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Offset 2, 8 lines modified		Offset 2, 8 lines modified
2	·45e26d19cacdf5597afdce217f26bf7e·90439660·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_amd64.deb	2	·45e26d19cacdf5597afdce217f26bf7e·90439660·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_amd64.deb
3	·940214afba0041bda2383a7d51e39d0a·4866076·libs·optional·libmia-2.4-4_2.4.7-13_amd64.deb	3	·940214afba0041bda2383a7d51e39d0a·4866076·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	·961fe969a14575fe485418c80af07d57·35761360·debug·optional·mia-tools-dbgsym_2.4.7-13_amd64.deb	7	·961fe969a14575fe485418c80af07d57·35761360·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	·~~849f5~~a~~0c3~~6e27c~~8e9~~7~~f1f~~0~~ec0d044559~~·194~~8716~~·science·optional·mia-tools_2.4.7-13_amd64.deb	9	·3e259a7d26dfc618718d0f22215238f4·1949868·science·optional·mia-tools_2.4.7-13_amd64.deb


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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·····7556·2023-08-29·09:00:00.000000·control.tar.xz
3	-rw-r--r--···0········0········0··194~~0956~~·2023-08-29·09:00:00.000000·data.tar.xz	3	-rw-r--r--···0········0········0··1942120·2023-08-29·09:00:00.000000·data.tar.xz


Offset 5, 21 lines modified		Offset 5, 21 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2ddeform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options]	6	.B··mia\-2ddeform·\-i·<in\-file>·\-o·<out\-file>·\-t·<transformation>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2ddeform	8	.B·mia\-2ddeform
9	This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.·Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation·formula·is·'x·->·x·-·v(x)'	9	This·program·is·used·to·deform·a·2D·image·using·a·deformation·vector·field.·Input·image·and·deformation·field·must·be·of·the·same·size.·The·transformation·formula·is·'x·->·x·-·v(x)'
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(~~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	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	15	.IP·"\-o·\-\-out-file=(required,·output);·io"
16	transformed··image	16	transformed··image
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-t·\-\-transformation=(~~inp~~ut,·requi~~red~~);·io"	18	.IP·"\-t·\-\-transformation=(required,·input);·io"
19	transformation·vector·field	19	transformation·vector·field
20	·For·supported·file·types·see·PLUGINS:2dvf/io	20	·For·supported·file·types·see·PLUGINS:2dvf/io
21	.IP·"\-p·\-\-interpolator=bspline:d=3"	21	.IP·"\-p·\-\-interpolator=bspline:d=3"
22	image·interpolator·kernel	22	image·interpolator·kernel
23	·For·supported·plugins·see·PLUGINS:1d/splinekernel	23	·For·supported·plugins·see·PLUGINS:1d/splinekernel
24	.RE	24	.RE
25	.SS·Help·&·Info	25	.SS·Help·&·Info


Offset 5, 21 lines modified		Offset 5, 21 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2ddistance·\-i·<in\-file>·\-d·<distance\-file>·\-o·<out\-file>·[options]	6	.B··mia\-2ddistance·\-i·<in\-file>·\-d·<distance\-file>·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2ddistance	8	.B·mia\-2ddistance
9	This·program·evaluate·the·average·or·maximum·distance·of·a·mask·given·by·a·binary·image·to·an·image·representing·a·distance·map·and·prints·the·result·to·stdout.·The·distance·map·can·be·obtained·by·running·the·filter·'diatance'·on·a·binary·image.	9	This·program·evaluate·the·average·or·maximum·distance·of·a·mask·given·by·a·binary·image·to·an·image·representing·a·distance·map·and·prints·the·result·to·stdout.·The·distance·map·can·be·obtained·by·running·the·filter·'diatance'·on·a·binary·image.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(~~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 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=(ou~~tput~~,·requ~~ired~~);·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, 24 lines modified		Offset 64, 24 lines modified

64	.IP·"···\-\-version"	64	.IP·"···\-\-version"
65	print·the·version·number·and·exit	65	print·the·version·number·and·exit

