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Offset 2, 8 lines modified		Offset 2, 8 lines modified
2	·d3fb1bca81b098eaec0974551e882e8e·90458048·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_amd64.deb	2	·d3fb1bca81b098eaec0974551e882e8e·90458048·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_amd64.deb
3	·a76f72bb63085f77a8c09124d0c3fec8·4863508·libs·optional·libmia-2.4-4_2.4.7-13_amd64.deb	3	·a76f72bb63085f77a8c09124d0c3fec8·4863508·libs·optional·libmia-2.4-4_2.4.7-13_amd64.deb
4	·7c46a0e14db6dffadbcf769b82bad8af·205268·libdevel·optional·libmia-2.4-dev_2.4.7-13_amd64.deb	4	·7c46a0e14db6dffadbcf769b82bad8af·205268·libdevel·optional·libmia-2.4-dev_2.4.7-13_amd64.deb
5	·4b782e2ec1f353f4e22ba18dde5f87d4·7070244·doc·optional·libmia-2.4-doc_2.4.7-13_all.deb	5	·4b782e2ec1f353f4e22ba18dde5f87d4·7070244·doc·optional·libmia-2.4-doc_2.4.7-13_all.deb
6	·b98296a28e5f8232780a9f392da185d1·26308·science·optional·mia-doctools_2.4.7-13_all.deb	6	·b98296a28e5f8232780a9f392da185d1·26308·science·optional·mia-doctools_2.4.7-13_all.deb
7	·148918b4674ff14b005793a2b2c0cb41·35771548·debug·optional·mia-tools-dbgsym_2.4.7-13_amd64.deb	7	·148918b4674ff14b005793a2b2c0cb41·35771548·debug·optional·mia-tools-dbgsym_2.4.7-13_amd64.deb
8	·ef14b850ff950efe4b75de8ac685e6e7·96460·doc·optional·mia-tools-doc_2.4.7-13_all.deb	8	·ef14b850ff950efe4b75de8ac685e6e7·96460·doc·optional·mia-tools-doc_2.4.7-13_all.deb
9	·688a23fde~~df5~~d96~~35ecc~~1~~593~~d0~~b8b2~~8b·19~~49816~~·science·optional·mia-tools_2.4.7-13_amd64.deb	9	·4d83ae587db6141df18bb6db0301918d·1950004·science·optional·mia-tools_2.4.7-13_amd64.deb


Offset 1, 3 lines modified		Offset 1, 3 lines modified
1	-rw-r--r--···0········0········0········4·2023-08-29·09:00:00.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2023-08-29·09:00:00.000000·debian-binary
2	-rw-r--r--···0········0········0·····7568·2023-08-29·09:00:00.000000·control.tar.xz	2	-rw-r--r--···0········0········0·····7568·2023-08-29·09:00:00.000000·control.tar.xz
3	-rw-r--r--···0········0········0··1942~~056~~·2023-08-29·09:00:00.000000·data.tar.xz	3	-rw-r--r--···0········0········0··1942244·2023-08-29·09:00:00.000000·data.tar.xz


Offset 5, 18 lines modified		Offset 5, 18 lines modified
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=(~~req~~uired,·in~~put~~);·io"	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=(~~req~~uired,·in~~put~~);·io"	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, 21 lines modified		Offset 5, 21 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=(~~inp~~ut,·requi~~red~~);·io"	12	.IP·"\-1·\-\-file1=(required,·input);·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=(~~inp~~ut,·requi~~red~~);·io"	15	.IP·"\-2·\-\-file2=(required,·input);·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=(ou~~tput~~,·requ~~ired~~);·io"	18	.IP·"\-o·\-\-out-file=(required,·output);·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

23	.RS·10	23	.RS·10
24	.I	24	.I


Offset 14, 15 lines modified		Offset 14, 15 lines modified
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-g·\-\-green=(input);·io"	15	.IP·"\-g·\-\-green=(input);·io"
16	input·image·for·green·channel	16	input·image·for·green·channel
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-r·\-\-red=(input);·io"	18	.IP·"\-r·\-\-red=(input);·io"
19	input·image·for·red·channel	19	input·image·for·red·channel
20	·For·supported·file·types·see·PLUGINS:2dimage/io	20	·For·supported·file·types·see·PLUGINS:2dimage/io
21	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	21	.IP·"\-o·\-\-out-file=(output,·required);·io"
22	combined·output·image	22	combined·output·image
23	·For·supported·file·types·see·PLUGINS:2dimage/io	23	·For·supported·file·types·see·PLUGINS:2dimage/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 15, 15 lines modified		Offset 15, 15 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=(~~req~~uired,·in~~put~~);·string"	21	.IP·"\-i·\-\-in-file=(input,·required);·string"
22	input·perfusion·data·set	22	input·perfusion·data·set

