | 13 | original·segmentation·set |
| 14 | .IP·"\-k·\-\-skip=2" | 14 | .IP·"\-k·\-\-skip=2" |
| 15 | images·to·skip·atthe·bgin·of·the·series | 15 | images·to·skip·atthe·bgin·of·the·series |
| 16 | .IP·"\-r·\-\-reference=20" | 16 | .IP·"\-r·\-\-reference=20" |
| 17 | reference·image | 17 | reference·image |
| Offset 7, 18 lines modified | Offset 7, 18 lines modified | ||
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dmyoset\-all2one\-nonrigid | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS· | 11 | .SS· |
| 12 | File-IO | 12 | File-IO |
| 13 | .RS | 13 | .RS |
| 14 | .IP·"\-i·\-\-in-file=( | 14 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 15 | input·perfusion·data·set | 15 | input·perfusion·data·set |
| 16 | .IP·"\-o·\-\-out-file=( | 16 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 17 | output·perfusion·data·set | 17 | 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 | .RE | 20 | .RE |
| 21 | .SS· | 21 | .SS· |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dsegcompare·\-i·<in\-file>·\-r·<ref\-file>·[options] | 6 | .B··mia\-2dsegcompare·\-i·<in\-file>·\-r·<ref\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dsegcompare | 8 | .B·mia\-2dsegcompare |
| 9 | 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. | 9 | 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. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-r·\-\-ref-file=( | 14 | .IP·"\-r·\-\-ref-file=(required,·input);·string" |
| 15 | reference··segmentation·set | 15 | reference··segmentation·set |
| 16 | .RE | 16 | .RE |
| 17 | .SS·Help·&·Info | 17 | .SS·Help·&·Info |
| 18 | .RS | 18 | .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: |
| Offset 16, 15 lines modified | Offset 16, 15 lines modified | ||
| 16 | ·changes·are:·p=2,·and·exp | 16 | ·changes·are:·p=2,·and·exp |
| 17 | .SH·OPTIONS | 17 | .SH·OPTIONS |
| 18 | .RS | 18 | .RS |
| 19 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 19 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 20 | image·to·be·segmented | 20 | image·to·be·segmented |
| 21 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 21 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 22 | .IP·"\-o·\-\-out-file=( | 22 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 23 | class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values | 23 | class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values |
| 24 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 24 | ·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·classes | 26 | number·of·classes |
| 27 | .IP·"\-b·\-\-bias-correct" | 27 | .IP·"\-b·\-\-bias-correct" |
| 28 | apply·bias·field·correction | 28 | apply·bias·field·correction |
| Offset 852, 15 lines modified | Offset 852, 15 lines modified | ||
| 852 | Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation. | 852 | Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation. |
| 853 | .RE | 853 | .RE |
| 854 | .RE | 854 | .RE |
| 855 | .RS·14 | 855 | .RS·14 |
| 856 | .I | 856 | .I |
| 857 | varfile | 857 | varfile |
| 858 | =( | 858 | =(output,·required,·io) |
| 859 | .RS·2 | 859 | .RS·2 |
| 860 | name·of·the·output·file·to·save·the·variation·image·too.. | 860 | name·of·the·output·file·to·save·the·variation·image·too.. |
| 861 | For·supported·file·types·see·PLUGINS:2dimage/io | 861 | For·supported·file·types·see·PLUGINS:2dimage/io |
| 862 | .RE | 862 | .RE |
| 863 | .RE | 863 | .RE |
| 864 | .RS·14 | 864 | .RS·14 |
| Offset 9, 15 lines modified | Offset 9, 15 lines modified | ||
| 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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 14 | image·to·be·segmented | 14 | image·to·be·segmented |
| 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 16 | .IP·"\-o·\-\-out-file=( | 16 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 17 | class·label·image·based·on·merging·local·labels | 17 | class·label·image·based·on·merging·local·labels |
| 18 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 18 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 19 | .RE | 19 | .RE |
| 20 | .SS·Help·&·Info | 20 | .SS·Help·&·Info |
| 21 | .RS | 21 | .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: |
| Offset 11, 15 lines modified | Offset 11, 15 lines modified | ||
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(required,·input);·string" | 12 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-p·\-\-override-imagepath" | 14 | .IP·"\-p·\-\-override-imagepath" |
| 15 | Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation·set,·assume·the·files·are·located·in·the·current·directory | 15 | Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation·set,·assume·the·files·are·located·in·the·current·directory |
| 16 | .IP·"\-o·\-\-out-file=( | 16 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 17 | output·segmentation·set | 17 | output·segmentation·set |
| 18 | .IP·"\-c·\-\-cropped-base=crop" | 18 | .IP·"\-c·\-\-cropped-base=crop" |
| 19 | Base·name·for·the·cropped·image·files,·the·file·type·and·numbering·will·be·based·on·the·input·image·file·type·and·numbering. | 19 | Base·name·for·the·cropped·image·files,·the·file·type·and·numbering·will·be·based·on·the·input·image·file·type·and·numbering. |
| 20 | .IP·"\-e·\-\-enlarge=5" | 20 | .IP·"\-e·\-\-enlarge=5" |
| 21 | Enlarge·the·area·around·the·obtained·sbounding·box·by·this·number·of·pixels·in·each·direction | 21 | Enlarge·the·area·around·the·obtained·sbounding·box·by·this·number·of·pixels·in·each·direction |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dsegseriesstats·\-o·<original>·\-g·<registered>·[options] | 6 | .B··mia\-2dsegseriesstats·\-o·<original>·\-g·<registered>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dsegseriesstats | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-original=( | 12 | .IP·"\-o·\-\-original=(required,·input);·string" |
| 13 | original·segmentation·set | 13 | original·segmentation·set |
| 14 | .IP·"\-g·\-\-registered=( | 14 | .IP·"\-g·\-\-registered=(required,·input);·string" |