66	.RE	66	.RE
67	.SS·IO	67	.SS·IO
68	.RS	68	.RS
69	.IP·"\-i·\-\-in-image=(~~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=(ou~~tput~~,·requ~~ired~~);·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=(ou~~tput~~,·requ~~ired~~);·io"	78	.IP·"\-O·\-\-inverse-transform=(required,·output);·io"
79	inverse·output·transformation	79	inverse·output·transformation
80	·For·supported·file·types·see·PLUGINS:2dtransform/io	80	·For·supported·file·types·see·PLUGINS:2dtransform/io
81	.RE	81	.RE
82	.SS·Processing	82	.SS·Processing
83	.RS	83	.RS
84	.IP·"···\-\-threads=\-1"	84	.IP·"···\-\-threads=\-1"
85	Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).	85	Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).


Offset 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 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 5, 18 lines modified		Offset 5, 18 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dimagecombine\-dice·\-1·<in\-file\-1>·\-2·<in\-file\-2>·[options]	6	.B··mia\-2dimagecombine\-dice·\-1·<in\-file\-1>·\-2·<in\-file\-2>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimagecombine\-dice	8	.B·mia\-2dimagecombine\-dice
9	This·program·evaluate·the·dice·index·of·two·binary·masks·given·as·binary·images.·The·result·is·written·to·stdout.	9	This·program·evaluate·the·dice·index·of·two·binary·masks·given·as·binary·images.·The·result·is·written·to·stdout.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-1·\-\-in-file-1=(~~req~~uired,·in~~put~~);·io"	12	.IP·"\-1·\-\-in-file-1=(input,·required);·io"
13	input·image·1	13	input·image·1
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-2·\-\-in-file-2=(~~req~~uired,·in~~put~~);·io"	15	.IP·"\-2·\-\-in-file-2=(input,·required);·io"
16	input·image·2	16	input·image·2
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 7, 15 lines modified		Offset 7, 15 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=(required,·output);·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
Offset 348, 15 lines modified		Offset 348, 15 lines modified
348	.TP·10	348	.TP·10
349	.B·combiner	349	.B·combiner
350	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:·	350	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:·
351	.P	351	.P
352	.RS·14	352	.RS·14
353	.I	353	.I
354	image	354	image
355	=(~~inp~~ut,·requi~~red~~,·io)	355	=(required,·input,·io)
356	.RS·2	356	.RS·2
357	second·image·that·is·needed·in·the·combiner.	357	second·image·that·is·needed·in·the·combiner.
358	For·supported·file·types·see·PLUGINS:2dimage/io	358	For·supported·file·types·see·PLUGINS:2dimage/io

359	.RE	359	.RE
360	.RE	360	.RE
361	.RS·14	361	.RS·14
Offset 692, 15 lines modified		Offset 692, 15 lines modified
692	.TP·10	692	.TP·10
693	.B·labelmap	693	.B·labelmap
694	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·	694	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
695	.P	695	.P
696	.RS·14	696	.RS·14
697	.I	697	.I
698	map	698	map
699	=(~~inp~~ut,·requi~~red~~,·string)	699	=(required,·input,·string)
700	.RS·2	700	.RS·2
701	Label·mapping·file.	701	Label·mapping·file.

702	.RE	702	.RE
703	.RE	703	.RE
704	.TP·10	704	.TP·10
705	.B·labelscale	705	.B·labelscale
Offset 718, 15 lines modified		Offset 718, 15 lines modified
718	.TP·10	718	.TP·10
719	.B·load	719	.B·load
720	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·	720	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
721	.P	721	.P
722	.RS·14	722	.RS·14
723	.I	723	.I
724	file	724	file
725	=(~~inp~~ut,·requi~~red~~,·io)	725	=(required,·input,·io)
726	.RS·2	726	.RS·2
727	name·of·the·input·file·to·load·from..	727	name·of·the·input·file·to·load·from..
728	For·supported·file·types·see·PLUGINS:2dimage/io	728	For·supported·file·types·see·PLUGINS:2dimage/io

