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Offset 2, 8 lines modified		Offset 2, 8 lines modified
2	·436ccfd672256f7316d377a9488b8268·89312180·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_armhf.deb	2	·436ccfd672256f7316d377a9488b8268·89312180·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_armhf.deb
3	·e9a80d7353aeb08464b51eb12a154019·4125212·libs·optional·libmia-2.4-4_2.4.7-13_armhf.deb	3	·e9a80d7353aeb08464b51eb12a154019·4125212·libs·optional·libmia-2.4-4_2.4.7-13_armhf.deb
4	·781a7255a4d9f4c6bdbcdc737631225a·205268·libdevel·optional·libmia-2.4-dev_2.4.7-13_armhf.deb	4	·781a7255a4d9f4c6bdbcdc737631225a·205268·libdevel·optional·libmia-2.4-dev_2.4.7-13_armhf.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	·33d8090fb6312d4f34354418ab27a438·34631944·debug·optional·mia-tools-dbgsym_2.4.7-13_armhf.deb	7	·33d8090fb6312d4f34354418ab27a438·34631944·debug·optional·mia-tools-dbgsym_2.4.7-13_armhf.deb
8	·391a637d2504ceec837f73882035078d·96428·doc·optional·mia-tools-doc_2.4.7-13_all.deb	8	·391a637d2504ceec837f73882035078d·96428·doc·optional·mia-tools-doc_2.4.7-13_all.deb
9	·c~~bd69d~~7a~~e66fd127~~d~~4458e51005f9~~ceb·1732~~056~~·science·optional·mia-tools_2.4.7-13_armhf.deb	9	·ac7af3a7f7e3294ad53ab823eb8acc28·1732608·science·optional·mia-tools_2.4.7-13_armhf.deb


Offset 1, 3 lines modified		Offset 1, 3 lines modified
1	-rw-r--r--···0········0········0········4·2023-08-29·09:00:00.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2023-08-29·09:00:00.000000·debian-binary
2	-rw-r--r--···0········0········0·····7576·2023-08-29·09:00:00.000000·control.tar.xz	2	-rw-r--r--···0········0········0·····7568·2023-08-29·09:00:00.000000·control.tar.xz
3	-rw-r--r--···0········0········0··1724288·2023-08-29·09:00:00.000000·data.tar.xz	3	-rw-r--r--···0········0········0··1724848·2023-08-29·09:00:00.000000·data.tar.xz


Offset 5, 21 lines modified		Offset 5, 21 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-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=(~~req~~uired,·in~~put~~);·io"	12	.IP·"\-1·\-\-file1=(input,·required);·io"
13	input·mask·image·1	13	input·mask·image·1
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-2·\-\-file2=(~~req~~uired,·in~~put~~);·io"	15	.IP·"\-2·\-\-file2=(input,·required);·io"
16	input·mask·image·2	16	input·mask·image·2
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	18	.IP·"\-o·\-\-out-file=(required,·output);·io"
19	output·mask·image	19	output·mask·image
20	·For·supported·file·types·see·PLUGINS:2dimage/io	20	·For·supported·file·types·see·PLUGINS:2dimage/io
21	.IP·"\-p·\-\-operation=nor"	21	.IP·"\-p·\-\-operation=nor"
22	Operation·to·be·applied	22	Operation·to·be·applied

23	.RS·10	23	.RS·10
24	.I	24	.I


Offset 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=(~~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·"\-o·\-\-out-file=(required,·output);·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=(~~req~~uired,·in~~put~~);·io"	18	.IP·"\-t·\-\-transformation=(input,·required);·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, 18 lines modified		Offset 5, 18 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=(~~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·"\-d·\-\-distance-file=(~~inp~~ut,·requi~~red~~);·io"	15	.IP·"\-d·\-\-distance-file=(required,·input);·io"
16	distance·field·image·(floating·point)	16	distance·field·image·(floating·point)
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-o·\-\-out-file=(output,·required);·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