| 15 | registered·segmentation·set | 15 | 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·set | 17 | 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): |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-2dsegshift | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 16 | input·segmentation·set | 16 | input·segmentation·set |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-g·\-\-image-file=crop" | 18 | .IP·"\-g·\-\-image-file=crop" |
| 19 | output·image·filename·base | 19 | output·image·filename·base |
| 20 | .IP·"\-S·\-\-shift=[0,0]" | 20 | .IP·"\-S·\-\-shift=[0,0]" |
| 21 | shift·of·segmentation | 21 | shift·of·segmentation |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-2dsegshiftperslice | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-file=( | 14 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 15 | output·segmentation·set | 15 | output·segmentation·set |
| 16 | .IP·"\-g·\-\-image-file=crop" | 16 | .IP·"\-g·\-\-image-file=crop" |
| 17 | output·image·filename·base | 17 | 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· |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dseries\-mincorr·\-i·<in\-set>·\-o·<out\-set>·[options] | 6 | .B··mia\-2dseries\-mincorr·\-i·<in\-set>·\-o·<out\-set>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dseries\-mincorr | 8 | .B·mia\-2dseries\-mincorr |
| 9 | Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal·correlation·of·the·time-intensity·curve·between·neighboring·pixels. | 9 | Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal·correlation·of·the·time-intensity·curve·between·neighboring·pixels. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-set=( | 12 | .IP·"\-i·\-\-in-set=(required,·input);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-set=(output,·required);·io" | 14 | .IP·"\-o·\-\-out-set=(output,·required);·io" |
| 15 | output·image·of·minimal·correlation | 15 | output·image·of·minimal·correlation |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 17 | .IP·"\-k·\-\-skip=2" | 17 | .IP·"\-k·\-\-skip=2" |
| 18 | skip·images·at·beginning·of·series | 18 | skip·images·at·beginning·of·series |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dseries\-sectionmask | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-file=(required,·output);·io" | 14 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 15 | output·image·containing·the·mask | 15 | output·image·containing·the·mask |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·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·mask | 18 | Frame·number·for·which·to·extract·the·mask |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dseries2dordermedian·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter> | 6 | .B··mia\-2dseries2dordermedian·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter> |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dseries2dordermedian | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-file=( | 14 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 15 | output·image·name | 15 | output·image·name |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 17 | .IP·"\-k·\-\-skip=0" | 17 | .IP·"\-k·\-\-skip=0" |
| 18 | Skip·files·at·the·beginning | 18 | Skip·files·at·the·beginning |
| 19 | .IP·"\-e·\-\-enlarge-boundary=5" | 19 | .IP·"\-e·\-\-enlarge-boundary=5" |
| 20 | Enlarge·cropbox·by·number·of·pixels | 20 | Enlarge·cropbox·by·number·of·pixels |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dseries2sets | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-directory=( | 12 | .IP·"\-o·\-\-out-directory=(required,·output);·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·directory | 15 | don't·copy·image·files·to·output·directory |
| 16 | .RE | 16 | .RE |
| 17 | .SS·Help·&·Info | 17 | .SS·Help·&·Info |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-2dseriesgradMAD | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-file=( | 14 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 15 | output·file·name | 15 | output·file·name |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 17 | .IP·"\-k·\-\-skip=0" | 17 | .IP·"\-k·\-\-skip=0" |
| 18 | Skip·files·at·the·beginning | 18 | Skip·files·at·the·beginning |
| 19 | .IP·"\-e·\-\-enlarge-boundary=5" | 19 | .IP·"\-e·\-\-enlarge-boundary=5" |
| 20 | Enlarge·cropbox·by·number·of·pixels | 20 | Enlarge·cropbox·by·number·of·pixels |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dseriesgradvariation | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-file=( | 14 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 15 | output·file·name | 15 | output·file·name |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 17 | .IP·"\-k·\-\-skip=0" | 17 | .IP·"\-k·\-\-skip=0" |
| 18 | Skip·files·at·the·beginning | 18 | Skip·files·at·the·beginning |
| 19 | .IP·"\-e·\-\-enlarge-boundary=5" | 19 | .IP·"\-e·\-\-enlarge-boundary=5" |
| 20 | Enlarge·cropbox·by·number·of·pixels | 20 | Enlarge·cropbox·by·number·of·pixels |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dseriessmoothgradMAD | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·segmentation·set | 13 | input·segmentation·set |
| 14 | .IP·"\-o·\-\-out-file=(required,·output);·io" | 14 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 15 | output·file·name | 15 | output·file·name |
| 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 17 | .IP·"\-k·\-\-skip=0" | 17 | .IP·"\-k·\-\-skip=0" |
| 18 | Skip·files·at·the·beginning | 18 | Skip·files·at·the·beginning |
| Offset 6, 24 lines modified | Offset 6, 24 lines modified | ||
| 6 | .B··mia\-2dstack\-cmeans\-presegment·\-i·<in\-file>·\-o·<out\-mask>·\-L·<label>·[options] | 6 | .B··mia\-2dstack\-cmeans\-presegment·\-i·<in\-file>·\-o·<out\-mask>·\-L·<label>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dstack\-cmeans\-presegment | 8 | .B·mia\-2dstack\-cmeans\-presegment |
| 9 | 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. | 9 | 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. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 14 | input·image(s)·to·be·filtered | 14 | input·image(s)·to·be·filtered |