729	.RE	729	.RE
730	.RE	730	.RE
731	.TP·10	731	.TP·10
Offset 757, 15 lines modified		Offset 757, 15 lines modified
757	.RE	757	.RE

758	.RE	758	.RE
759	.RE	759	.RE
760	.RS·14	760	.RS·14
761	.I	761	.I
762	input	762	input
763	=(~~inp~~ut,·requi~~red~~,·io)	763	=(required,·input,·io)
764	.RS·2	764	.RS·2
765	second·input·image·file·name.	765	second·input·image·file·name.
766	For·supported·file·types·see·PLUGINS:2dimage/io	766	For·supported·file·types·see·PLUGINS:2dimage/io

767	.RE	767	.RE
768	.RE	768	.RE
769	.RS·14	769	.RS·14
Offset 780, 25 lines modified		Offset 780, 25 lines modified
780	.TP·10	780	.TP·10
781	.B·maxflow	781	.B·maxflow
782	This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·	782	This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·
783	.P	783	.P
784	.RS·14	784	.RS·14
785	.I	785	.I
786	sink-flow	786	sink-flow
787	=(~~inp~~ut,·requi~~red~~,·io)	787	=(required,·input,·io)
788	.RS·2	788	.RS·2
789	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.	789	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.
790	For·supported·file·types·see·PLUGINS:2dimage/io	790	For·supported·file·types·see·PLUGINS:2dimage/io

791	.RE	791	.RE
792	.RE	792	.RE
793	.RS·14	793	.RS·14
794	.I	794	.I
795	source-flow	795	source-flow
796	=(~~inp~~ut,·requi~~red~~,·io)	796	=(required,·input,·io)
797	.RS·2	797	.RS·2
798	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.	798	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.
799	For·supported·file·types·see·PLUGINS:2dimage/io	799	For·supported·file·types·see·PLUGINS:2dimage/io

800	.RE	800	.RE
801	.RE	801	.RE
802	.TP·10	802	.TP·10
Offset 987, 15 lines modified		Offset 987, 15 lines modified
987	For·supported·plug-ins·see·PLUGINS:2dimage/shape	987	For·supported·plug-ins·see·PLUGINS:2dimage/shape

988	.RE	988	.RE
989	.RE	989	.RE
990	.RS·14	990	.RS·14
991	.I	991	.I
992	seed	992	seed
993	=(~~inp~~ut,·requi~~red~~,·io)	993	=(required,·input,·io)
994	.RS·2	994	.RS·2
995	seed·image·(bit·valued).	995	seed·image·(bit·valued).
996	For·supported·file·types·see·PLUGINS:2dimage/io	996	For·supported·file·types·see·PLUGINS:2dimage/io

997	.RE	997	.RE
998	.RE	998	.RE
999	.TP·10	999	.TP·10
Offset 1168, 15 lines modified		Offset 1168, 15 lines modified
1168	For·supported·plug-ins·see·PLUGINS:2dimage/shape	1168	For·supported·plug-ins·see·PLUGINS:2dimage/shape

1169	.RE	1169	.RE
1170	.RE	1170	.RE
1171	.RS·14	1171	.RS·14
Max diff block lines reached; 494/3504 bytes (14.10%) of diff not shown.