23	.IP·"\-o·\-\-out-file=(required,·output);·string"	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


Offset 7, 18 lines modified		Offset 7, 18 lines modified
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimagefilter	8	.B·mia\-2dimagefilter
9	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	9	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
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=(~~inp~~ut,·requi~~red~~);·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=(ou~~tput~~,·requ~~ired~~);·io"	17	.IP·"\-o·\-\-out-file=(required,·output);·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=(~~inp~~ut,·requi~~red~~);·io"	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-file=(ou~~tput~~,·requ~~ired~~);·io"	16	.IP·"\-o·\-\-out-file=(required,·output);·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=(~~inp~~ut,·requi~~red~~);·io"	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 6, 18 lines modified		Offset 6, 18 lines modified
6	.B··mia\-2dimageregistration·\-i·<in\-image>·\-r·<ref\-image>·\-t·<transformation>·[options]·<PLUGINS:2dimage/fullcost>	6	.B··mia\-2dimageregistration·\-i·<in\-image>·\-r·<ref\-image>·\-t·<transformation>·[options]·<PLUGINS:2dimage/fullcost>
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimageregistration	8	.B·mia\-2dimageregistration
9	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.	9	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.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File-IO	11	.SS·File-IO
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-image=(~~inp~~ut,·requi~~red~~);·io"	13	.IP·"\-i·\-\-in-image=(required,·input);·io"
14	test·image·to·be·registered	14	test·image·to·be·registered
15	·For·supported·file·types·see·PLUGINS:2dimage/io	15	·For·supported·file·types·see·PLUGINS:2dimage/io
16	.IP·"\-r·\-\-ref-image=(~~inp~~ut,·requi~~red~~);·io"	16	.IP·"\-r·\-\-ref-image=(required,·input);·io"
17	reference·image·to·be·registered·to	17	reference·image·to·be·registered·to
18	·For·supported·file·types·see·PLUGINS:2dimage/io	18	·For·supported·file·types·see·PLUGINS:2dimage/io
19	.IP·"\-o·\-\-out-image=(output);·io"	19	.IP·"\-o·\-\-out-image=(output);·io"
20	registered·output·image	20	registered·output·image
21	·For·supported·file·types·see·PLUGINS:2dimage/io	21	·For·supported·file·types·see·PLUGINS:2dimage/io
22	.IP·"\-t·\-\-transformation=(required,·output);·io"	22	.IP·"\-t·\-\-transformation=(required,·output);·io"
23	output·transformation·comprising·the·registration	23	output·transformation·comprising·the·registration


Offset 11, 15 lines modified		Offset 11, 15 lines modified
11	.RS	11	.RS
12	.IP·"\-1·\-\-first=(input,·required);·io"	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=(input,·required);·io"	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=(ou~~tput~~,·requ~~ired~~);·io"	18	.IP·"\-o·\-\-out-file=(required,·output);·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)

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\-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=(~~req~~uired,·in~~put~~);·io"	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 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dmyocard\-icaseries·\-i·<in\-file>·[options]	6	.B··mia\-2dmyocard\-icaseries·\-i·<in\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmyocard\-icaseries	8	.B·mia\-2dmyocard\-icaseries
9	This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this·program·is·essentially·the·same·without·the·registration·bits.	9	This·program·is·used·to·run·a·ICA·on·a·series·of·myocardial·perfusion·images·given·in·a·segmentation·set·in·order·to·create·sythetic·references·that·can·be·used·for·motion·correction·by·image·registration.·If·the·aim·is·to·run·a·full·motion·compensation·then·it·is·better·run·mia-2dmyoica-nonrigid,·since·this·program·is·essentially·the·same·without·the·registration·bits.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File-IO	11	.SS·File-IO
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-file=(~~req~~uired,·in~~put~~);·string"	13	.IP·"\-i·\-\-in-file=(input,·required);·string"
14	input·perfusion·data·set	14	input·perfusion·data·set

15	.IP·"\-r·\-\-references=(output);·string"	15	.IP·"\-r·\-\-references=(output);·string"
16	File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images.	16	File·name·base·for·the·reference·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images.