| 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 15 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 16 | .IP·"\-p·\-\-out-probmap=(output);·string" | 16 | .IP·"\-p·\-\-out-probmap=(output);·string" |
| 17 | Save·probability·map·to·this·file | 17 | Save·probability·map·to·this·file |
| 18 | .IP·"\-t·\-\-type=png" | 18 | .IP·"\-t·\-\-type=png" |
| 19 | output·file·name·type | 19 | output·file·name·type |
| 20 | .IP·"\-o·\-\-out-mask=( | 20 | .IP·"\-o·\-\-out-mask=(required,·output);·string" |
| 21 | output·file·name·base | 21 | output·file·name·base |
| 22 | .RE | 22 | .RE |
| 23 | .SS·Help·&·Info | 23 | .SS·Help·&·Info |
| 24 | .RS | 24 | .RS |
| 25 | .IP·"\-V·\-\-verbose=warning" | 25 | .IP·"\-V·\-\-verbose=warning" |
| 26 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: | 26 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: |
| Offset 13, 15 lines modified | Offset 13, 15 lines modified | ||
| 13 | .SH·OPTIONS | 13 | .SH·OPTIONS |
| 14 | .SS· | 14 | .SS· |
| 15 | File-IO | 15 | File-IO |
| 16 | .RS | 16 | .RS |
| 17 | .IP·"\-i·\-\-in-file=(required,·input);·string" | 17 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 18 | input·point·set | 18 | input·point·set |
| 19 | .IP·"\-o·\-\-out-file=( | 19 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 20 | output·point·set | 20 | output·point·set |
| 21 | .IP·"\-t·\-\-transformation=(required,·input);·io" | 21 | .IP·"\-t·\-\-transformation=(required,·input);·io" |
| 22 | transformation·describing·the·monitored·change | 22 | transformation·describing·the·monitored·change |
| 23 | ·For·supported·file·types·see·PLUGINS:2dtransform/io | 23 | ·For·supported·file·types·see·PLUGINS:2dtransform/io |
| 24 | .RE | 24 | .RE |
| 25 | .SS· | 25 | .SS· |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-2dtransform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options] | 6 | .B··mia\-2dtransform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-2dtransform | 8 | .B·mia\-2dtransform |
| 9 | This·program·is·used·to·deform·a·2D·image·using·a·given·transformation. | 9 | This·program·is·used·to·deform·a·2D·image·using·a·given·transformation. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·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 | output·image | 16 | output·image |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-t·\-\-transformation=( | 18 | .IP·"\-t·\-\-transformation=(input,·required);·io" |
| 19 | transformation·file·name | 19 | transformation·file·name |
| 20 | ·For·supported·file·types·see·PLUGINS:2dtransform/io | 20 | ·For·supported·file·types·see·PLUGINS:2dtransform/io |
| 21 | .IP·"\-p·\-\-interpolator=" | 21 | .IP·"\-p·\-\-interpolator=" |
| 22 | override·the·interpolator·provided·by·the·transformation | 22 | 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·overridden. | 24 | override·the·boundary·conditions·provided·by·the·transformation.·This·is·only·used·if·the·interpolator·is·overridden. |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dcombine\-imageseries | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-file=( | 12 | .IP·"\-o·\-\-out-file=(output,·required);·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/io | 14 | ·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·images | 16 | Operation·to·be·applied·when·combining·the·images |
| 17 | .RS·10 | 17 | .RS·10 |
| 18 | .I | 18 | .I |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dcombine\-mr\-segmentations | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·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/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-o·\-\-out-file=( | 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/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| 20 | .RS | 20 | .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: |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-3ddeform | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-image=(required,·input);·io" | 12 | .IP·"\-i·\-\-in-image=(required,·input);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-o·\-\-out-image=( | 15 | .IP·"\-o·\-\-out-image=(required,·output);·io" |
| 16 | transformed·image | 16 | transformed·image |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" | 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" |
| 19 | transformation·vector·field | 19 | transformation·vector·field |
| 20 | ·For·supported·file·types·see·PLUGINS:3dvf/io | 20 | ·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·kernel | 22 | image·interpolator·kernel |
| Offset 33, 15 lines modified | Offset 33, 15 lines modified | ||
| 33 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 33 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 34 | .IP·"\-r·\-\-ref-labels=(input,·required);·io" | 34 | .IP·"\-r·\-\-ref-labels=(input,·required);·io" |
| 35 | reference·label·image | 35 | reference·label·image |
| 36 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 36 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 37 | .IP·"\-l·\-\-label-map=(input);·string" | 37 | .IP·"\-l·\-\-label-map=(input);·string" |
| 38 | optional·mapping·of·label·numbers | 38 | optional·mapping·of·label·numbers |
| 39 | .IP·"\-o·\-\-out-file=( | 39 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 40 | output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label. | 40 | output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label. |
| 41 | .RE | 41 | .RE |
| 42 | .SS·Help·&·Info | 42 | .SS·Help·&·Info |
| 43 | .RS | 43 | .RS |
| 44 | .IP·"\-V·\-\-verbose=warning" | 44 | .IP·"\-V·\-\-verbose=warning" |
| 45 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: | 45 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: |
| Offset 6, 18 lines modified | Offset 6, 18 lines modified | ||
| 6 | .B··mia\-3ddistance·\-i·<in\-file>·\-r·<ref\-file>·\-o·<out\-file>·[options] | 6 | .B··mia\-3ddistance·\-i·<in\-file>·\-r·<ref\-file>·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3ddistance | 8 | .B·mia\-3ddistance |
| 9 | 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. | 9 | 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. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File·IO | 11 | .SS·File·IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 14 | input·image(s)·that·contain·the·source·pixel·mask | 14 | input·image(s)·that·contain·the·source·pixel·mask |