Offset 5, 15 lines modified		Offset 5, 15 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dimageseries\-maximum\-intensity\-projection·\-o·<out\-file>·[options]	6	.B··mia\-2dimageseries\-maximum\-intensity\-projection·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimageseries\-maximum\-intensity\-projection	8	.B·mia\-2dimageseries\-maximum\-intensity\-projection
9	This·program·is·used·to·evaluate·the·per-pixel·maximum·intensity·of·an·image·series.	9	This·program·is·used·to·evaluate·the·per-pixel·maximum·intensity·of·an·image·series.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	12	.IP·"\-o·\-\-out-file=(output,·required);·io"
13	output·image	13	output·image
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.RE	15	.RE
16	.SS·Help·&·Info	16	.SS·Help·&·Info
17	.RS	17	.RS
18	.IP·"\-V·\-\-verbose=warning"	18	.IP·"\-V·\-\-verbose=warning"
19	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	19	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 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 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dmultiimageto3d	8	.B·mia\-2dmultiimageto3d
9	This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image.	9	This·program·is·used·to·convert·a·2D·multi-image·file·to·a·3D·image.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(input,·required);·io"	12	.IP·"\-i·\-\-in-file=(input,·required);·io"
13	input·images	13	input·images
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-o·\-\-out-file=(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: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 146, 139 lines modified		Offset 146, 139 lines modified
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)·····1474·2023-08-29·09:00:00.000000·./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)·····1565·2023-08-29·09:00:00.000000·./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)·····1745·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddeform.1.gz	153	-rw-r--r--···0·root·········(0)·root·········(0)·····1746·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddeform.1.gz
154	-rw-r--r--···0·root·········(0)·root·········(0)·····1691·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddistance.1.gz	154	-rw-r--r--···0·root·········(0)·root·········(0)·····1690·2023-08-29·09:00:00.000000·./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)·····3498·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz	156	-rw-r--r--···0·root·········(0)·root·········(0)·····3499·2023-08-29·09:00:00.000000·./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)·····1543·2023-08-29·09:00:00.000000·./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)·····1805·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz
160	-rw-r--r--···0·root·········(0)·root·········(0)·····1592·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz	160	-rw-r--r--···0·root·········(0)·root·········(0)·····1590·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz
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)·····1620·2023-08-29·09:00:00.000000·./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)·····6185·2023-08-29·09:00:00.000000·./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
166	-rw-r--r--···0·root·········(0)·root·········(0)·····6379·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilterstack.1.gz	166	-rw-r--r--···0·root·········(0)·root·········(0)·····6379·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilterstack.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	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
168	-rw-r--r--···0·root·········(0)·root·········(0)·····5278·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageregistration.1.gz	168	-rw-r--r--···0·root·········(0)·root·········(0)·····5276·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageregistration.1.gz
169	-rw-r--r--···0·root·········(0)·root·········(0)·····1490·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageselect.1.gz	169	-rw-r--r--···0·root·········(0)·root·········(0)·····1490·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageselect.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	170	-rw-r--r--···0·root·········(0)·root·········(0)·····1426·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz
171	-rw-r--r--···0·root·········(0)·root·········(0)·····1946·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz	171	-rw-r--r--···0·root·········(0)·root·········(0)·····1946·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagestack-cmeans.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	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
173	-rw-r--r--···0·root·········(0)·root·········(0)·····1672·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dlerp.1.gz	173	-rw-r--r--···0·root·········(0)·root·········(0)·····1669·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dlerp.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	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)·····2777·2023-08-29·09:00:00.000000·./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)·····5396·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageregistration.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
177	-rw-r--r--···0·root·········(0)·root·········(0)·····1856·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz	177	-rw-r--r--···0·root·········(0)·root·········(0)·····1861·2023-08-29·09:00:00.000000·./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)·····1815·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz
181	-rw-r--r--···0·root·········(0)·root·········(0)·····1733·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-segment.1.gz	181	-rw-r--r--···0·root·········(0)·root·········(0)·····1738·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-segment.1.gz
182	-rw-r--r--···0·root·········(0)·root·········(0)·····6381·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyoica-full.1.gz	182	-rw-r--r--···0·root·········(0)·root·········(0)·····6387·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyoica-full.1.gz
183	-rw-r--r--···0·root·········(0)·root·········(0)·····5451·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz	183	-rw-r--r--···0·root·········(0)·root·········(0)·····5456·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz


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 13, 18 lines modified		Offset 13, 18 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=(ou~~tput~~,·requ~~ired~~);·io"	22	.IP·"\-o·\-\-out-file=(required,·output);·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 5, 21 lines modified		Offset 5, 21 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dsegmentcropbox·\-i·<in\-file>·\-o·<out\-file>·[options]	6	.B··mia\-2dsegmentcropbox·\-i·<in\-file>·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dsegmentcropbox	8	.B·mia\-2dsegmentcropbox
9	This·program·is·used·on·a·segmentation·set·and·evaluates·a·bounding·box·that·encloses·the·segmentation·in·all·slices.·This·bounding·box·is·then·used·to·crop·the·original·images,·correct·the·segmentation·and·store·a·new·segmentation·set·with·the·cropped·images.·The·cropped·images·will·be·of·the·same·type·as·the·original·images.·If·no·segmentation·is·given·in·the·set,·the·result·is·undefined.	9	This·program·is·used·on·a·segmentation·set·and·evaluates·a·bounding·box·that·encloses·the·segmentation·in·all·slices.·This·bounding·box·is·then·used·to·crop·the·original·images,·correct·the·segmentation·and·store·a·new·segmentation·set·with·the·cropped·images.·The·cropped·images·will·be·of·the·same·type·as·the·original·images.·If·no·segmentation·is·given·in·the·set,·the·result·is·undefined.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·string"	12	.IP·"\-i·\-\-in-file=(required,·input);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-p·\-\-override-imagepath"	14	.IP·"\-p·\-\-override-imagepath"
15	Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation·set,·assume·the·files·are·located·in·the·current·directory	15	Instead·of·using·the·path·of·the·image·files·as·given·in·the·segmentation·set,·assume·the·files·are·located·in·the·current·directory

16	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	16	.IP·"\-o·\-\-out-file=(required,·output);·string"
17	output·segmentation·set	17	output·segmentation·set

18	.IP·"\-c·\-\-cropped-base=crop"	18	.IP·"\-c·\-\-cropped-base=crop"
19	Base·name·for·the·cropped·image·files,·the·file·type·and·numbering·will·be·based·on·the·input·image·file·type·and·numbering.	19	Base·name·for·the·cropped·image·files,·the·file·type·and·numbering·will·be·based·on·the·input·image·file·type·and·numbering.

20	.IP·"\-e·\-\-enlarge=5"	20	.IP·"\-e·\-\-enlarge=5"
21	Enlarge·the·area·around·the·obtained·sbounding·box·by·this·number·of·pixels·in·each·direction	21	Enlarge·the·area·around·the·obtained·sbounding·box·by·this·number·of·pixels·in·each·direction


Offset 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


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=(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=(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 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=(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=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 43, 18 lines modified		Offset 43, 18 lines modified

43	.IP·"\-T·\-\-rho-thresh=0.85"	43	.IP·"\-T·\-\-rho-thresh=0.85"
44	correlation·threshold·for·neighborhood·analysis	44	correlation·threshold·for·neighborhood·analysis

45	.RE	45	.RE
46	.SS·File-IO	46	.SS·File-IO
47	.RS	47	.RS
48	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·string"	48	.IP·"\-i·\-\-in-file=(required,·input);·string"
49	input·perfusion·data·set	49	input·perfusion·data·set

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

54	.IP·"···\-\-save-cropped=(output);·string"	54	.IP·"···\-\-save-cropped=(output);·string"
55	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base	55	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base


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

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


Offset 18, 15 lines modified		Offset 18, 15 lines modified
18	.SH·OPTIONS	18	.SH·OPTIONS
19	.SS·	19	.SS·
20	File-IO	20	File-IO
21	.RS	21	.RS
22	.IP·"\-i·\-\-in-file=(required,·input);·string"	22	.IP·"\-i·\-\-in-file=(required,·input);·string"
23	input·perfusion·data·set	23	input·perfusion·data·set

24	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	24	.IP·"\-o·\-\-out-file=(required,·output);·string"
25	output·perfusion·data·set	25	output·perfusion·data·set

26	.IP·"\-r·\-\-registered=reg"	26	.IP·"\-r·\-\-registered=reg"
27	file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set	27	file·name·base·for·registered·files,·the·image·file·type·is·the·same·as·given·in·the·input·data·set

28	.RE	28	.RE
29	.SS·	29	.SS·


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=(~~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=(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	.RE	26	.RE
27	.SS·	27	.SS·