17	.IP·"\-c·\-\-save-cropped=(output);·string"	17	.IP·"\-c·\-\-save-cropped=(output);·string"
18	save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base	18	save·cropped·set·of·the·original·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base


Offset 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dmyocard\-segment·\-i·<in\-file>·\-o·<out\-file>·[options]	6	.B··mia\-2dmyocard\-segment·\-i·<in\-file>·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmyocard\-segment	8	.B·mia\-2dmyocard\-segment
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=(~~req~~uired,·in~~put~~);·string"	13	.IP·"\-i·\-\-in-file=(input,·required);·string"
14	input·perfusion·data·set	14	input·perfusion·data·set

15	.IP·"\-o·\-\-out-file=(required,·output);·io"	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


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143	-rw-r--r--···0·root·········(0)·root·········(0)····10430·2020-04-26·10:42:08.000000·./usr/share/doc/mia-tools/changelog.gz	143	-rw-r--r--···0·root·········(0)·root·········(0)····10430·2020-04-26·10:42:08.000000·./usr/share/doc/mia-tools/changelog.gz
144	-rw-r--r--···0·root·········(0)·root·········(0)·····1127·2023-08-29·09:00:00.000000·./usr/share/doc/mia-tools/copyright	144	-rw-r--r--···0·root·········(0)·root·········(0)·····1127·2023-08-29·09:00:00.000000·./usr/share/doc/mia-tools/copyright
145	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/	145	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/
146	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/	146	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/
147	-rw-r--r--···0·root·········(0)·root·········(0)······425·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/mia-tools	147	-rw-r--r--···0·root·········(0)·root·········(0)······425·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/mia-tools
148	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/	148	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/
149	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/man1/	149	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/man1/
150	-rw-r--r--···0·root·········(0)·root·········(0)·····1474·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2davgmasked.1.gz	150	-rw-r--r--···0·root·········(0)·root·········(0)·····1472·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2davgmasked.1.gz
151	-rw-r--r--···0·root·········(0)·root·········(0)·····1565·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dbinarycombine.1.gz	151	-rw-r--r--···0·root·········(0)·root·········(0)·····1566·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dbinarycombine.1.gz
152	-rw-r--r--···0·root·········(0)·root·········(0)·····2633·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dcost.1.gz	152	-rw-r--r--···0·root·········(0)·root·········(0)·····2633·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dcost.1.gz
153	-rw-r--r--···0·root·········(0)·root·········(0)·····1751·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddeform.1.gz	153	-rw-r--r--···0·root·········(0)·root·········(0)·····1751·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddeform.1.gz
154	-rw-r--r--···0·root·········(0)·root·········(0)·····1696·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddistance.1.gz	154	-rw-r--r--···0·root·········(0)·root·········(0)·····1696·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddistance.1.gz
155	-rw-r--r--···0·root·········(0)·root·········(0)·····1867·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz	155	-rw-r--r--···0·root·········(0)·root·········(0)·····1867·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz
156	-rw-r--r--···0·root·········(0)·root·········(0)·····3501·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz	156	-rw-r--r--···0·root·········(0)·root·········(0)·····3501·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz
157	-rw-r--r--···0·root·········(0)·root·········(0)·····1913·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid.1.gz	157	-rw-r--r--···0·root·········(0)·root·········(0)·····1913·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid.1.gz
158	-rw-r--r--···0·root·········(0)·root·········(0)·····1547·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dforce.1.gz	158	-rw-r--r--···0·root·········(0)·root·········(0)·····1543·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dforce.1.gz
159	-rw-r--r--···0·root·········(0)·root·········(0)·····1810·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz	159	-rw-r--r--···0·root·········(0)·root·········(0)·····1810·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz
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161	-rw-r--r--···0·root·········(0)·root·········(0)·····3457·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dgroundtruthreg.1.gz	161	-rw-r--r--···0·root·········(0)·root·········(0)·····3462·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dgroundtruthreg.1.gz
162	-rw-r--r--···0·root·········(0)·root·········(0)·····1470·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecombine-dice.1.gz	162	-rw-r--r--···0·root·········(0)·root·········(0)·····1469·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecombine-dice.1.gz
163	-rw-r--r--···0·root·········(0)·root·········(0)·····1620·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecombiner.1.gz	163	-rw-r--r--···0·root·········(0)·root·········(0)·····1624·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecombiner.1.gz
164	-rw-r--r--···0·root·········(0)·root·········(0)·····1774·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecreator.1.gz	164	-rw-r--r--···0·root·········(0)·root·········(0)·····1774·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecreator.1.gz
165	-rw-r--r--···0·root·········(0)·root·········(0)·····6179·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilter.1.gz	165	-rw-r--r--···0·root·········(0)·root·········(0)·····6177·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilter.1.gz
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167	-rw-r--r--···0·root·········(0)·root·········(0)·····1442·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefullstats.1.gz	167	-rw-r--r--···0·root·········(0)·root·········(0)·····1442·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefullstats.1.gz
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170	-rw-r--r--···0·root·········(0)·root·········(0)·····1428·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz	170	-rw-r--r--···0·root·········(0)·root·········(0)·····1428·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz
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172	-rw-r--r--···0·root·········(0)·root·········(0)·····1622·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagestats.1.gz	172	-rw-r--r--···0·root·········(0)·root·········(0)·····1622·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagestats.1.gz
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174	-rw-r--r--···0·root·········(0)·root·········(0)·····3672·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz	174	-rw-r--r--···0·root·········(0)·root·········(0)·····3672·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz
175	-rw-r--r--···0·root·········(0)·root·········(0)·····2776·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmulti-force.1.gz	175	-rw-r--r--···0·root·········(0)·root·········(0)·····2776·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmulti-force.1.gz
176	-rw-r--r--···0·root·········(0)·root·········(0)·····5397·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageregistration.1.gz	176	-rw-r--r--···0·root·········(0)·root·········(0)·····5396·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageregistration.1.gz
177	-rw-r--r--···0·root·········(0)·root·········(0)·····1857·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz	177	-rw-r--r--···0·root·········(0)·root·········(0)·····1857·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz
178	-rw-r--r--···0·root·········(0)·root·········(0)·····1540·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimagevar.1.gz	178	-rw-r--r--···0·root·········(0)·root·········(0)·····1540·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimagevar.1.gz
179	-rw-r--r--···0·root·········(0)·root·········(0)·····2193·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-ica.1.gz	179	-rw-r--r--···0·root·········(0)·root·········(0)·····2193·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-ica.1.gz
180	-rw-r--r--···0·root·········(0)·root·········(0)·····1815·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz	180	-rw-r--r--···0·root·········(0)·root·········(0)·····1817·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz


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=(~~req~~uired,·in~~put~~);·io"	12	.IP·"\-i·\-\-in-file=(input,·required);·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, 15 lines modified		Offset 5, 15 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dmultiimageregistration·\-o·<out\-transform>·[options]·<PLUGINS:2dimage/fullcost>	6	.B··mia\-2dmultiimageregistration·\-o·<out\-transform>·[options]·<PLUGINS:2dimage/fullcost>
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmultiimageregistration	8	.B·mia\-2dmultiimageregistration
9	This·program·runs·a·non-rigid·registration·based·on·the·given·cost·criteria·and·a·given·transformation·model.·Other·than·mia-2dnonrigidreg·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-2dnonrigidreg·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=(requ~~ired~~,·ou~~tput~~);·io"	12	.IP·"\-o·\-\-out-transform=(output,·required);·io"
13	output·transformation	13	output·transformation
14	·For·supported·file·types·see·PLUGINS:2dtransform/io	14	·For·supported·file·types·see·PLUGINS:2dtransform/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 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=(input,·required);·io"	19	.IP·"\-i·\-\-in-file=(input,·required);·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=(requ~~ired~~,·ou~~tput~~);·io"	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 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=(~~inp~~ut,·requi~~red~~);·string"	20	.IP·"\-i·\-\-in-file=(required,·input);·string"
21	input·perfusion·data·set	21	input·perfusion·data·set

22	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	22	.IP·"\-o·\-\-out-file=(required,·output);·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 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=(~~inp~~ut,·requi~~red~~);·string"	19	.IP·"\-i·\-\-in-file=(required,·input);·string"
20	input·perfusion·data·set	20	input·perfusion·data·set

21	.IP·"\-o·\-\-out-file=(output,·required);·string"	21	.IP·"\-o·\-\-out-file=(output,·required);·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 15, 15 lines modified		Offset 15, 15 lines modified
15	.RE	15	.RE

16	·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.	16	·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.