| 15 | .IP·"\-r·\-\-ref-file=( | 15 | .IP·"\-r·\-\-ref-file=(input,·required);·string" |
| 16 | reference·mask·to·evaluate·the·distance·from | 16 | reference·mask·to·evaluate·the·distance·from |
| 17 | .IP·"\-o·\-\-out-file=(output,·required);·string" | 17 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 18 | output·file·name | 18 | output·file·name |
| 19 | .RE | 19 | .RE |
| 20 | .SS·Help·&·Info | 20 | .SS·Help·&·Info |
| Offset 27, 15 lines modified | Offset 27, 15 lines modified | ||
| 27 | .SH·OPTIONS | 27 | .SH·OPTIONS |
| 28 | .SS· | 28 | .SS· |
| 29 | File-IO | 29 | File-IO |
| 30 | .RS | 30 | .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=( | 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=(input,·required);·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/io | 37 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 38 | .RE | 38 | .RE |
| 39 | .SS· | 39 | .SS· |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-3dfield2norm·\-i·<in\-vectorfield>·\-o·<out\-image>·[options] | 6 | .B··mia\-3dfield2norm·\-i·<in\-vectorfield>·\-o·<out\-image>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dfield2norm | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-vectorfield=( | 12 | .IP·"\-i·\-\-in-vectorfield=(input,·required);·io" |
| 13 | input·vector·field | 13 | input·vector·field |
| 14 | ·For·supported·file·types·see·PLUGINS:3dvf/io | 14 | ·For·supported·file·types·see·PLUGINS:3dvf/io |
| 15 | .IP·"\-o·\-\-out-image=( | 15 | .IP·"\-o·\-\-out-image=(output,·required);·io" |
| 16 | output·image·comprising·the·per·voxel·norm·of·each·image | 16 | output·image·comprising·the·per·voxel·norm·of·each·image |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| 20 | .RS | 20 | .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: |
| Offset 64, 24 lines modified | Offset 64, 24 lines modified | ||
| 64 | .IP·"···\-\-version" | 64 | .IP·"···\-\-version" |
| 65 | print·the·version·number·and·exit | 65 | print·the·version·number·and·exit |
| 66 | .RE | 66 | .RE |
| 67 | .SS·IO | 67 | .SS·IO |
| 68 | .RS | 68 | .RS |
| 69 | .IP·"\-i·\-\-in-image=( | 69 | .IP·"\-i·\-\-in-image=(input,·required);·io" |
| 70 | test·image | 70 | test·image |
| 71 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 71 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 72 | .IP·"\-r·\-\-ref-image=( | 72 | .IP·"\-r·\-\-ref-image=(input,·required);·io" |
| 73 | reference·image | 73 | reference·image |
| 74 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 74 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 75 | .IP·"\-o·\-\-transform=( | 75 | .IP·"\-o·\-\-transform=(output,·required);·io" |
| 76 | output·transformation | 76 | output·transformation |
| 77 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 77 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 78 | .IP·"\-O·\-\-inverse-transform=( | 78 | .IP·"\-O·\-\-inverse-transform=(output,·required);·io" |
| 79 | inverse·output·transformation | 79 | inverse·output·transformation |
| 80 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 80 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 81 | .RE | 81 | .RE |
| 82 | .SS·Processing | 82 | .SS·Processing |
| 83 | .RS | 83 | .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). |
| Offset 11, 15 lines modified | Offset 11, 15 lines modified | ||
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-src-file=(input,·required);·io" | 12 | .IP·"\-i·\-\-src-file=(input,·required);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·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·image | 16 | output·force·norm·image |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-o·\-\-out-file=( | 18 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 19 | reference·image | 19 | reference·image |
| 20 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 20 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 21 | .IP·"\-c·\-\-cost=ssd" | 21 | .IP·"\-c·\-\-cost=ssd" |
| 22 | cost·function·to·use | 22 | cost·function·to·use |
| 23 | ·For·supported·plugins·see·PLUGINS:3dimage/cost | 23 | ·For·supported·plugins·see·PLUGINS:3dimage/cost |
| 24 | .RE | 24 | .RE |
| 25 | .SS·Help·&·Info | 25 | .SS·Help·&·Info |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-3dfuzzysegment·\-i·<in\-file>·[options] | 6 | .B··mia\-3dfuzzysegment·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dfuzzysegment | 8 | .B·mia\-3dfuzzysegment |
| 9 | This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image | 9 | This·program·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image(s)·to·be·segmenetd | 13 | input·image(s)·to·be·segmenetd |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·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/io | 17 | ·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\-uniformity | 19 | image·corrected·for·intensity·non\-uniformity |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dimageaddattributes | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image(s)·to·be·filtered | 13 | input·image(s)·to·be·filtered |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·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 | output·image(s)·with·the·added·attributes | 16 | output·image(s)·with·the·added·attributes |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-a·\-\-attr=( | 18 | .IP·"\-a·\-\-attr=(required,·input);·io" |
| 19 | 2D·image·providing·the·attributes | 19 | 2D·image·providing·the·attributes |
| 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 20 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 21 | .RE | 21 | .RE |
| 22 | .SS·Help·&·Info | 22 | .SS·Help·&·Info |
| 23 | .RS | 23 | .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: |
| Offset 14, 15 lines modified | Offset 14, 15 lines modified | ||
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-2·\-\-image2=(input,·required);·io" | 15 | .IP·"\-2·\-\-image2=(input,·required);·io" |
