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Offset 2, 8 lines modified		Offset 2, 8 lines modified
2	·52805b13b8ae5a75ab60b24aaced691c·84142188·debug·optional·libmia-2.4-4-dbgsym_2.4.7-7_i386.deb	2	·52805b13b8ae5a75ab60b24aaced691c·84142188·debug·optional·libmia-2.4-4-dbgsym_2.4.7-7_i386.deb
3	·36ec4b9f794433c315cdb73da6cd64f2·4814076·libs·optional·libmia-2.4-4_2.4.7-7_i386.deb	3	·36ec4b9f794433c315cdb73da6cd64f2·4814076·libs·optional·libmia-2.4-4_2.4.7-7_i386.deb
4	·2ecb6f27dae64ecaaaec1444d245b10f·207284·libdevel·optional·libmia-2.4-dev_2.4.7-7_i386.deb	4	·2ecb6f27dae64ecaaaec1444d245b10f·207284·libdevel·optional·libmia-2.4-dev_2.4.7-7_i386.deb
5	·1eb0506f4126b557e52618b41827549b·4755804·doc·optional·libmia-2.4-doc_2.4.7-7_all.deb	5	·1eb0506f4126b557e52618b41827549b·4755804·doc·optional·libmia-2.4-doc_2.4.7-7_all.deb
6	·dcec706416c22847a9b49bd728ecb998·28924·science·optional·mia-doctools_2.4.7-7_all.deb	6	·dcec706416c22847a9b49bd728ecb998·28924·science·optional·mia-doctools_2.4.7-7_all.deb
7	·a08a1e9e2cf3e5be21163f2c4bf70000·31844188·debug·optional·mia-tools-dbgsym_2.4.7-7_i386.deb	7	·a08a1e9e2cf3e5be21163f2c4bf70000·31844188·debug·optional·mia-tools-dbgsym_2.4.7-7_i386.deb
8	·6f733997b452ba9ce1bb30102ca81bfc·98996·doc·optional·mia-tools-doc_2.4.7-7_all.deb	8	·6f733997b452ba9ce1bb30102ca81bfc·98996·doc·optional·mia-tools-doc_2.4.7-7_all.deb
9	·~~8a6~~43c4b819ff8a587253~~adfa018d~~215·193~~8612~~·science·optional·mia-tools_2.4.7-7_i386.deb	9	·9d70f4073e05dbb8e0fe8a02c3834f2f·1939024·science·optional·mia-tools_2.4.7-7_i386.deb


Offset 1, 3 lines modified		Offset 1, 3 lines modified
1	-rw-r--r--···0········0········0········4·2021-01-11·21:49:29.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2021-01-11·21:49:29.000000·debian-binary
2	-rw-r--r--···0········0········0·····7532·2021-01-11·21:49:29.000000·control.tar.xz	2	-rw-r--r--···0········0········0·····7528·2021-01-11·21:49:29.000000·control.tar.xz
3	-rw-r--r--···0········0········0··193~~0888~~·2021-01-11·21:49:29.000000·data.tar.xz	3	-rw-r--r--···0········0········0··1931304·2021-01-11·21:49:29.000000·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=(~~inp~~ut,·requi~~red~~);·io"	12	.IP·"\-i·\-\-in-files=(required,·input);·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=(~~inp~~ut,·requi~~red~~);·io"	15	.IP·"\-m·\-\-mask-file=(required,·input);·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=(requ~~ired~~,·ou~~tput~~);·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

23	.RS·10	23	.RS·10
24	.I	24	.I


Offset 24, 21 lines modified		Offset 24, 21 lines modified
24	}	24	}

25	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.	25	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.
26	.SH·OPTIONS	26	.SH·OPTIONS
27	.SS·	27	.SS·
28	File-IO	28	File-IO
29	.RS	29	.RS
30	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·string"	30	.IP·"\-i·\-\-in-file=(required,·input);·string"
31	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.	31	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	.IP·"\-o·\-\-out-file=(required,·output);·string"	32	.IP·"\-o·\-\-out-file=(required,·output);·string"
33	output·strains·file,·for·a·format·description·see·above.	33	output·strains·file,·for·a·format·description·see·above.

34	.IP·"\-t·\-\-transformation=(~~inp~~ut,·requi~~red~~);·io"	34	.IP·"\-t·\-\-transformation=(required,·input);·io"
35	transformation·of·which·the·quantity·will·be·evaluated.	35	transformation·of·which·the·quantity·will·be·evaluated.
36	·For·supported·file·types·see·PLUGINS:2dtransform/io	36	·For·supported·file·types·see·PLUGINS:2dtransform/io
37	.RE	37	.RE
38	.SS·	38	.SS·
39	Parameters	39	Parameters
40	.RS	40	.RS
41	.IP·"\-q·\-\-quantity=strain"	41	.IP·"\-q·\-\-quantity=strain"


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=(~~inp~~ut,·requi~~red~~);·io"	69	.IP·"\-i·\-\-in-image=(required,·input);·io"
70	test·image	70	test·image
71	·For·supported·file·types·see·PLUGINS:2dimage/io	71	·For·supported·file·types·see·PLUGINS:2dimage/io
72	.IP·"\-r·\-\-ref-image=(~~inp~~ut,·requi~~red~~);·io"	72	.IP·"\-r·\-\-ref-image=(required,·input);·io"
73	reference·image	73	reference·image
74	·For·supported·file·types·see·PLUGINS:2dimage/io	74	·For·supported·file·types·see·PLUGINS:2dimage/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:2dtransform/io	77	·For·supported·file·types·see·PLUGINS:2dtransform/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 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=(~~inp~~ut,·requi~~red~~);·io"	13	.IP·"\-i·\-\-in-file=(required,·input);·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 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=(ou~~tput~~,·requ~~ired~~);·io"	21	.IP·"\-o·\-\-out-file=(required,·output);·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 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=(requ~~ired~~,·ou~~tput~~);·io"	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 826, 15 lines modified		Offset 826, 15 lines modified
826	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.	826	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.