17	.SH·OPTIONS	17	.SH·OPTIONS
18	.SS·File-IO	18	.SS·File-IO
19	.RS	19	.RS
20	.IP·"\-i·\-\-in-file=(~~req~~uired,·in~~put~~);·string"	20	.IP·"\-i·\-\-in-file=(input,·required);·string"
21	input·perfusion·data·set	21	input·perfusion·data·set

22	.IP·"\-o·\-\-out-file=(required,·output);·string"	22	.IP·"\-o·\-\-out-file=(required,·output);·string"
23	output·perfusion·data·set	23	output·perfusion·data·set

24	.IP·"\-r·\-\-registered="	24	.IP·"\-r·\-\-registered="
25	file·name·base·for·registered·files	25	file·name·base·for·registered·files


Offset 15, 15 lines modified		Offset 15, 15 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=(~~req~~uired,·in~~put~~);·string"	21	.IP·"\-i·\-\-in-file=(input,·required);·string"
22	input·perfusion·data·set	22	input·perfusion·data·set

23	.IP·"\-o·\-\-out-file=(output,·required);·string"	23	.IP·"\-o·\-\-out-file=(output,·required);·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,·the·image·file·type·is·the·same·as·given·in·the·input·data·set	26	file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set


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=(requ~~ired~~,·ou~~tput~~);·io"	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 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=(requ~~ired~~,·ou~~tput~~);·string"	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 8, 15 lines modified		Offset 8, 15 lines modified
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=(required,·input);·string"	12	.IP·"\-i·\-\-in-file=(required,·input);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	14	.IP·"\-o·\-\-out-file=(output,·required);·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

19	.RE	19	.RE
20	.SS·Help·&·Info	20	.SS·Help·&·Info


Offset 8, 15 lines modified		Offset 8, 15 lines modified
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=(required,·input);·string"	12	.IP·"\-i·\-\-in-file=(required,·input);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	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 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=(required,·input);·string"	12	.IP·"\-i·\-\-in-file=(required,·input);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·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

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 8, 15 lines modified		Offset 8, 15 lines modified
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=(input,·required);·string"	12	.IP·"\-i·\-\-in-file=(input,·required);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·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

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 6, 15 lines modified		Offset 6, 15 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=(~~req~~uired,·in~~put~~);·io"	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·"\-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


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=(~~inp~~ut,·requi~~red~~);·string"	16	.IP·"\-i·\-\-in-file=(required,·input);·string"
17	input·point·set	17	input·point·set

18	.IP·"\-o·\-\-out-file=(output,·required);·string"	18	.IP·"\-o·\-\-out-file=(output,·required);·string"
19	output·point·set	19	output·point·set

20	.IP·"\-t·\-\-transformation=(~~inp~~ut,·requi~~red~~);·io"	20	.IP·"\-t·\-\-transformation=(required,·input);·io"
21	transformation·describing·the·monitored·change	21	transformation·describing·the·monitored·change
22	·For·supported·file·types·see·PLUGINS:2dtransform/io	22	·For·supported·file·types·see·PLUGINS:2dtransform/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\-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=(required,·input);·io"	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=(ou~~tput~~,·requ~~ired~~);·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=(required,·input);·io"	18	.IP·"\-t·\-\-transformation=(required,·input);·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


Offset 403, 15 lines modified		Offset 403, 15 lines modified
403	.TP·10	403	.TP·10
404	.B·combiner	404	.B·combiner
405	Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·	405	Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
406	.P	406	.P
407	.RS·14	407	.RS·14
408	.I	408	.I
409	image	409	image
410	=(~~req~~uired,·in~~put~~,·io)	410	=(input,·required,·io)
411	.RS·2	411	.RS·2
412	second·image·that·is·needed·in·the·combiner.	412	second·image·that·is·needed·in·the·combiner.
413	For·supported·file·types·see·PLUGINS:3dimage/io	413	For·supported·file·types·see·PLUGINS:3dimage/io