| 16 | input·image··2·to·be·combined | 16 | input·image··2·to·be·combined |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-c·\-\-combiner=(required);·factory" | 18 | .IP·"\-c·\-\-combiner=(required);·factory" |
| 19 | combiner·operation | 19 | combiner·operation |
| 20 | ·For·supported·plugins·see·PLUGINS:3dimage/combiner | 20 | ·For·supported·plugins·see·PLUGINS:3dimage/combiner |
| 21 | .IP·"\-o·\-\-out-file=( | 21 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 22 | output·image·file | 22 | output·image·file |
| 23 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 23 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 24 | .RE | 24 | .RE |
| 25 | .SS·Help·&·Info | 25 | .SS·Help·&·Info |
| 26 | .RS | 26 | .RS |
| 27 | .IP·"\-V·\-\-verbose=warning" | 27 | .IP·"\-V·\-\-verbose=warning" |
| 28 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: | 28 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-3dimagecreator·\-o·<out\-file>·[options] | 6 | .B··mia\-3dimagecreator·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dimagecreator | 8 | .B·mia\-3dimagecreator |
| 9 | This·program·creates·a·3D·image·that·contains·an·object·created·by·one·of·the·object·creator·plug-ins·(creator/3dimage) | 9 | This·program·creates·a·3D·image·that·contains·an·object·created·by·one·of·the·object·creator·plug-ins·(creator/3dimage) |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-file=( | 12 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 13 | output·file·for·create·object | 13 | output·file·for·create·object |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-s·\-\-size=[128,128,128]" | 15 | .IP·"\-s·\-\-size=[128,128,128]" |
| 16 | size·of·the·object | 16 | size·of·the·object |
| 17 | .IP·"\-r·\-\-repn=ubyte" | 17 | .IP·"\-r·\-\-repn=ubyte" |
| 18 | input·pixel·type· | 18 | input·pixel·type· |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dlandmarks\-distances | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file-1=( | 12 | .IP·"\-i·\-\-in-file-1=(input,·required);·io" |
| 13 | input·landmark·set·1 | 13 | input·landmark·set·1 |
| 14 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io | 14 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io |
| 15 | .IP·"\-o·\-\-in-file-2=( | 15 | .IP·"\-o·\-\-in-file-2=(input,·required);·io" |
| 16 | input·landmark·set·2 | 16 | input·landmark·set·2 |
| 17 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io | 17 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
| 20 | .RS | 20 | .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: |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-3dlandmarks\-transform | 8 | .B·mia\-3dlandmarks\-transform |
| 9 | 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). | 9 | 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). |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·landmark·set | 13 | input·landmark·set |
| 14 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io | 14 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 16 | output·landmark·set | 16 | output·landmark·set |
| 17 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io | 17 | ·For·supported·file·types·see·PLUGINS:3dlandmarklist/io |
| 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" | 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" |
| 19 | transformation·file | 19 | transformation·file |
| 20 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 20 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 21 | .RE | 21 | .RE |
| 22 | .SS·Help·&·Info | 22 | .SS·Help·&·Info |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dlerp | 8 | .B·mia\-3dlerp |
| 9 | merge·two·images·by·linear·combination. | 9 | merge·two·images·by·linear·combination. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-1·\-\-first=( | 12 | .IP·"\-1·\-\-first=(required,·input);·io" |
| 13 | first·input·image· | 13 | first·input·image· |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-2·\-\-second=( | 15 | .IP·"\-2·\-\-second=(required,·input);·io" |
| 16 | second·input·image· | 16 | second·input·image· |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-o·\-\-out-file=( | 18 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 19 | linearly·interpolated·image | 19 | linearly·interpolated·image |
| 20 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 20 | ·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 | .RE | 23 | .RE |
| 24 | .SS·Help·&·Info | 24 | .SS·Help·&·Info |
| Offset 1280, 15 lines modified | Offset 1280, 15 lines modified | ||
| 1280 | .TP·10 | 1280 | .TP·10 |
| 1281 | .B·tee | 1281 | .B·tee |
| 1282 | Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:· | 1282 | Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:· |
| 1283 | .P | 1283 | .P |
| 1284 | .RS·14 | 1284 | .RS·14 |
| 1285 | .I | 1285 | .I |
| 1286 | file | 1286 | file |
| 1287 | =( | 1287 | =(output,·required,·io) |
| 1288 | .RS·2 | 1288 | .RS·2 |
| 1289 | name·of·the·output·file·to·save·the·image·too.. | 1289 | name·of·the·output·file·to·save·the·image·too.. |
| 1290 | For·supported·file·types·see·PLUGINS:3dimage/io | 1290 | For·supported·file·types·see·PLUGINS:3dimage/io |
| 1291 | .RE | 1291 | .RE |
| 1292 | .RE | 1292 | .RE |
| 1293 | .TP·10 | 1293 | .TP·10 |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dmaskseeded | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·io" |
| 13 | input·image(s)·to·be·filtered | 13 | input·image(s)·to·be·filtered |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" | 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 16 | output·image(s)·that·have·been·filtered | 16 | output·image(s)·that·have·been·filtered |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-s·\-\-seed=[0,0,0]" | 18 | .IP·"\-s·\-\-seed=[0,0,0]" |
| 19 | seed·point | 19 | seed·point |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-3dnonrigidreg\-alt·\-o·<out\-transform>·[options]·<PLUGINS:3dimage/fullcost> | 6 | .B··mia\-3dnonrigidreg\-alt·\-o·<out\-transform>·[options]·<PLUGINS:3dimage/fullcost> |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dnonrigidreg\-alt | 8 | .B·mia\-3dnonrigidreg\-alt |
| 9 | This·program·runs·a·non-rigid·registration·based·on·the·given·cost·criteria·and·a·given·transformation·model.·Other·than·mia-3dnonrigidreg·it·doesn't·support·specific·command·line·parameters·to·provide·the·images.·Instead·the·images·are·specified·dirctly·when·defining·the·cost·function.·Hence,·image·registrations·can·be·executed·that·optimize·the·aligmnet·of··more·than·one·image·pair·at·the·same·time.·Note,·however,·that·all·input·images·must·be·of·the·same·dimension·(in·pixels) | 9 | This·program·runs·a·non-rigid·registration·based·on·the·given·cost·criteria·and·a·given·transformation·model.·Other·than·mia-3dnonrigidreg·it·doesn't·support·specific·command·line·parameters·to·provide·the·images.·Instead·the·images·are·specified·dirctly·when·defining·the·cost·function.·Hence,·image·registrations·can·be·executed·that·optimize·the·aligmnet·of··more·than·one·image·pair·at·the·same·time.·Note,·however,·that·all·input·images·must·be·of·the·same·dimension·(in·pixels) |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-transform=( | 12 | .IP·"\-o·\-\-out-transform=(required,·output);·io" |
| 13 | output·transformation | 13 | output·transformation |
| 14 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 14 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 15 | .IP·"\-l·\-\-levels=3" | 15 | .IP·"\-l·\-\-levels=3" |
| 16 | multi\-resolution·levels | 16 | multi\-resolution·levels |
| 17 | .IP·"\-O·\-\-optimizer=gsl:opt=gd,step=0.1" | 17 | .IP·"\-O·\-\-optimizer=gsl:opt=gd,step=0.1" |
| 18 | Optimizer·used·for·minimization | 18 | Optimizer·used·for·minimization |
| Offset 64, 18 lines modified | Offset 64, 18 lines modified | ||
| 64 | .IP·"···\-\-version" | 64 | .IP·"···\-\-version" |
| 65 | print·the·version·number·and·exit | 65 | print·the·version·number·and·exit |
| 66 | .RE | 66 | .RE |
| 67 | .SS·IO | 67 | .SS·IO |
| 68 | .RS | 68 | .RS |
| 69 | .IP·"\-i·\-\-in-image=( | 69 | .IP·"\-i·\-\-in-image=(input,·required);·io" |
| 70 | test·image | 70 | test·image |
| 71 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 71 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 72 | .IP·"\-r·\-\-ref-image=( | 72 | .IP·"\-r·\-\-ref-image=(input,·required);·io" |
| 73 | reference·image | 73 | reference·image |
| 74 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 74 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 75 | .IP·"\-o·\-\-out-image=(output,·required);·io" | 75 | .IP·"\-o·\-\-out-image=(output,·required);·io" |
| 76 | registered·output·image | 76 | registered·output·image |
| 77 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 77 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 78 | .IP·"\-t·\-\-transformation=(output);·io" | 78 | .IP·"\-t·\-\-transformation=(output);·io" |
| 79 | output·transformation | 79 | output·transformation |
| Offset 6, 15 lines modified | Offset 6, 15 lines modified | ||
| 6 | .B··mia\-3dpropose\-boundingbox·\-i·<in\-file>·[options] | 6 | .B··mia\-3dpropose\-boundingbox·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dpropose\-boundingbox | 8 | .B·mia\-3dpropose\-boundingbox |
| 9 | 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. | 9 | 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. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 14 | input·image(s)·to·be·filtered | 14 | input·image(s)·to·be·filtered |
| 15 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 15 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 16 | .RE | 16 | .RE |
| 17 | .SS·Help·&·Info | 17 | .SS·Help·&·Info |
| 18 | .RS | 18 | .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: |
| Offset 14, 18 lines modified | Offset 14, 18 lines modified | ||
| 14 | .UE | 14 | .UE |
| 15 | .RE | 15 | .RE |
| 16 | ·changes·are:·p=2,·and·exp | 16 | ·changes·are:·p=2,·and·exp |
| 17 | .SH·OPTIONS | 17 | .SH·OPTIONS |
| 18 | .SS·File-IO | 18 | .SS·File-IO |
| 19 | .RS | 19 | .RS |
| 20 | .IP·"\-i·\-\-in-file=( | 20 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 21 | image·to·be·segmented | 21 | image·to·be·segmented |
| 22 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 22 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 23 | .IP·"\-c·\-\-class-file=( | 23 | .IP·"\-c·\-\-class-file=(required,·output);·io" |
| 24 | class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values | 24 | class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values |
| 25 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 25 | ·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. |
| 28 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 28 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 29 | .RE | 29 | .RE |
| 30 | .SS·Help·&·Info | 30 | .SS·Help·&·Info |
| Offset 7, 15 lines modified | Offset 7, 15 lines modified | ||
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dserial\-nonrigid | 8 | .B·mia\-3dserial\-nonrigid |
| 9 | 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.· | 9 | 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.· |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS· | 11 | .SS· |
| 12 | File-IO | 12 | File-IO |
| 13 | .RS | 13 | .RS |
| 14 | .IP·"\-i·\-\-in-file=( | 14 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 15 | input·perfusion·data·set | 15 | input·perfusion·data·set |
| 16 | .IP·"\-o·\-\-out-file=(output);·string" | 16 | .IP·"\-o·\-\-out-file=(output);·string" |
| 17 | file·name·for·registered·fiels | 17 | file·name·for·registered·fiels |
| 18 | .RE | 18 | .RE |
| 19 | .SS· | 19 | .SS· |
| Offset 7, 18 lines modified | Offset 7, 18 lines modified | ||
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dseries\-track\-intensity | 8 | .B·mia\-3dseries\-track\-intensity |
| 9 | This·program·tracks·the·intensity·of·a·pixel·at·the·given·coordinates. | 9 | This·program·tracks·the·intensity·of·a·pixel·at·the·given·coordinates. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS· | 11 | .SS· |
| 12 | File-IO | 12 | File-IO |
| 13 | .RS | 13 | .RS |
| 14 | .IP·"\-i·\-\-in-file=( | 14 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 15 | input·perfusion·data·set | 15 | input·perfusion·data·set |