827	.RE	827	.RE
828	.RE	828	.RE
829	.RS·14	829	.RS·14
830	.I	830	.I
831	varfile	831	varfile
832	=(requ~~ired~~,·ou~~tput~~,·io)	832	=(output,·required,·io)
833	.RS·2	833	.RS·2
834	name·of·the·output·file·to·save·the·variation·image·too..	834	name·of·the·output·file·to·save·the·variation·image·too..
835	For·supported·file·types·see·PLUGINS:2dimage/io	835	For·supported·file·types·see·PLUGINS:2dimage/io

836	.RE	836	.RE
837	.RE	837	.RE
838	.RS·14	838	.RS·14
Offset 862, 15 lines modified		Offset 862, 15 lines modified
862	.TP·10	862	.TP·10
863	.B·medianmad	863	.B·medianmad
864	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·	864	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
865	.P	865	.P
866	.RS·14	866	.RS·14
867	.I	867	.I
868	madfile	868	madfile
869	=(requ~~ired~~,·ou~~tput~~,·io)	869	=(output,·required,·io)
870	.RS·2	870	.RS·2
871	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..	871	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
872	For·supported·file·types·see·PLUGINS:2dimage/io	872	For·supported·file·types·see·PLUGINS:2dimage/io

873	.RE	873	.RE
874	.RE	874	.RE
875	.RS·14	875	.RS·14
Offset 1181, 15 lines modified		Offset 1181, 15 lines modified
1181	.TP·10	1181	.TP·10
1182	.B·tee	1182	.B·tee
1183	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·	1183	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1184	.P	1184	.P
1185	.RS·14	1185	.RS·14
1186	.I	1186	.I
1187	file	1187	file
1188	=(requ~~ired~~,·ou~~tput~~,·io)	1188	=(output,·required,·io)
1189	.RS·2	1189	.RS·2
1190	name·of·the·output·file·to·save·the·image·too..	1190	name·of·the·output·file·to·save·the·image·too..
1191	For·supported·file·types·see·PLUGINS:2dimage/io	1191	For·supported·file·types·see·PLUGINS:2dimage/io

1192	.RE	1192	.RE
1193	.RE	1193	.RE
1194	.TP·10	1194	.TP·10


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 388, 15 lines modified		Offset 388, 15 lines modified
388	.TP·10	388	.TP·10
389	.B·combiner	389	.B·combiner
390	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:·	390	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:·
391	.P	391	.P
392	.RS·14	392	.RS·14
393	.I	393	.I
394	image	394	image
395	=(~~inp~~ut,·requi~~red~~,·io)	395	=(required,·input,·io)
396	.RS·2	396	.RS·2
397	second·image·that·is·needed·in·the·combiner.	397	second·image·that·is·needed·in·the·combiner.
398	For·supported·file·types·see·PLUGINS:2dimage/io	398	For·supported·file·types·see·PLUGINS:2dimage/io

399	.RE	399	.RE
400	.RE	400	.RE
401	.RS·14	401	.RS·14
Offset 732, 15 lines modified		Offset 732, 15 lines modified
732	.TP·10	732	.TP·10
733	.B·labelmap	733	.B·labelmap
734	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·	734	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
735	.P	735	.P
736	.RS·14	736	.RS·14
737	.I	737	.I
738	map	738	map
739	=(~~inp~~ut,·requi~~red~~,·string)	739	=(required,·input,·string)
740	.RS·2	740	.RS·2
741	Label·mapping·file.	741	Label·mapping·file.

742	.RE	742	.RE
743	.RE	743	.RE
744	.TP·10	744	.TP·10
745	.B·labelscale	745	.B·labelscale
Offset 758, 15 lines modified		Offset 758, 15 lines modified
758	.TP·10	758	.TP·10
759	.B·load	759	.B·load
760	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·	760	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
761	.P	761	.P
762	.RS·14	762	.RS·14
763	.I	763	.I
764	file	764	file
765	=(~~inp~~ut,·requi~~red~~,·io)	765	=(required,·input,·io)
766	.RS·2	766	.RS·2
767	name·of·the·input·file·to·load·from..	767	name·of·the·input·file·to·load·from..
768	For·supported·file·types·see·PLUGINS:2dimage/io	768	For·supported·file·types·see·PLUGINS:2dimage/io

769	.RE	769	.RE
770	.RE	770	.RE
771	.TP·10	771	.TP·10
Offset 797, 15 lines modified		Offset 797, 15 lines modified
797	.RE	797	.RE