414	.RE	414	.RE
415	.RE	415	.RE
416	.RS·14	416	.RS·14


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=(requ~~ired~~,·ou~~tput~~);·io"	15	.IP·"\-o·\-\-out-image=(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·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 24, 18 lines modified		Offset 24, 18 lines modified
24	········cat(result)	24	········cat(result)
25	····}	25	····}


26	.SH·OPTIONS	26	.SH·OPTIONS
27	.SS·File-IO	27	.SS·File-IO
28	.RS	28	.RS
29	.IP·"\-i·\-\-in-labels=(~~inp~~ut,·requi~~red~~);·io"	29	.IP·"\-i·\-\-in-labels=(required,·input);·io"
30	input·label·image	30	input·label·image
31	·For·supported·file·types·see·PLUGINS:3dimage/io	31	·For·supported·file·types·see·PLUGINS:3dimage/io
32	.IP·"\-r·\-\-ref-labels=(~~inp~~ut,·requi~~red~~);·io"	32	.IP·"\-r·\-\-ref-labels=(required,·input);·io"
33	reference·label·image	33	reference·label·image
34	·For·supported·file·types·see·PLUGINS:3dimage/io	34	·For·supported·file·types·see·PLUGINS:3dimage/io
35	.IP·"\-l·\-\-label-map=(input);·string"	35	.IP·"\-l·\-\-label-map=(input);·string"
36	optional·mapping·of·label·numbers	36	optional·mapping·of·label·numbers

37	.IP·"\-o·\-\-out-file=(required,·output);·string"	37	.IP·"\-o·\-\-out-file=(required,·output);·string"
38	output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.	38	output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.


Offset 8, 15 lines modified		Offset 8, 15 lines modified
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=(input,·required);·io"	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=(ou~~tput~~,·requ~~ired~~);·io"	15	.IP·"\-o·\-\-out-image=(required,·output);·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, 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=(~~req~~uired,·in~~put~~);·io"	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=(~~req~~uired,·in~~put~~);·io"	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=(required,·output);·io"	75	.IP·"\-o·\-\-transform=(required,·output);·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=(required,·output);·io"	78	.IP·"\-O·\-\-inverse-transform=(required,·output);·io"
79	inverse·output·transformation	79	inverse·output·transformation


Offset 20, 15 lines modified		Offset 20, 15 lines modified
20	.RS	20	.RS
21	.IP·"\-i·\-\-in-image=(input,·required);·io"	21	.IP·"\-i·\-\-in-image=(input,·required);·io"
22	input·image	22	input·image
23	·For·supported·file·types·see·PLUGINS:3dimage/io	23	·For·supported·file·types·see·PLUGINS:3dimage/io
24	.IP·"\-r·\-\-ref-image=(input,·required);·io"	24	.IP·"\-r·\-\-ref-image=(input,·required);·io"
25	reference·image·	25	reference·image·
26	·For·supported·file·types·see·PLUGINS:3dimage/io	26	·For·supported·file·types·see·PLUGINS:3dimage/io
27	.IP·"\-o·\-\-out-transformation=(requ~~ired~~,·ou~~tput~~);·io"	27	.IP·"\-o·\-\-out-transformation=(output,·required);·io"
28	output·transformation·comprising·the·registering·transformation·field	28	output·transformation·comprising·the·registering·transformation·field
29	·For·supported·file·types·see·PLUGINS:3dtransform/io	29	·For·supported·file·types·see·PLUGINS:3dtransform/io
30	.IP·"\-d·\-\-out-image=(output);·io"	30	.IP·"\-d·\-\-out-image=(output);·io"
31	save·deformed·image	31	save·deformed·image
32	·For·supported·file·types·see·PLUGINS:3dimage/io	32	·For·supported·file·types·see·PLUGINS:3dimage/io
33	.RE	33	.RE
34	.SS·Help·&·Info	34	.SS·Help·&·Info


Offset 8, 15 lines modified		Offset 8, 15 lines modified
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=(required,·input);·io"	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=(ou~~tput~~,·requ~~ired~~);·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=(required,·input);·io"	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