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=(output,·required);·string"	32	.IP·"\-o·\-\-out-file=(output,·required);·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=(output,·required);·io"	75	.IP·"\-o·\-\-transform=(output,·required);·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=(output,·required);·io"	78	.IP·"\-O·\-\-inverse-transform=(output,·required);·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·(test)·image·to·be·registered	21	input·(test)·image·to·be·registered
22	·For·supported·file·types·see·PLUGINS:2dimage/io	22	·For·supported·file·types·see·PLUGINS:2dimage/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:2dimage/io	25	·For·supported·file·types·see·PLUGINS:2dimage/io
26	.IP·"\-o·\-\-out-transformation=(output);·io"	26	.IP·"\-o·\-\-out-transformation=(output);·io"
27	output·transformation·comprising·the·registration	27	output·transformation·comprising·the·registration
28	·For·supported·file·types·see·PLUGINS:2dvf/io	28	·For·supported·file·types·see·PLUGINS:2dvf/io
29	.IP·"\-d·\-\-out-image=(output);·io"	29	.IP·"\-d·\-\-out-image=(output);·io"
30	output·image·deformed·according·to·the·transformation	30	output·image·deformed·according·to·the·transformation


Offset 11, 15 lines modified		Offset 11, 15 lines modified
11	.RS	11	.RS
12	.IP·"\-i·\-\-src-file=(required,·input);·io"	12	.IP·"\-i·\-\-src-file=(required,·input);·io"
13	input·image	13	input·image
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-r·\-\-ref-file=(required,·input);·io"	15	.IP·"\-r·\-\-ref-file=(required,·input);·io"
16	reference·image	16	reference·image
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	18	.IP·"\-o·\-\-out-file=(output,·required);·io"
19	output·force·norm·image	19	output·force·norm·image
20	·For·supported·file·types·see·PLUGINS:2dimage/io	20	·For·supported·file·types·see·PLUGINS:2dimage/io
21	.IP·"\-c·\-\-cost=(required);·string"	21	.IP·"\-c·\-\-cost=(required);·string"
22	cost·function·to·use	22	cost·function·to·use

23	.RE	23	.RE
24	.SS·Help·&·Info	24	.SS·Help·&·Info


Offset 15, 18 lines modified		Offset 15, 18 lines modified
15	.RE	15	.RE

16	·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.	16	·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.
17	.SH·OPTIONS	17	.SH·OPTIONS
18	.SS·	18	.SS·
19	File-IO	19	File-IO
20	.RS	20	.RS
21	.IP·"\-i·\-\-in-file=(~~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=(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·registered·files	26	file·name·base·for·registered·files

27	.RE	27	.RE
28	.SS·	28	.SS·


Offset 7, 18 lines modified		Offset 7, 18 lines modified
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimagefilter	8	.B·mia\-2dimagefilter
9	This·program·runs·a·series·filters·on·a·given·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·Ware·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run	9	This·program·runs·a·series·filters·on·a·given·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·Ware·run·in·the·order·in·which·they·are·given.·To·obtain·a·list·of·available·filters·you·may·run
10	···'mia-plugin-help·filter/2dimage'	10	···'mia-plugin-help·filter/2dimage'
11	from·the·command·line	11	from·the·command·line
12	.SH·OPTIONS	12	.SH·OPTIONS
13	.RS	13	.RS
14	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·io"	14	.IP·"\-i·\-\-in-file=(required,·input);·io"
15	input·image(s)·to·be·filtered	15	input·image(s)·to·be·filtered
16	·For·supported·file·types·see·PLUGINS:2dimage/io	16	·For·supported·file·types·see·PLUGINS:2dimage/io
17	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	17	.IP·"\-o·\-\-out-file=(required,·output);·io"
18	output·image(s)·that·have·been·filtered	18	output·image(s)·that·have·been·filtered
19	·For·supported·file·types·see·PLUGINS:2dimage/io	19	·For·supported·file·types·see·PLUGINS:2dimage/io
20	.RE	20	.RE
21	.SS·Help·&·Info	21	.SS·Help·&·Info
22	.RS	22	.RS
23	.IP·"\-V·\-\-verbose=warning"	23	.IP·"\-V·\-\-verbose=warning"
24	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	24	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 6, 15 lines modified		Offset 6, 15 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=(~~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-file=(output,·required);·io"	16	.IP·"\-o·\-\-out-file=(output,·required);·io"
17	output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option	17	output·file·name·base,·the·file·type·is·set··accurding·to·the·'type'·option
18	·For·supported·file·types·see·PLUGINS:2dimage/io	18	·For·supported·file·types·see·PLUGINS:2dimage/io
19	.IP·"\-t·\-\-type="	19	.IP·"\-t·\-\-type="
20	output·file·type,·if·not·given·the·input·type·is·used	20	output·file·type,·if·not·given·the·input·type·is·used