798	.RE	798	.RE
799	.RE	799	.RE
800	.RS·14	800	.RS·14
801	.I	801	.I
802	input	802	input
803	=(~~inp~~ut,·requi~~red~~,·io)	803	=(required,·input,·io)
804	.RS·2	804	.RS·2
805	second·input·image·file·name.	805	second·input·image·file·name.
806	For·supported·file·types·see·PLUGINS:2dimage/io	806	For·supported·file·types·see·PLUGINS:2dimage/io

807	.RE	807	.RE
808	.RE	808	.RE
809	.RS·14	809	.RS·14
Offset 820, 25 lines modified		Offset 820, 25 lines modified
820	.TP·10	820	.TP·10
821	.B·maxflow	821	.B·maxflow
822	This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·	822	This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·
823	.P	823	.P
824	.RS·14	824	.RS·14
825	.I	825	.I
826	sink-flow	826	sink-flow
827	=(~~inp~~ut,·requi~~red~~,·io)	827	=(required,·input,·io)
828	.RS·2	828	.RS·2
829	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.	829	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.
830	For·supported·file·types·see·PLUGINS:2dimage/io	830	For·supported·file·types·see·PLUGINS:2dimage/io

831	.RE	831	.RE
832	.RE	832	.RE
833	.RS·14	833	.RS·14
834	.I	834	.I
835	source-flow	835	source-flow
836	=(~~inp~~ut,·requi~~red~~,·io)	836	=(required,·input,·io)
837	.RS·2	837	.RS·2
838	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.	838	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.
839	For·supported·file·types·see·PLUGINS:2dimage/io	839	For·supported·file·types·see·PLUGINS:2dimage/io

840	.RE	840	.RE
841	.RE	841	.RE
842	.TP·10	842	.TP·10
Offset 866, 15 lines modified		Offset 866, 15 lines modified
866	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.	866	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.

867	.RE	867	.RE
868	.RE	868	.RE
869	.RS·14	869	.RS·14
870	.I	870	.I
871	varfile	871	varfile
872	=(ou~~tput~~,·requ~~ired~~,·io)	872	=(required,·output,·io)
873	.RS·2	873	.RS·2
874	name·of·the·output·file·to·save·the·variation·image·too..	874	name·of·the·output·file·to·save·the·variation·image·too..
875	For·supported·file·types·see·PLUGINS:2dimage/io	875	For·supported·file·types·see·PLUGINS:2dimage/io

876	.RE	876	.RE
877	.RE	877	.RE
878	.RS·14	878	.RS·14
Offset 902, 15 lines modified		Offset 902, 15 lines modified
902	.TP·10	902	.TP·10
903	.B·medianmad	903	.B·medianmad
Max diff block lines reached; 1373/5136 bytes (26.73%) of diff not shown.


Offset 5, 15 lines modified		Offset 5, 15 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dimageselect·\-i·<in\-file>·\-o·<out\-file>·[options]	6	.B··mia\-2dimageselect·\-i·<in\-file>·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
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=(~~req~~uired,·in~~put~~);·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=(output,·required);·io"	15	.IP·"\-o·\-\-out-file=(output,·required);·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