| 16 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 16 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 17 | .IP·"\-o·\-\-out-file=( | 17 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 18 | file·name·for·output·intensity·slopes | 18 | file·name·for·output·intensity·slopes |
| 19 | .RE | 19 | .RE |
| 20 | .SS·Help·&·Info | 20 | .SS·Help·&·Info |
| 21 | .RS | 21 | .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: |
| Offset 10, 21 lines modified | Offset 10, 21 lines modified | ||
| 10 | ···id;time;x;y;z;reserved | 10 | ···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·OPTIONS | 12 | .SH·OPTIONS |
| 13 | .SS· | 13 | .SS· |
| 14 | File-IO | 14 | File-IO |
| 15 | .RS | 15 | .RS |
| 16 | .IP·"\-i·\-\-in-file=( | 16 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 17 | input·point·set | 17 | input·point·set |
| 18 | .IP·"\-o·\-\-out-file=( | 18 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 19 | output·point·set | 19 | output·point·set |
| 20 | .IP·"\-t·\-\-transformation=( | 20 | .IP·"\-t·\-\-transformation=(input,·required);·io" |
| 21 | transformation·describing·the·monitored·change | 21 | transformation·describing·the·monitored·change |
| 22 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 22 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 23 | .RE | 23 | .RE |
| 24 | .SS· | 24 | .SS· |
| 25 | Parameters | 25 | Parameters |
| 26 | .RS | 26 | .RS |
| 27 | .IP·"\-T·\-\-time-step=1" | 27 | .IP·"\-T·\-\-time-step=1" |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-3dtransform | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image | 13 | input·image |
| 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 16 | transformed·image | 16 | transformed·image |
| 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" | 18 | .IP·"\-t·\-\-transformation=(required,·input);·io" |
| 19 | transformation·file | 19 | transformation·file |
| 20 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 20 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 21 | .IP·"\-p·\-\-interpolator=" | 21 | .IP·"\-p·\-\-interpolator=" |
| 22 | override·the·interpolator·provided·by·the·transformation | 22 | override·the·interpolator·provided·by·the·transformation |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-3dtransform2vf·\-i·<in\-file>·\-o·<out\-file>·[options] | 6 | .B··mia\-3dtransform2vf·\-i·<in\-file>·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dtransform2vf | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·transformation· | 13 | input·transformation· |
| 14 | ·For·supported·file·types·see·PLUGINS:3dtransform/io | 14 | ·For·supported·file·types·see·PLUGINS:3dtransform/io |
| 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" | 15 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 16 | output·vector·field· | 16 | output·vector·field· |
| 17 | ·For·supported·file·types·see·PLUGINS:3dvf/io | 17 | ·For·supported·file·types·see·PLUGINS:3dvf/io |
| 18 | .RE | 18 | .RE |
| 19 | .SS·Help·&·Info | 19 | .SS·Help·&·Info |
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| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-3dvectorfieldcreate·\-o·<out\-file>·[options] | 6 | .B··mia\-3dvectorfieldcreate·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dvectorfieldcreate | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-o·\-\-out-file=( | 12 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 13 | output·file·for·the·vector·field | 13 | output·file·for·the·vector·field |
| 14 | ·For·supported·file·types·see·PLUGINS:3dvf/io | 14 | ·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·field | 16 | size·of·the·vector·field |
| 17 | .IP·"\-y·\-\-ftype=0" | 17 | .IP·"\-y·\-\-ftype=0" |
| 18 | vector·field·type | 18 | vector·field·type |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-3dvfcompare | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-1·\-\-in-file-1=( | 12 | .IP·"\-1·\-\-in-file-1=(required,·input);·io" |
| 13 | input·vector·field·1 | 13 | input·vector·field·1 |
| 14 | ·For·supported·file·types·see·PLUGINS:3dvf/io | 14 | ·For·supported·file·types·see·PLUGINS:3dvf/io |
| 15 | .IP·"\-2·\-\-in-file-2=( | 15 | .IP·"\-2·\-\-in-file-2=(required,·input);·io" |
| 16 | input·vector·field·2 | 16 | input·vector·field·2 |
| 17 | ·For·supported·file·types·see·PLUGINS:3dvf/io | 17 | ·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·ignored | 19 | Maximum·difference·between·vector·to·be·ignored |
| 20 | .RE | 20 | .RE |
| 21 | .SS·Help·&·Info | 21 | .SS·Help·&·Info |
| Offset 8, 15 lines modified | Offset 8, 15 lines modified | ||
| 8 | .B·mia\-cmeans | 8 | .B·mia\-cmeans |
| 9 | This·Program·reads·a·histogram·from·stdin·and·evaluates·a·cmeans·classification·of·the·intensity·values·into·the·given·number·of·classes. | 9 | This·Program·reads·a·histogram·from·stdin·and·evaluates·a·cmeans·classification·of·the·intensity·values·into·the·given·number·of·classes. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·file·name·containing·the·histogram | 13 | input·file·name·containing·the·histogram |
| 14 | .IP·"\-o·\-\-out-file=( | 14 | .IP·"\-o·\-\-out-file=(output,·required);·string" |
| 15 | output·file·name·to·store·probabilities | 15 | output·file·name·to·store·probabilities |
| 16 | .IP·"\-n·\-\-nclasses=3" | 16 | .IP·"\-n·\-\-nclasses=3" |
| 17 | number·of·classes·to·partition·into | 17 | number·of·classes·to·partition·into |
| 18 | .IP·"\-m·\-\-max-iter=100" | 18 | .IP·"\-m·\-\-max-iter=100" |
| 19 | maximum·number·of·iterations | 19 | maximum·number·of·iterations |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-filenumberpattern·\-i·<in\-file>·[options] | 6 | .B··mia\-filenumberpattern·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-filenumberpattern | 8 | .B·mia\-filenumberpattern |
| 9 | This·program·is·used·to·extract·a·extract·the·number·pattern·for·file012312.ext·type·file·names. | 9 | This·program·is·used·to·extract·a·extract·the·number·pattern·for·file012312.ext·type·file·names. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·image·example·name | 13 | input·image·example·name |
| 14 | .RE | 14 | .RE |
| 15 | .SS·Help·&·Info | 15 | .SS·Help·&·Info |