Offset 10, 15 lines modified		Offset 10, 15 lines modified
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·	11	.SS·
12	File-IO	12	File-IO
13	.RS	13	.RS
14	.IP·"\-i·\-\-in-file=(input,·required);·string"	14	.IP·"\-i·\-\-in-file=(input,·required);·string"
15	input·perfusion·data·set	15	input·perfusion·data·set

16	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·string"	16	.IP·"\-o·\-\-out-file=(output,·required);·string"
17	output·perfusion·data·set	17	output·perfusion·data·set

18	.IP·"···\-\-out-filebase=reg"	18	.IP·"···\-\-out-filebase=reg"
19	file·name·basae·for·registered·files,·file·type·is·deducted·from·the·image·file·type·in·the·input·data·set.	19	file·name·basae·for·registered·files,·file·type·is·deducted·from·the·image·file·type·in·the·input·data·set.

20	.RE	20	.RE
21	.SS·	21	.SS·


Offset 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dsegment\-fuzzyw·\-i·<in\-file>·[options]	6	.B··mia\-2dsegment\-fuzzyw·\-i·<in\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dsegment\-fuzzyw	8	.B·mia\-2dsegment\-fuzzyw
9	This·program·is·a··implementation·of·a·fuzzy·c-means·segmentation·algorithm	9	This·program·is·a··implementation·of·a·fuzzy·c-means·segmentation·algorithm
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File·I/O	11	.SS·File·I/O
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·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·"\-c·\-\-cls-file=(output);·io"	16	.IP·"\-c·\-\-cls-file=(output);·io"
17	class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values	17	class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values
18	·For·supported·file·types·see·PLUGINS:2dimage/io	18	·For·supported·file·types·see·PLUGINS:2dimage/io
19	.IP·"\-o·\-\-out-file=(output);·io"	19	.IP·"\-o·\-\-out-file=(output);·io"
20	B\-field·corrected·image	20	B\-field·corrected·image
Offset 374, 15 lines modified		Offset 374, 15 lines modified
374	.TP·10	374	.TP·10
375	.B·combiner	375	.B·combiner
376	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:·	376	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:·
377	.P	377	.P
378	.RS·14	378	.RS·14
379	.I	379	.I
380	image	380	image
381	=(~~inp~~ut,·requi~~red~~,·io)	381	=(required,·input,·io)
382	.RS·2	382	.RS·2
383	second·image·that·is·needed·in·the·combiner.	383	second·image·that·is·needed·in·the·combiner.
384	For·supported·file·types·see·PLUGINS:2dimage/io	384	For·supported·file·types·see·PLUGINS:2dimage/io

385	.RE	385	.RE
386	.RE	386	.RE
387	.RS·14	387	.RS·14
Offset 718, 15 lines modified		Offset 718, 15 lines modified
718	.TP·10	718	.TP·10
719	.B·labelmap	719	.B·labelmap
720	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·	720	Image·filter·to·remap·label·id's.·Only·applicable·to·images·with·integer·valued·intensities/labels.,·supported·parameters·are:·
721	.P	721	.P
722	.RS·14	722	.RS·14
723	.I	723	.I
724	map	724	map
725	=(~~inp~~ut,·requi~~red~~,·string)	725	=(required,·input,·string)
726	.RS·2	726	.RS·2
727	Label·mapping·file.	727	Label·mapping·file.

728	.RE	728	.RE
729	.RE	729	.RE
730	.TP·10	730	.TP·10
731	.B·labelscale	731	.B·labelscale
Offset 744, 15 lines modified		Offset 744, 15 lines modified
744	.TP·10	744	.TP·10
745	.B·load	745	.B·load
746	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·	746	Load·the·input·image·from·a·file·and·use·it·to·replace·the·current·image·in·the·pipeline.,·supported·parameters·are:·
747	.P	747	.P
748	.RS·14	748	.RS·14
749	.I	749	.I
750	file	750	file
751	=(~~inp~~ut,·requi~~red~~,·io)	751	=(required,·input,·io)
752	.RS·2	752	.RS·2
753	name·of·the·input·file·to·load·from..	753	name·of·the·input·file·to·load·from..
754	For·supported·file·types·see·PLUGINS:2dimage/io	754	For·supported·file·types·see·PLUGINS:2dimage/io