Offset 6, 18 lines modified		Offset 6, 18 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=(~~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·"\-o·\-\-out-probmap=(requ~~ired~~,·ou~~tput~~);·string"	16	.IP·"\-o·\-\-out-probmap=(output,·required);·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
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 11, 15 lines modified		Offset 11, 15 lines modified
11	.RS	11	.RS
12	.IP·"\-1·\-\-first=(required,·input);·io"	12	.IP·"\-1·\-\-first=(required,·input);·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=(required,·input);·io"	15	.IP·"\-2·\-\-second=(required,·input);·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\-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 143, 142 lines modified		Offset 143, 142 lines modified
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)·····1127·2021-01-11·21:49:29.000000·./usr/share/doc/mia-tools/copyright	144	-rw-r--r--···0·root·········(0)·root·········(0)·····1127·2021-01-11·21:49:29.000000·./usr/share/doc/mia-tools/copyright
145	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/lintian/	145	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/lintian/
146	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/lintian/overrides/	146	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/lintian/overrides/
147	-rw-r--r--···0·root·········(0)·root·········(0)······425·2021-01-11·21:49:29.000000·./usr/share/lintian/overrides/mia-tools	147	-rw-r--r--···0·root·········(0)·root·········(0)······425·2021-01-11·21:49:29.000000·./usr/share/lintian/overrides/mia-tools
148	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/man/	148	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-01-11·21:49:29.000000·./usr/share/man/
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/
150	-rw-r--r--···0·root·········(0)·root·········(0)·····1472·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2davgmasked.1.gz	150	-rw-r--r--···0·root·········(0)·root·········(0)·····1474·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2davgmasked.1.gz
151	-rw-r--r--···0·root·········(0)·root·········(0)·····1571·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dbinarycombine.1.gz	151	-rw-r--r--···0·root·········(0)·root·········(0)·····1570·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dbinarycombine.1.gz
152	-rw-r--r--···0·root·········(0)·root·········(0)·····2633·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dcost.1.gz	152	-rw-r--r--···0·root·········(0)·root·········(0)·····2633·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dcost.1.gz
153	-rw-r--r--···0·root·········(0)·root·········(0)·····1745·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2ddeform.1.gz	153	-rw-r--r--···0·root·········(0)·root·········(0)·····1745·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2ddeform.1.gz
154	-rw-r--r--···0·root·········(0)·root·········(0)·····1691·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2ddistance.1.gz	154	-rw-r--r--···0·root·········(0)·root·········(0)·····1690·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2ddistance.1.gz
155	-rw-r--r--···0·root·········(0)·root·········(0)·····1871·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz	155	-rw-r--r--···0·root·········(0)·root·········(0)·····1867·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz
156	-rw-r--r--···0·root·········(0)·root·········(0)·····3~~501~~·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz	156	-rw-r--r--···0·root·········(0)·root·········(0)·····3499·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz
157	-rw-r--r--···0·root·········(0)·root·········(0)·····1915·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dfluid.1.gz	157	-rw-r--r--···0·root·········(0)·root·········(0)·····1915·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dfluid.1.gz
158	-rw-r--r--···0·root·········(0)·root·········(0)·····1543·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dforce.1.gz	158	-rw-r--r--···0·root·········(0)·root·········(0)·····1543·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dforce.1.gz
159	-rw-r--r--···0·root·········(0)·root·········(0)·····1810·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz	159	-rw-r--r--···0·root·········(0)·root·········(0)·····1805·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz
160	-rw-r--r--···0·root·········(0)·root·········(0)·····1592·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz	160	-rw-r--r--···0·root·········(0)·root·········(0)·····1590·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz
161	-rw-r--r--···0·root·········(0)·root·········(0)·····3457·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dgroundtruthreg.1.gz	161	-rw-r--r--···0·root·········(0)·root·········(0)·····3457·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dgroundtruthreg.1.gz
162	-rw-r--r--···0·root·········(0)·root·········(0)·····1469·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagecombine-dice.1.gz	162	-rw-r--r--···0·root·········(0)·root·········(0)·····1470·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagecombine-dice.1.gz
163	-rw-r--r--···0·root·········(0)·root·········(0)·····1620·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagecombiner.1.gz	163	-rw-r--r--···0·root·········(0)·root·········(0)·····1620·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagecombiner.1.gz
164	-rw-r--r--···0·root·········(0)·root·········(0)·····1772·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagecreator.1.gz	164	-rw-r--r--···0·root·········(0)·root·········(0)·····1772·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagecreator.1.gz
165	-rw-r--r--···0·root·········(0)·root·········(0)·····6177·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagefilter.1.gz	165	-rw-r--r--···0·root·········(0)·root·········(0)·····6181·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagefilter.1.gz
166	-rw-r--r--···0·root·········(0)·root·········(0)·····6373·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagefilterstack.1.gz	166	-rw-r--r--···0·root·········(0)·root·········(0)·····6370·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagefilterstack.1.gz
167	-rw-r--r--···0·root·········(0)·root·········(0)·····1442·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagefullstats.1.gz	167	-rw-r--r--···0·root·········(0)·root·········(0)·····1442·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagefullstats.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	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
169	-rw-r--r--···0·root·········(0)·root·········(0)·····1494·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimageselect.1.gz	169	-rw-r--r--···0·root·········(0)·root·········(0)·····1490·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimageselect.1.gz
170	-rw-r--r--···0·root·········(0)·root·········(0)·····1426·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz	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
171	-rw-r--r--···0·root·········(0)·root·········(0)·····1952·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz	171	-rw-r--r--···0·root·········(0)·root·········(0)·····1955·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz
172	-rw-r--r--···0·root·········(0)·root·········(0)·····1622·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagestats.1.gz	172	-rw-r--r--···0·root·········(0)·root·········(0)·····1622·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dimagestats.1.gz
173	-rw-r--r--···0·root·········(0)·root·········(0)·····1672·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dlerp.1.gz	173	-rw-r--r--···0·root·········(0)·root·········(0)·····1669·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dlerp.1.gz
174	-rw-r--r--···0·root·········(0)·root·········(0)·····3668·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz	174	-rw-r--r--···0·root·········(0)·root·········(0)·····3668·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz
175	-rw-r--r--···0·root·········(0)·root·········(0)·····2777·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmulti-force.1.gz	175	-rw-r--r--···0·root·········(0)·root·········(0)·····2777·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmulti-force.1.gz
176	-rw-r--r--···0·root·········(0)·root·········(0)·····5396·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmultiimageregistration.1.gz	176	-rw-r--r--···0·root·········(0)·root·········(0)·····5397·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmultiimageregistration.1.gz
177	-rw-r--r--···0·root·········(0)·root·········(0)·····1860·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz	177	-rw-r--r--···0·root·········(0)·root·········(0)·····1856·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz
178	-rw-r--r--···0·root·········(0)·root·········(0)·····1542·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmultiimagevar.1.gz	178	-rw-r--r--···0·root·········(0)·root·········(0)·····1540·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmultiimagevar.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	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
180	-rw-r--r--···0·root·········(0)·root·········(0)·····1815·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz	180	-rw-r--r--···0·root·········(0)·root·········(0)·····1817·2021-01-11·21:49:29.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz


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=(~~req~~uired,·in~~put~~);·io"	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=(~~req~~uired,·in~~put~~);·io"	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=(requ~~ired~~,·ou~~tput~~);·string"	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 17, 15 lines modified		Offset 17, 15 lines modified
17	·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	·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.
18	.SH·OPTIONS	18	.SH·OPTIONS
19	.SS·File-IO	19	.SS·File-IO
20	.RS	20	.RS
21	.IP·"\-i·\-\-in-file=(input,·required);·string"	21	.IP·"\-i·\-\-in-file=(input,·required);·string"
22	input·perfusion·data·set	22	input·perfusion·data·set

23	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·string"	23	.IP·"\-o·\-\-out-file=(output,·required);·string"
24	output·perfusion·data·set	24	output·perfusion·data·set

25	.IP·"\-r·\-\-registered="	25	.IP·"\-r·\-\-registered="
26	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.	26	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.