Offset 5, 15 lines modified		Offset 5, 15 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dimagefullstats·\-i·<in\-file>·[options]	6	.B··mia\-2dimagefullstats·\-i·<in\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimagefullstats	8	.B·mia\-2dimagefullstats
9	This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·Min·and·Max·of·the·intensity·values.	9	This·progranm·is·used·to·evaluate·some·statistics·of·an·image.·Output·is·Mean,·Variation,·Median,·Min·and·Max·of·the·intensity·values.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·io"	12	.IP·"\-i·\-\-in-file=(required,·input);·io"
13	input·image	13	input·image
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.RE	15	.RE
16	.SS·Help·&·Info	16	.SS·Help·&·Info
17	.RS	17	.RS
18	.IP·"\-V·\-\-verbose=warning"	18	.IP·"\-V·\-\-verbose=warning"
19	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	19	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 6, 24 lines modified		Offset 6, 24 lines modified
6	.B··mia\-2dimageregistration·\-i·<in\-image>·\-r·<ref\-image>·\-t·<transformation>·[options]·<PLUGINS:2dimage/fullcost>	6	.B··mia\-2dimageregistration·\-i·<in\-image>·\-r·<ref\-image>·\-t·<transformation>·[options]·<PLUGINS:2dimage/fullcost>
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimageregistration	8	.B·mia\-2dimageregistration
9	This·program·runs·registration·of·two·images·optimizing·a·transformation·of·the·given·transformation·model·by·optimizing·certain·cost·measures·that·are·given·as·free·parameters.	9	This·program·runs·registration·of·two·images·optimizing·a·transformation·of·the·given·transformation·model·by·optimizing·certain·cost·measures·that·are·given·as·free·parameters.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File-IO	11	.SS·File-IO
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-image=(~~req~~uired,·in~~put~~);·io"	13	.IP·"\-i·\-\-in-image=(input,·required);·io"
14	test·image·to·be·registered	14	test·image·to·be·registered
15	·For·supported·file·types·see·PLUGINS:2dimage/io	15	·For·supported·file·types·see·PLUGINS:2dimage/io
16	.IP·"\-r·\-\-ref-image=(~~req~~uired,·in~~put~~);·io"	16	.IP·"\-r·\-\-ref-image=(input,·required);·io"
17	reference·image·to·be·registered·to	17	reference·image·to·be·registered·to
18	·For·supported·file·types·see·PLUGINS:2dimage/io	18	·For·supported·file·types·see·PLUGINS:2dimage/io
19	.IP·"\-o·\-\-out-image=(output);·io"	19	.IP·"\-o·\-\-out-image=(output);·io"
20	registered·output·image	20	registered·output·image
21	·For·supported·file·types·see·PLUGINS:2dimage/io	21	·For·supported·file·types·see·PLUGINS:2dimage/io
22	.IP·"\-t·\-\-transformation=(requ~~ired~~,·ou~~tput~~);·io"	22	.IP·"\-t·\-\-transformation=(output,·required);·io"
23	output·transformation·comprising·the·registration	23	output·transformation·comprising·the·registration
24	·For·supported·file·types·see·PLUGINS:2dtransform/io	24	·For·supported·file·types·see·PLUGINS:2dtransform/io
25	.RE	25	.RE
26	.SS·Help·&·Info	26	.SS·Help·&·Info
27	.RS	27	.RS
28	.IP·"\-V·\-\-verbose=warning"	28	.IP·"\-V·\-\-verbose=warning"
29	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	29	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 144, 141 lines modified		Offset 144, 141 lines modified
144	-rw-r--r--···0·root·········(0)·root·········(0)·····1127·2023-08-29·09:00:00.000000·./usr/share/doc/mia-tools/copyright	144	-rw-r--r--···0·root·········(0)·root·········(0)·····1127·2023-08-29·09:00:00.000000·./usr/share/doc/mia-tools/copyright
145	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/	145	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/
146	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/	146	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/
147	-rw-r--r--···0·root·········(0)·root·········(0)······425·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/mia-tools	147	-rw-r--r--···0·root·········(0)·root·········(0)······425·2023-08-29·09:00:00.000000·./usr/share/lintian/overrides/mia-tools
148	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/	148	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/
149	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/man1/	149	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-08-29·09:00:00.000000·./usr/share/man/man1/