755	.RE	755	.RE
756	.RE	756	.RE
757	.TP·10	757	.TP·10
Offset 783, 15 lines modified		Offset 783, 15 lines modified
783	.RE	783	.RE

784	.RE	784	.RE
785	.RE	785	.RE
786	.RS·14	786	.RS·14
787	.I	787	.I
788	input	788	input
789	=(~~inp~~ut,·requi~~red~~,·io)	789	=(required,·input,·io)
790	.RS·2	790	.RS·2
791	second·input·image·file·name.	791	second·input·image·file·name.
792	For·supported·file·types·see·PLUGINS:2dimage/io	792	For·supported·file·types·see·PLUGINS:2dimage/io

793	.RE	793	.RE
794	.RE	794	.RE
795	.RS·14	795	.RS·14
Offset 806, 25 lines modified		Offset 806, 25 lines modified
806	.TP·10	806	.TP·10
807	.B·maxflow	807	.B·maxflow
808	This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·	808	This·filter·implements·the·uses·the·max-flow·min-cut·algorithmfor·image·segmentation,·supported·parameters·are:·
809	.P	809	.P
810	.RS·14	810	.RS·14
811	.I	811	.I
812	sink-flow	812	sink-flow
813	=(~~inp~~ut,·requi~~red~~,·io)	813	=(required,·input,·io)
814	.RS·2	814	.RS·2
815	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.	815	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·sink.
816	For·supported·file·types·see·PLUGINS:2dimage/io	816	For·supported·file·types·see·PLUGINS:2dimage/io

817	.RE	817	.RE
818	.RE	818	.RE
819	.RS·14	819	.RS·14
820	.I	820	.I
821	source-flow	821	source-flow
822	=(~~inp~~ut,·requi~~red~~,·io)	822	=(required,·input,·io)
823	.RS·2	823	.RS·2
824	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.	824	Image·of·float·type·to·define·the·per\-pixel·flow·to·the·source.
825	For·supported·file·types·see·PLUGINS:2dimage/io	825	For·supported·file·types·see·PLUGINS:2dimage/io

826	.RE	826	.RE
827	.RE	827	.RE
828	.TP·10	828	.TP·10
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	=(ou~~tput~~,·requ~~ired~~,·io)	858	=(required,·output,·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
Max diff block lines reached; 1357/4902 bytes (27.68%) of diff not shown.


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=(~~req~~uired,·in~~put~~);·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=(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=(~~inp~~ut,·requi~~red~~);·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=(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=(required,·output);·io"	16	.IP·"\-o·\-\-out-file=(required,·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	.RE	19	.RE
20	.SS·Help·&·Info	20	.SS·Help·&·Info


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=(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·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 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 24, 24 lines modified		Offset 24, 24 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=(requ~~ired~~,·ou~~tput~~);·string"	37	.IP·"\-o·\-\-out-file=(output,·required);·string"
38	output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.	38	output·file·name·to·write·the·distances·to.·The·output·file·is·a·csv·file,·containing·distances·listed·for·each·label.

39	.RE	39	.RE
40	.SS·Help·&·Info	40	.SS·Help·&·Info
41	.RS	41	.RS
42	.IP·"\-V·\-\-verbose=warning"	42	.IP·"\-V·\-\-verbose=warning"
43	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	43	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 12, 15 lines modified		Offset 12, 15 lines modified
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-file=(required,·input);·string"	13	.IP·"\-i·\-\-in-file=(required,·input);·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=(required,·input);·string"	15	.IP·"\-r·\-\-ref-file=(required,·input);·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:


Offset 30, 15 lines modified		Offset 30, 15 lines modified
30	.RS	30	.RS
31	.IP·"\-i·\-\-in-file=(input);·string"	31	.IP·"\-i·\-\-in-file=(input);·string"
32	input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.	32	input·point·set,·if·this·parameter·is·given·a·sparse·evaluation·of·the·quantity·will·be·done,·otherwise·the·quantity·is·evaluated·for·each·grid·point·of·the·transformation·range.