27	.IP·"···\-\-save-cropped=(output);·string"	27	.IP·"···\-\-save-cropped=(output);·string"
28	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base	28	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base


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=(~~req~~uired,·in~~put~~);·string"	12	.IP·"\-1·\-\-first=(input,·required);·string"
13	first·segmentation·set	13	first·segmentation·set

14	.IP·"\-2·\-\-second=(~~req~~uired,·in~~put~~);·string"	14	.IP·"\-2·\-\-second=(input,·required);·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 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=(requ~~ired~~,·ou~~tput~~);·io"	15	.IP·"\-o·\-\-out-file=(output,·required);·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 17, 15 lines modified		Offset 17, 15 lines modified
17	This·version·of·the·program·runs·all·registrations·in·parallel.	17	This·version·of·the·program·runs·all·registrations·in·parallel.
18	.SH·OPTIONS	18	.SH·OPTIONS
19	.SS·File-IO	19	.SS·File-IO
20	.RS	20	.RS
21	.IP·"\-i·\-\-in-file=(required,·input);·string"	21	.IP·"\-i·\-\-in-file=(required,·input);·string"
22	input·perfusion·data·set	22	input·perfusion·data·set

23	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·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·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.	26	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.

27	.IP·"···\-\-save-cropped=(output);·string"	27	.IP·"···\-\-save-cropped=(output);·string"
28	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base	28	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base


Offset 16, 15 lines modified		Offset 16, 15 lines modified

16	.SH·OPTIONS	16	.SH·OPTIONS
17	.SS·File-IO	17	.SS·File-IO
18	.RS	18	.RS
19	.IP·"\-i·\-\-in-file=(required,·input);·string"	19	.IP·"\-i·\-\-in-file=(required,·input);·string"
20	input·perfusion·data·set	20	input·perfusion·data·set

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

25	.IP·"···\-\-save-cropped="	25	.IP·"···\-\-save-cropped="
26	save·cropped·set·to·this·file	26	save·cropped·set·to·this·file


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dmyoica\-nonrigid2	8	.B·mia\-2dmyoica\-nonrigid2
9	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	9	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
10	Special·note·to·this·implemnentation:·the·registration·is·always·run·from·the·original·images·to·avoid·the·accumulation·of·interpolation·errors.	10	Special·note·to·this·implemnentation:·the·registration·is·always·run·from·the·original·images·to·avoid·the·accumulation·of·interpolation·errors.
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=(~~req~~uired,·in~~put~~);·string"	15	.IP·"\-i·\-\-in-file=(input,·required);·string"
16	input·perfusion·data·set	16	input·perfusion·data·set

17	.IP·"\-o·\-\-out-file=(output,·required);·string"	17	.IP·"\-o·\-\-out-file=(output,·required);·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


Offset 43, 15 lines modified		Offset 43, 15 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=(~~req~~uired,·in~~put~~);·string"	48	.IP·"\-i·\-\-in-file=(input,·required);·string"
49	input·perfusion·data·set	49	input·perfusion·data·set

50	.IP·"\-o·\-\-out-file=(required,·output);·string"	50	.IP·"\-o·\-\-out-file=(required,·output);·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.


Offset 18, 15 lines modified		Offset 18, 15 lines modified

18	.SH·OPTIONS	18	.SH·OPTIONS
19	.SS·File-IO	19	.SS·File-IO
20	.RS	20	.RS
21	.IP·"\-i·\-\-in-file=(input,·required);·string"	21	.IP·"\-i·\-\-in-file=(input,·required);·string"
22	input·perfusion·data·set	22	input·perfusion·data·set

23	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	23	.IP·"\-o·\-\-out-file=(required,·output);·string"
24	output·perfusion·data·set	24	output·perfusion·data·set

25	.IP·"\-r·\-\-registered="	25	.IP·"\-r·\-\-registered="
26	file·name·base·for·registered·files	26	file·name·base·for·registered·files

27	.IP·"···\-\-save-references="	27	.IP·"···\-\-save-references="
28	save·synthetic·reference·images·to·this·file·base	28	save·synthetic·reference·images·to·this·file·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=(~~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=(requ~~ired~~,·ou~~tput~~);·string"	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·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 13, 15 lines modified		Offset 13, 15 lines modified
13	Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,	13	Mohamed·N.·Ahmed·et.·al,·"A·Modified·Fuzzy·C-Means·Algorithm·for·Bias·Field·estimation·and·Segmentation·of·MRI·Data",·IEEE·Trans.·on·Medical·Imaging,·Vol.·21,·No.·3,·March·2002,
14	.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	.RS	18	.RS
19	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·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=(output,·required);·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