150	-rw-r--r--···0·root·········(0)·root·········(0)·····1474·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2davgmasked.1.gz	150	-rw-r--r--···0·root·········(0)·root·········(0)·····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)·····1570·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dbinarycombine.1.gz	151	-rw-r--r--···0·root·········(0)·root·········(0)·····1571·2023-08-29·09:00:00.000000·./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)·····1746·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddeform.1.gz	153	-rw-r--r--···0·root·········(0)·root·········(0)·····1751·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddeform.1.gz
154	-rw-r--r--···0·root·········(0)·root·········(0)·····1690·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2ddistance.1.gz	154	-rw-r--r--···0·root·········(0)·root·········(0)·····1695·2023-08-29·09:00:00.000000·./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)·····1869·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz
156	-rw-r--r--···0·root·········(0)·root·········(0)·····3~~498~~·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz	156	-rw-r--r--···0·root·········(0)·root·········(0)·····3501·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz
157	-rw-r--r--···0·root·········(0)·root·········(0)·····1915·2023-08-29·09:00:00.000000·./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)·····1547·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dforce.1.gz
159	-rw-r--r--···0·root·········(0)·root·········(0)·····1810·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz	159	-rw-r--r--···0·root·········(0)·root·········(0)·····1810·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfuzzysegment.1.gz
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)·····1592·2023-08-29·09:00:00.000000·./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)·····3457·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dgroundtruthreg.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	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
163	-rw-r--r--···0·root·········(0)·root·········(0)·····1625·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecombiner.1.gz	163	-rw-r--r--···0·root·········(0)·root·········(0)·····1625·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecombiner.1.gz
164	-rw-r--r--···0·root·········(0)·root·········(0)·····1774·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecreator.1.gz	164	-rw-r--r--···0·root·········(0)·root·········(0)·····1774·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagecreator.1.gz
165	-rw-r--r--···0·root·········(0)·root·········(0)·····6179·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilter.1.gz	165	-rw-r--r--···0·root·········(0)·root·········(0)·····6177·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilter.1.gz
166	-rw-r--r--···0·root·········(0)·root·········(0)·····6374·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagefilterstack.1.gz	166	-rw-r--r--···0·root·········(0)·root·········(0)·····6373·2023-08-29·09:00:00.000000·./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)·····5276·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageregistration.1.gz	168	-rw-r--r--···0·root·········(0)·root·········(0)·····5274·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageregistration.1.gz
169	-rw-r--r--···0·root·········(0)·root·········(0)·····1494·2023-08-29·09:00:00.000000·./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)·····1428·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz
171	-rw-r--r--···0·root·········(0)·root·········(0)·····1952·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz	171	-rw-r--r--···0·root·········(0)·root·········(0)·····1955·2023-08-29·09:00:00.000000·./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)·····1674·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dlerp.1.gz	173	-rw-r--r--···0·root·········(0)·root·········(0)·····1674·2023-08-29·09:00:00.000000·./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)·····3668·2023-08-29·09:00:00.000000·./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)·····1857·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz	177	-rw-r--r--···0·root·········(0)·root·········(0)·····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)·····1817·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz	180	-rw-r--r--···0·root·········(0)·root·········(0)·····1817·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz
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	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