| 16 | .RS | 16 | .RS |
| 17 | .IP·"\-V·\-\-verbose=warning" | 17 | .IP·"\-V·\-\-verbose=warning" |
| 18 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: | 18 | verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are: |
| Offset 9, 15 lines modified | Offset 9, 15 lines modified | ||
| 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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File·I/O | 11 | .SS·File·I/O |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" | 13 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 14 | input·mesh·to·be·adapted | 14 | input·mesh·to·be·adapted |
| 15 | ·For·supported·file·types·see·PLUGINS:mesh/io | 15 | ·For·supported·file·types·see·PLUGINS:mesh/io |
| 16 | .IP·"\-o·\-\-out-file=( | 16 | .IP·"\-o·\-\-out-file=(required,·output);·io" |
| 17 | output·image·containing·the·binary·mask | 17 | output·image·containing·the·binary·mask |
| 18 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 18 | ·For·supported·file·types·see·PLUGINS:3dimage/io |
| 19 | .RE | 19 | .RE |
| 20 | .SS·Help·&·Info | 20 | .SS·Help·&·Info |
| 21 | .RS | 21 | .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: |
| Offset 5, 21 lines modified | Offset 5, 21 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-meshdistance\-to\-stackmask | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-mesh=( | 12 | .IP·"\-i·\-\-in-mesh=(input,·required);·io" |
| 13 | input·mesh | 13 | input·mesh |
| 14 | ·For·supported·file·types·see·PLUGINS:mesh/io | 14 | ·For·supported·file·types·see·PLUGINS:mesh/io |
| 15 | .IP·"\-r·\-\-ref-mask=( | 15 | .IP·"\-r·\-\-ref-mask=(input,·required);·io" |
| 16 | reference·binary·mask | 16 | reference·binary·mask |
| 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 17 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 18 | .IP·"\-o·\-\-out-mesh=( | 18 | .IP·"\-o·\-\-out-mesh=(required,·output);·io" |
| 19 | output·mesh | 19 | output·mesh |
| 20 | ·For·supported·file·types·see·PLUGINS:mesh/io | 20 | ·For·supported·file·types·see·PLUGINS:mesh/io |
| 21 | .RE | 21 | .RE |
| 22 | .SS·Help·&·Info | 22 | .SS·Help·&·Info |
| 23 | .RS | 23 | .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: |
| Offset 5, 18 lines modified | Offset 5, 18 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .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·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-multihist | 8 | .B·mia\-multihist |
| 9 | This·program·evaluates·the·histogram·over·a·series·of·2D·images | 9 | This·program·evaluates·the·histogram·over·a·series·of·2D·images |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(required,·input);·io" |
| 13 | input·image(s)·to·be·filtered | 13 | input·image(s)·to·be·filtered |
| 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io | 14 | ·For·supported·file·types·see·PLUGINS:2dimage/io |
| 15 | .IP·"\-o·\-\-out-histogram=( | 15 | .IP·"\-o·\-\-out-histogram=(required,·output);·string" |
| 16 | output·file·name | 16 | output·file·name |
| 17 | .IP·"···\-\-min=0" | 17 | .IP·"···\-\-min=0" |
| 18 | minimum·of·histogram·range | 18 | minimum·of·histogram·range |
| 19 | .IP·"···\-\-max=65535" | 19 | .IP·"···\-\-max=65535" |
| 20 | maximum·of·histogram·range | 20 | maximum·of·histogram·range |
| Offset 6, 15 lines modified | Offset 6, 15 lines modified | ||
| 6 | .B··mia\-myowavelettest·\-i·<in\-file>·[options] | 6 | .B··mia\-myowavelettest·\-i·<in\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-myowavelettest | 8 | .B·mia\-myowavelettest |
| 9 | This·program·runs·the·wavelet·based·slope-statistics·on·the·mixing·matrix·of·a·ICA·perfusion·series. | 9 | This·program·runs·the·wavelet·based·slope-statistics·on·the·mixing·matrix·of·a·ICA·perfusion·series. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(required,·input);·string" |
| 14 | input·data·set | 14 | input·data·set |
| 15 | .RE | 15 | .RE |
| 16 | .SS·Help·&·Info | 16 | .SS·Help·&·Info |
| 17 | .RS | 17 | .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: |
| Offset 5, 15 lines modified | Offset 5, 15 lines modified | ||
| 5 | .SH·SYNOPSIS | 5 | .SH·SYNOPSIS |
| 6 | .B··mia\-raw2volume·\-i·<in\-file>·\-o·<out\-file>·\-s·<size>·[options] | 6 | .B··mia\-raw2volume·\-i·<in\-file>·\-o·<out\-file>·\-s·<size>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-raw2volume | 8 | .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·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .RS | 11 | .RS |
| 12 | .IP·"\-i·\-\-in-file=( | 12 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 13 | input·file·name | 13 | input·file·name |
| 14 | .IP·"\-o·\-\-out-file=(output,·required);·io" | 14 | .IP·"\-o·\-\-out-file=(output,·required);·io" |
| 15 | output·file·name | 15 | output·file·name |
| 16 | ·For·supported·file·types·see·PLUGINS:3dimage/io | 16 | ·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· |
| Offset 6, 18 lines modified | Offset 6, 18 lines modified | ||
| 6 | .B··mia\-wavelettrans·\-i·<in\-file>·\-o·<out\-file>·[options] | 6 | .B··mia\-wavelettrans·\-i·<in\-file>·\-o·<out\-file>·[options] |
| 7 | .SH·DESCRIPTION | 7 | .SH·DESCRIPTION |
| 8 | .B·mia\-wavelettrans | 8 | .B·mia\-wavelettrans |
| 9 | This·program·runs·the·a·column-wise·discret·wavelet·forward·transform·on·the·data·given·by·an·input·text·file. | 9 | This·program·runs·the·a·column-wise·discret·wavelet·forward·transform·on·the·data·given·by·an·input·text·file. |
| 10 | .SH·OPTIONS | 10 | .SH·OPTIONS |
| 11 | .SS·File-IO | 11 | .SS·File-IO |
| 12 | .RS | 12 | .RS |
| 13 | .IP·"\-i·\-\-in-file=( | 13 | .IP·"\-i·\-\-in-file=(input,·required);·string" |
| 14 | input·data·set | 14 | input·data·set |
| 15 | .IP·"\-o·\-\-out-file=( | 15 | .IP·"\-o·\-\-out-file=(required,·output);·string" |
| 16 | output·data·set | 16 | output·data·set |
| 17 | .IP·"\-s·\-\-save-wave=(output);·string" | 17 | .IP·"\-s·\-\-save-wave=(output);·string" |
| 18 | base·name·of·the·output·files·that·will·store·the·wavelet·coefficients·as·matrix | 18 | base·name·of·the·output·files·that·will·store·the·wavelet·coefficients·as·matrix |
| 19 | .RE | 19 | .RE |
| 20 | .SS·Help·&·Info | 20 | .SS·Help·&·Info |