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	=(requ~~ired~~,·ou~~tput~~,·io)	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 888, 15 lines modified		Offset 888, 15 lines modified
888	.TP·10	888	.TP·10
889	.B·medianmad	889	.B·medianmad
890	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·	890	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
891	.P	891	.P
892	.RS·14	892	.RS·14
893	.I	893	.I
894	madfile	894	madfile
895	=(requ~~ired~~,·ou~~tput~~,·io)	895	=(output,·required,·io)
896	.RS·2	896	.RS·2
897	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..	897	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
898	For·supported·file·types·see·PLUGINS:2dimage/io	898	For·supported·file·types·see·PLUGINS:2dimage/io

899	.RE	899	.RE
900	.RE	900	.RE
901	.RS·14	901	.RS·14
Offset 1207, 15 lines modified		Offset 1207, 15 lines modified
1207	.TP·10	1207	.TP·10
1208	.B·tee	1208	.B·tee
1209	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·	1209	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1210	.P	1210	.P
1211	.RS·14	1211	.RS·14
1212	.I	1212	.I
1213	file	1213	file
1214	=(requ~~ired~~,·ou~~tput~~,·io)	1214	=(output,·required,·io)
1215	.RS·2	1215	.RS·2
1216	name·of·the·output·file·to·save·the·image·too..	1216	name·of·the·output·file·to·save·the·image·too..
1217	For·supported·file·types·see·PLUGINS:2dimage/io	1217	For·supported·file·types·see·PLUGINS:2dimage/io

1218	.RE	1218	.RE
1219	.RE	1219	.RE
1220	.TP·10	1220	.TP·10


Offset 13, 15 lines modified		Offset 13, 15 lines modified
13	Dunmore·CJ,·Wollny·G,·Skinner·MM.·(2018)·MIA-Clustering:·a·novel·method·for·segmentation·of·paleontological·material.·PeerJ·6:e4374.	13	Dunmore·CJ,·Wollny·G,·Skinner·MM.·(2018)·MIA-Clustering:·a·novel·method·for·segmentation·of·paleontological·material.·PeerJ·6:e4374.
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~~);·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=(output);·io"	22	.IP·"\-o·\-\-out-file=(output);·io"
23	class·label·image·based·on·merging·local·labels	23	class·label·image·based·on·merging·local·labels
24	·For·supported·file·types·see·PLUGINS:2dimage/io	24	·For·supported·file·types·see·PLUGINS:2dimage/io
25	.IP·"\-G·\-\-out-global-crisp=(output);·io"	25	.IP·"\-G·\-\-out-global-crisp=(output);·io"
26	class·label·image·based·on·global·segmentation	26	class·label·image·based·on·global·segmentation


Offset 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dsegment\-local\-kmeans·\-i·<in\-file>·[options]	6	.B··mia\-2dsegment\-local\-kmeans·\-i·<in\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dsegment\-local\-kmeans	8	.B·mia\-2dsegment\-local\-kmeans
9	This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.	9	This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.
10	.SH·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	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=(output);·io"	16	.IP·"\-o·\-\-out-file=(output);·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	.IP·"\-O·\-\-out-file2=(output);·io"	19	.IP·"\-O·\-\-out-file2=(output);·io"
20	class·label·image·based·on·classifying·by·using·the·interpolated·class·centers·	20	class·label·image·based·on·classifying·by·using·the·interpolated·class·centers·


Offset 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dsegment\-per\-pixel\-kmeans·\-i·<in\-file>·\-o·<out\-file>·[options]	6	.B··mia\-2dsegment\-per\-pixel\-kmeans·\-i·<in\-file>·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dsegment\-per\-pixel\-kmeans	8	.B·mia\-2dsegment\-per\-pixel\-kmeans
9	This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.	9	This·program·runs·the·segmentation·of·a·2D·image·by·applying·a·localized·k-means·approach·that·helps·to·overcome·intensity·inhomogeneities·in·the·image.·The·approach·evaluates·a·global·k-means·clustering,·and·then·separates·the·image·into·overlapping·regions·where·more·k-means·iterations·are·run·only·including·the·locally·present·classes,·i.e.·the·classes·that·relatively·contain·more·pixels·than·a·given·threshold.
10	.SH·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	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=(output,·required);·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


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

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

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\-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=(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 833, 15 lines modified		Offset 833, 15 lines modified
833	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.	833	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.

834	.RE	834	.RE
835	.RE	835	.RE
836	.RS·14	836	.RS·14
837	.I	837	.I
838	varfile	838	varfile
839	=(ou~~tput~~,·requ~~ired~~,·io)	839	=(required,·output,·io)
840	.RS·2	840	.RS·2
841	name·of·the·output·file·to·save·the·variation·image·too..	841	name·of·the·output·file·to·save·the·variation·image·too..
842	For·supported·file·types·see·PLUGINS:2dimage/io	842	For·supported·file·types·see·PLUGINS:2dimage/io

843	.RE	843	.RE
844	.RE	844	.RE
845	.RS·14	845	.RS·14
Offset 869, 15 lines modified		Offset 869, 15 lines modified
869	.TP·10	869	.TP·10
870	.B·medianmad	870	.B·medianmad
871	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·	871	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
872	.P	872	.P
873	.RS·14	873	.RS·14
874	.I	874	.I
875	madfile	875	madfile
876	=(ou~~tput~~,·requ~~ired~~,·io)	876	=(required,·output,·io)
877	.RS·2	877	.RS·2
878	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..	878	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
879	For·supported·file·types·see·PLUGINS:2dimage/io	879	For·supported·file·types·see·PLUGINS:2dimage/io

880	.RE	880	.RE
881	.RE	881	.RE
882	.RS·14	882	.RS·14
Offset 1188, 15 lines modified		Offset 1188, 15 lines modified
1188	.TP·10	1188	.TP·10
1189	.B·tee	1189	.B·tee
1190	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·	1190	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1191	.P	1191	.P
1192	.RS·14	1192	.RS·14
1193	.I	1193	.I
1194	file	1194	file
1195	=(ou~~tput~~,·requ~~ired~~,·io)	1195	=(required,·output,·io)
1196	.RS·2	1196	.RS·2
1197	name·of·the·output·file·to·save·the·image·too..	1197	name·of·the·output·file·to·save·the·image·too..
1198	For·supported·file·types·see·PLUGINS:2dimage/io	1198	For·supported·file·types·see·PLUGINS:2dimage/io

1199	.RE	1199	.RE
1200	.RE	1200	.RE
1201	.TP·10	1201	.TP·10


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dstackfilter	8	.B·mia\-2dstackfilter
9	This·program·is·used·to·filter·and·convert·a·series·of·2D·gray·scale·images·in·a·3D·fashion·by·running·filters·(filter/2dimage)·as·given·on·the·command·line.	9	This·program·is·used·to·filter·and·convert·a·series·of·2D·gray·scale·images·in·a·3D·fashion·by·running·filters·(filter/2dimage)·as·given·on·the·command·line.
10	.SH·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: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·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	16	output·file·name·base,·the·actual·names·is·created·by·adding·the·file·number·based·on·output·order·and·the·extension·bysed·on·the·'type'·parameter
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-t·\-\-type=(required);·set"	18	.IP·"\-t·\-\-type=(required);·set"
19	output·file·type	19	output·file·type

20	.RS·10	20	.RS·10
21	.I	21	.I
Offset 856, 15 lines modified		Offset 856, 15 lines modified
856	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.	856	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.

857	.RE	857	.RE
858	.RE	858	.RE
859	.RS·14	859	.RS·14
860	.I	860	.I
861	varfile	861	varfile
862	=(ou~~tput~~,·requ~~ired~~,·io)	862	=(required,·output,·io)
863	.RS·2	863	.RS·2
864	name·of·the·output·file·to·save·the·variation·image·too..	864	name·of·the·output·file·to·save·the·variation·image·too..
865	For·supported·file·types·see·PLUGINS:2dimage/io	865	For·supported·file·types·see·PLUGINS:2dimage/io

866	.RE	866	.RE
867	.RE	867	.RE
868	.RS·14	868	.RS·14
Offset 892, 15 lines modified		Offset 892, 15 lines modified
892	.TP·10	892	.TP·10
893	.B·medianmad	893	.B·medianmad
894	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·	894	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
895	.P	895	.P
896	.RS·14	896	.RS·14
897	.I	897	.I
898	madfile	898	madfile
899	=(ou~~tput~~,·requ~~ired~~,·io)	899	=(required,·output,·io)
900	.RS·2	900	.RS·2
901	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..	901	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
902	For·supported·file·types·see·PLUGINS:2dimage/io	902	For·supported·file·types·see·PLUGINS:2dimage/io

903	.RE	903	.RE
904	.RE	904	.RE
905	.RS·14	905	.RS·14
Offset 1211, 15 lines modified		Offset 1211, 15 lines modified
1211	.TP·10	1211	.TP·10
1212	.B·tee	1212	.B·tee
1213	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·	1213	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1214	.P	1214	.P
1215	.RS·14	1215	.RS·14
1216	.I	1216	.I
1217	file	1217	file
1218	=(ou~~tput~~,·requ~~ired~~,·io)	1218	=(required,·output,·io)
1219	.RS·2	1219	.RS·2
1220	name·of·the·output·file·to·save·the·image·too..	1220	name·of·the·output·file·to·save·the·image·too..
1221	For·supported·file·types·see·PLUGINS:2dimage/io	1221	For·supported·file·types·see·PLUGINS:2dimage/io

1222	.RE	1222	.RE
1223	.RE	1223	.RE
1224	.TP·10	1224	.TP·10


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=(input,·required);·io"	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=(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=(input,·required);·io"	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


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-3dbrainextractT1	8	.B·mia\-3dbrainextractT1
9	This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter·segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to·obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the·brain·from·the·B0·field·corrected·images.	9	This·program·is·used·to·extract·the·brain·from·T1·MR·images.·It·first·runs·a·combined·fuzzy·c-means·clustering·and·B-field·correction·to·facilitate·a·3D·segmentation·of·3D·image.·Then·various·fiters·are·run·to·obtain·a·white·matter·segmentation·as·initial·mask·that·is·then·used·to·run·a·region·growing·to·obtain·a·mask·of·the·whole·brain.·Finally,·this·mask·is·used·to·extact·the·brain·from·the·B0·field·corrected·images.
10	.SH·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·image(s)·to·be·segmented	13	input·image(s)·to·be·segmented
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	brain·mask	16	brain·mask
17	·For·supported·file·types·see·PLUGINS:3dimage/io	17	·For·supported·file·types·see·PLUGINS:3dimage/io
18	.IP·"\-n·\-\-no-of-classes=3"	18	.IP·"\-n·\-\-no-of-classes=3"
19	number·of·classes	19	number·of·classes

20	.IP·"\-w·\-\-wm-class=2"	20	.IP·"\-w·\-\-wm-class=2"
21	index·of·white·matter	21	index·of·white·matter


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 717, 15 lines modified		Offset 717, 15 lines modified
717	lower·threshold·for·mask·growing.	717	lower·threshold·for·mask·growing.