Offset 5, 15 lines modified		Offset 5, 15 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dmyoseries\-dice·\-i·<input>·[options]	6	.B··mia\-2dmyoseries\-dice·\-i·<input>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmyoseries\-dice	8	.B·mia\-2dmyoseries\-dice
9	This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.	9	This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-input=(~~inp~~ut,·requi~~red~~);·string"	12	.IP·"\-i·\-\-input=(required,·input);·string"
13	original·segmentation·set	13	original·segmentation·set

14	.IP·"\-k·\-\-skip=2"	14	.IP·"\-k·\-\-skip=2"
15	images·to·skip·atthe·bgin·of·the·series	15	images·to·skip·atthe·bgin·of·the·series

16	.IP·"\-r·\-\-reference=20"	16	.IP·"\-r·\-\-reference=20"
17	reference·image	17	reference·image


Offset 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 11, 15 lines modified		Offset 11, 15 lines modified
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(required,·input);·string"	12	.IP·"\-i·\-\-in-file=(required,·input);·string"
13	input·segmentation·set	13	input·segmentation·set

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

16	.IP·"\-o·\-\-out-file=(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, 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 14, 15 lines modified		Offset 14, 15 lines modified
14	.UE	14	.UE
15	.RE	15	.RE

16	·The·software·may·first·run·a·linear·registration·and·then·a·non-linear·registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all·registrations·in·parallel.	16	·The·software·may·first·run·a·linear·registration·and·then·a·non-linear·registration·or·just·one·of·the·two.This·version·of·the·program·can·run·all·registrations·in·parallel.
17	.SH·OPTIONS	17	.SH·OPTIONS
18	.SS·File-IO	18	.SS·File-IO
19	.RS	19	.RS
20	.IP·"\-i·\-\-in-file=(~~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=(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·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.	25	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.


Offset 14, 18 lines modified		Offset 14, 18 lines modified
14	.UE	14	.UE
15	.RE	15	.RE

16	This·version·of·the·program·runs·all·registrations·in·parallel.	16	This·version·of·the·program·runs·all·registrations·in·parallel.
17	.SH·OPTIONS	17	.SH·OPTIONS
18	.SS·File-IO	18	.SS·File-IO
19	.RS	19	.RS
20	.IP·"\-i·\-\-in-file=(~~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·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.	25	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.

26	.IP·"···\-\-save-cropped=(output);·string"	26	.IP·"···\-\-save-cropped=(output);·string"
27	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base	27	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base


Offset 13, 18 lines modified		Offset 13, 18 lines modified
13	Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.	13	Wollny·G,·Kellman·P,·Santos·A,·Ledesma-Carbayo·M-J,·"Automatic·Motion·Compensation·of·Free·Breathing·acquired·Myocardial·Perfusion·Data·by·using·Independent·Component·Analysis"·Medical·Image·Analysis,·2012.
14	.UE	14	.UE
15	.RE	15	.RE

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

21	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	21	.IP·"\-o·\-\-out-file=(required,·output);·string"
22	output·perfusion·data·set	22	output·perfusion·data·set

23	.IP·"\-r·\-\-registered=reg"	23	.IP·"\-r·\-\-registered=reg"
24	file·name·base·for·registered·fiels	24	file·name·base·for·registered·fiels

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


Offset 8, 18 lines modified		Offset 8, 18 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=(requ~~ired~~,·ou~~tput~~);·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

21	.IP·"···\-\-save-cropped="	21	.IP·"···\-\-save-cropped="
22	save·cropped·set·to·this·file	22	save·cropped·set·to·this·file


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=(output,·required);·string"	50	.IP·"\-o·\-\-out-file=(output,·required);·string"
51	output·perfusion·data·set	51	output·perfusion·data·set

52	.IP·"\-r·\-\-registered="	52	.IP·"\-r·\-\-registered="
53	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.	53	File·name·base·for·the·registered·images.·Image·type·and·numbering·scheme·are·taken·from·the·input·images·as·given·in·the·input·data·set.


Offset 15, 18 lines modified		Offset 15, 18 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=(ou~~tput~~,·requ~~ired~~);·string"	22	.IP·"\-o·\-\-out-file=(required,·output);·string"
23	output·perfusion·data·set	23	output·perfusion·data·set

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

26	.IP·"···\-\-save-references="	26	.IP·"···\-\-save-references="
27	save·synthetic·reference·images·to·this·file·base	27	save·synthetic·reference·images·to·this·file·base


Offset 17, 15 lines modified		Offset 17, 15 lines modified
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=(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=reg"	25	.IP·"\-r·\-\-registered=reg"
26	file·name·base·for·registered·fiels	26	file·name·base·for·registered·fiels