33	.IP·"\-o·\-\-out-file=(required,·output);·string"	33	.IP·"\-o·\-\-out-file=(required,·output);·string"
34	output·strains·file,·for·a·format·description·see·above.	34	output·strains·file,·for·a·format·description·see·above.

35	.IP·"\-t·\-\-transformation=(~~inp~~ut,·requi~~red~~);·io"	35	.IP·"\-t·\-\-transformation=(required,·input);·io"
36	transformation·of·which·the·quantity·will·be·evaluated.	36	transformation·of·which·the·quantity·will·be·evaluated.
37	·For·supported·file·types·see·PLUGINS:3dtransform/io	37	·For·supported·file·types·see·PLUGINS:3dtransform/io
38	.RE	38	.RE
39	.SS·	39	.SS·
40	Parameters	40	Parameters
41	.RS	41	.RS
42	.IP·"\-q·\-\-quantity=strain"	42	.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=(~~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 14, 18 lines modified		Offset 14, 18 lines modified
14	.UE	14	.UE
15	.RE	15	.RE

16	·It·uses·SSD·as·the·sole·registration·criterion.	16	·It·uses·SSD·as·the·sole·registration·criterion.
17	.SH·OPTIONS	17	.SH·OPTIONS
18	.SS·File-IO	18	.SS·File-IO
19	.RS	19	.RS
20	.IP·"\-i·\-\-in-image=(~~inp~~ut,·requi~~red~~);·io"	20	.IP·"\-i·\-\-in-image=(required,·input);·io"
21	input·image	21	input·image
22	·For·supported·file·types·see·PLUGINS:3dimage/io	22	·For·supported·file·types·see·PLUGINS:3dimage/io
23	.IP·"\-r·\-\-ref-image=(~~inp~~ut,·requi~~red~~);·io"	23	.IP·"\-r·\-\-ref-image=(required,·input);·io"
24	reference·image·	24	reference·image·
25	·For·supported·file·types·see·PLUGINS:3dimage/io	25	·For·supported·file·types·see·PLUGINS:3dimage/io
26	.IP·"\-o·\-\-out-transformation=(required,·output);·io"	26	.IP·"\-o·\-\-out-transformation=(required,·output);·io"
27	output·transformation·comprising·the·registering·transformation·field	27	output·transformation·comprising·the·registering·transformation·field
28	·For·supported·file·types·see·PLUGINS:3dtransform/io	28	·For·supported·file·types·see·PLUGINS:3dtransform/io
29	.IP·"\-d·\-\-out-image=(output);·io"	29	.IP·"\-d·\-\-out-image=(output);·io"
30	save·deformed·image	30	save·deformed·image


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-3dgetslice	8	.B·mia\-3dgetslice
9	This·program·is·used·to·extract·2D·slices·from·a·3D·data·set·and·store·them·in·separate·files.·Output·files·will·be·numbered·according·to·their·slice·index.	9	This·program·is·used·to·extract·2D·slices·from·a·3D·data·set·and·store·them·in·separate·files.·Output·files·will·be·numbered·according·to·their·slice·index.
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·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=(requ~~ired~~,·ou~~tput~~);·io"	15	.IP·"\-o·\-\-out-file=(output,·required);·io"
16	output·image(s).·If·number·!=·1·than·this·is·used·as·a·base·name·and·should·be·given·without·extension·since·this·will·be·based·on·the·'\-\-type'·option.·If·number=1·then·this·exact·file·name·will·be·used.	16	output·image(s).·If·number·!=·1·than·this·is·used·as·a·base·name·and·should·be·given·without·extension·since·this·will·be·based·on·the·'\-\-type'·option.·If·number=1·then·this·exact·file·name·will·be·used.
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-t·\-\-type=png"	18	.IP·"\-t·\-\-type=png"
19	output·file·type·for·number·!=·1	19	output·file·type·for·number·!=·1

20	.RS·10	20	.RS·10
21	.I	21	.I