718	.RE	718	.RE
719	.RE	719	.RE
720	.RS·14	720	.RS·14
721	.I	721	.I
722	ref	722	ref
723	=(~~req~~uired,·in~~put~~,·io)	723	=(input,·required,·io)
724	.RS·2	724	.RS·2
725	reference·image·for·mask·region·growing.	725	reference·image·for·mask·region·growing.
726	For·supported·file·types·see·PLUGINS:3dimage/io	726	For·supported·file·types·see·PLUGINS:3dimage/io

727	.RE	727	.RE
728	.RE	728	.RE
729	.RS·14	729	.RS·14
Offset 798, 15 lines modified		Offset 798, 15 lines modified
798	.TP·10	798	.TP·10
799	.B·labelmap	799	.B·labelmap
800	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·	800	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
801	.P	801	.P
802	.RS·14	802	.RS·14
803	.I	803	.I
804	map	804	map
805	=(~~req~~uired,·in~~put~~,·string)	805	=(input,·required,·string)
806	.RS·2	806	.RS·2
807	Label·mapping·file.	807	Label·mapping·file.

808	.RE	808	.RE
809	.RE	809	.RE
810	.TP·10	810	.TP·10
811	.B·labelscale	811	.B·labelscale
Offset 824, 15 lines modified		Offset 824, 15 lines modified
824	.TP·10	824	.TP·10
825	.B·load	825	.B·load
826	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·	826	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
827	.P	827	.P
828	.RS·14	828	.RS·14
829	.I	829	.I
830	file	830	file
831	=(~~req~~uired,·in~~put~~,·io)	831	=(input,·required,·io)
832	.RS·2	832	.RS·2
833	name·of·the·input·file·to·load·from..	833	name·of·the·input·file·to·load·from..
834	For·supported·file·types·see·PLUGINS:3dimage/io	834	For·supported·file·types·see·PLUGINS:3dimage/io

835	.RE	835	.RE
836	.RE	836	.RE
837	.TP·10	837	.TP·10
Offset 851, 15 lines modified		Offset 851, 15 lines modified
851	.TP·10	851	.TP·10
852	.B·mask	852	.B·mask
853	Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·	853	Mask·an·image,·one·image·is·taken·from·the·parameters·list·and·the·other·from·the·normal·filter·input.·Both·images·must·be·of·the·same·dimensions·and·one·must·be·binary.·The·attributes·of·the·image·coming·through·the·filter·pipeline·are·preserved.·The·output·pixel·type·corresponds·to·the·input·image·that·is·not·binary.,·supported·parameters·are:·
854	.P	854	.P
855	.RS·14	855	.RS·14
856	.I	856	.I
857	input	857	input
858	=(~~req~~uired,·in~~put~~,·io)	858	=(input,·required,·io)
859	.RS·2	859	.RS·2
860	second·input·image·file·name.	860	second·input·image·file·name.
861	For·supported·file·types·see·PLUGINS:3dimage/io	861	For·supported·file·types·see·PLUGINS:3dimage/io

862	.RE	862	.RE
863	.RE	863	.RE
864	.TP·10	864	.TP·10
Offset 1241, 15 lines modified		Offset 1241, 15 lines modified
1241	For·supported·plug-ins·see·PLUGINS:3dimage/shape	1241	For·supported·plug-ins·see·PLUGINS:3dimage/shape

1242	.RE	1242	.RE
1243	.RE	1243	.RE
1244	.RS·14	1244	.RS·14
1245	.I	1245	.I
1246	seed	1246	seed
1247	=(~~req~~uired,·in~~put~~,·string)	1247	=(input,·required,·string)
1248	.RS·2	1248	.RS·2
1249	seed·input·image·containing·the·lables·for·the·initial·regions.	1249	seed·input·image·containing·the·lables·for·the·initial·regions.

1250	.RE	1250	.RE
1251	.RE	1251	.RE
1252	.TP·10	1252	.TP·10
1253	.B·tee	1253	.B·tee
Offset 1275, 15 lines modified		Offset 1275, 15 lines modified
1275	.TP·10	1275	.TP·10
1276	.B·transform	1276	.B·transform
1277	Transform·the·input·image·with·the·given·transformation.,·supported·parameters·are:·	1277	Transform·the·input·image·with·the·given·transformation.,·supported·parameters·are:·
1278	.P	1278	.P
1279	.RS·14	1279	.RS·14
1280	.I	1280	.I
1281	file	1281	file
1282	=(~~req~~uired,·in~~put~~,·io)	1282	=(input,·required,·io)
1283	.RS·2	1283	.RS·2
1284	Name·of·the·file·containing·the·transformation..	1284	Name·of·the·file·containing·the·transformation..
1285	For·supported·file·types·see·PLUGINS:3dtransform/io	1285	For·supported·file·types·see·PLUGINS:3dtransform/io

1286	.RE	1286	.RE
1287	.RE	1287	.RE
1288	.RS·14	1288	.RS·14


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