27	.IP·"···\-\-save-references"	27	.IP·"···\-\-save-references"
28	Save·synthetic·references·to·files·refXXXX.v	28	Save·synthetic·references·to·files·refXXXX.v


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=(required,·input);·string"	14	.IP·"\-i·\-\-in-file=(required,·input);·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 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=(~~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=(requ~~ired~~,·ou~~tput~~);·io"	22	.IP·"\-o·\-\-out-file=(output,·required);·io"
23	class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values	23	class·probability·images,·the·image·type·must·support·multiple·images·and·floating·point·values
24	·For·supported·file·types·see·PLUGINS:2dimage/io	24	·For·supported·file·types·see·PLUGINS:2dimage/io
25	.IP·"\-a·\-\-no-of-classes=3"	25	.IP·"\-a·\-\-no-of-classes=3"
26	number·of·classes	26	number·of·classes

27	.IP·"\-b·\-\-bias-correct"	27	.IP·"\-b·\-\-bias-correct"
28	apply·bias·field·correction	28	apply·bias·field·correction


Offset 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\-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=(~~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=(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\-2dseries\-sectionmask	8	.B·mia\-2dseries\-sectionmask
9	Evaluate·the·masks·for·the·sections·of·a·segmented·frame.	9	Evaluate·the·masks·for·the·sections·of·a·segmented·frame.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(required,·input);·string"	12	.IP·"\-i·\-\-in-file=(required,·input);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	14	.IP·"\-o·\-\-out-file=(output,·required);·io"
15	output·image·containing·the·mask	15	output·image·containing·the·mask
16	·For·supported·file·types·see·PLUGINS:2dimage/io	16	·For·supported·file·types·see·PLUGINS:2dimage/io
17	.IP·"\-f·\-\-frame=0"	17	.IP·"\-f·\-\-frame=0"
18	Frame·number·for·which·to·extract·the·mask	18	Frame·number·for·which·to·extract·the·mask

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


Offset 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dstack\-cmeans\-presegment·\-i·<in\-file>·\-o·<out\-mask>·\-L·<label>·[options]	6	.B··mia\-2dstack\-cmeans\-presegment·\-i·<in\-file>·\-o·<out\-mask>·\-L·<label>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dstack\-cmeans\-presegment	8	.B·mia\-2dstack\-cmeans\-presegment
9	This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram,·and·then·estimates·the·mask·for·one·(given)·class·based·on·class·probabilities.·This·program·accepts·only·images·of·eight·or·16·bit·integer·pixels.	9	This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram,·and·then·estimates·the·mask·for·one·(given)·class·based·on·class·probabilities.·This·program·accepts·only·images·of·eight·or·16·bit·integer·pixels.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File-IO	11	.SS·File-IO
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-file=(~~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·"\-p·\-\-out-probmap=(output);·string"	16	.IP·"\-p·\-\-out-probmap=(output);·string"
17	Save·probability·map·to·this·file	17	Save·probability·map·to·this·file

18	.IP·"\-t·\-\-type=png"	18	.IP·"\-t·\-\-type=png"
19	output·file·name·type	19	output·file·name·type


Offset 44, 15 lines modified		Offset 44, 15 lines modified
44	\(hy·logocal·xor	44	\(hy·logocal·xor
45	.RE	45	.RE
46	.RS·10	46	.RS·10
47	.I	47	.I
48	nxor	48	nxor
49	\(hy·logocal·nxor	49	\(hy·logocal·nxor
50	.RE	50	.RE
51	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	51	.IP·"\-o·\-\-out-file=(required,·output);·io"
52	output·mask·image	52	output·mask·image
53	·For·supported·file·types·see·PLUGINS:3dimage/io	53	·For·supported·file·types·see·PLUGINS:3dimage/io
54	.RE	54	.RE
55	.SS·Help·&·Info	55	.SS·Help·&·Info
56	.RS	56	.RS
57	.IP·"\-V·\-\-verbose=warning"	57	.IP·"\-V·\-\-verbose=warning"
58	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	58	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-3dcombine\-mr\-segmentations	8	.B·mia\-3dcombine\-mr\-segmentations
9	This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue·probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are·translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel·is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.	9	This·programs·takes·various·segmentation·masks·of·the·same·data·and·a·tissue·probability·image·set·and·combines·them·into·one·labeled·image.·The·masks·are·translated·to·labels·according·to·the·position·on·the·command·line.·If·a·voxel·is·set·as·belonging·to·more·then·one·mask,·the·probabilities·are·consulted.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(input,·required);·io"	12	.IP·"\-i·\-\-in-file=(input,·required);·io"
13	input·probability·images.·The·number·of·mask·images·must·correspond·to·the·number·of·probability·images·given·here.	13	input·probability·images.·The·number·of·mask·images·must·correspond·to·the·number·of·probability·images·given·here.
14	·For·supported·file·types·see·PLUGINS:3dimage/io	14	·For·supported·file·types·see·PLUGINS:3dimage/io
15	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	15	.IP·"\-o·\-\-out-file=(required,·output);·io"
16	output·image·that·contains·the·labeling.	16	output·image·that·contains·the·labeling.
17	·For·supported·file·types·see·PLUGINS:3dimage/io	17	·For·supported·file·types·see·PLUGINS:3dimage/io
18	.RE	18	.RE
19	.SS·Help·&·Info	19	.SS·Help·&·Info
20	.RS	20	.RS
21	.IP·"\-V·\-\-verbose=warning"	21	.IP·"\-V·\-\-verbose=warning"
22	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	22	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 70, 18 lines modified		Offset 70, 18 lines modified
70	.RS	70	.RS
71	.IP·"\-i·\-\-in-image=(input,·required);·io"	71	.IP·"\-i·\-\-in-image=(input,·required);·io"
72	test·image	72	test·image
73	·For·supported·file·types·see·PLUGINS:3dimage/io	73	·For·supported·file·types·see·PLUGINS:3dimage/io
74	.IP·"\-r·\-\-ref-image=(input,·required);·io"	74	.IP·"\-r·\-\-ref-image=(input,·required);·io"
75	reference·image	75	reference·image
76	·For·supported·file·types·see·PLUGINS:3dimage/io	76	·For·supported·file·types·see·PLUGINS:3dimage/io
77	.IP·"\-o·\-\-transform=(requ~~ired~~,·ou~~tput~~);·io"	77	.IP·"\-o·\-\-transform=(output,·required);·io"
78	output·transformation	78	output·transformation
79	·For·supported·file·types·see·PLUGINS:3dtransform/io	79	·For·supported·file·types·see·PLUGINS:3dtransform/io
80	.IP·"\-O·\-\-inverse-transform=(requ~~ired~~,·ou~~tput~~);·io"	80	.IP·"\-O·\-\-inverse-transform=(output,·required);·io"
81	inverse·output·transformation	81	inverse·output·transformation
82	·For·supported·file·types·see·PLUGINS:3dtransform/io	82	·For·supported·file·types·see·PLUGINS:3dtransform/io
83	.RE	83	.RE
84	.SS·Processing	84	.SS·Processing
85	.RS	85	.RS
86	.IP·"···\-\-threads=\-1"	86	.IP·"···\-\-threads=\-1"
87	Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).	87	Maxiumum·number·of·threads·to·use·for·processing,This·number·should·be·lower·or·equal·to·the·number·of·logical·processor·cores·in·the·machine.·(\-1:·automatic·estimation).


Offset 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=(~~req~~uired,·in~~put~~);·io"	20	.IP·"\-i·\-\-in-image=(input,·required);·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=(~~req~~uired,·in~~put~~);·io"	23	.IP·"\-r·\-\-ref-image=(input,·required);·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


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-3dimagefilter	8	.B·mia\-3dimagefilter
9	This·program·is·used·to·filter·and·convert·gray·scale·3D·images.	9	This·program·is·used·to·filter·and·convert·gray·scale·3D·images.
10	.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=(ou~~tput~~,·requ~~ired~~);·io"	15	.IP·"\-o·\-\-out-file=(required,·output);·io"
16	output·image(s)·that·have·been·filtered	16	output·image(s)·that·have·been·filtered
17	·For·supported·file·types·see·PLUGINS:3dimage/io	17	·For·supported·file·types·see·PLUGINS:3dimage/io
18	.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: