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/srv/reproducible-results/rbuild-debian/r-b-build.XgjVGAz1/b2/mia_2.4.7-13_amd64.changes ¶

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mia-tools_2.4.7-13_amd64.deb ¶

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file list ¶

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xz --list ¶


Offset 2, 8 lines modified		Offset 2, 8 lines modified
2	·415f9cc99d6ed4767b3714ea29758df0·90458180·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_amd64.deb	2	·415f9cc99d6ed4767b3714ea29758df0·90458180·debug·optional·libmia-2.4-4-dbgsym_2.4.7-13_amd64.deb
3	·9f5893a69b84f091a01dc5a56dc18e58·4864652·libs·optional·libmia-2.4-4_2.4.7-13_amd64.deb	3	·9f5893a69b84f091a01dc5a56dc18e58·4864652·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	·bc5152f28f153fa285bb77368dd26476·96444·doc·optional·mia-tools-doc_2.4.7-13_all.deb	8	·bc5152f28f153fa285bb77368dd26476·96444·doc·optional·mia-tools-doc_2.4.7-13_all.deb
9	·~~97eed2f~~e~~3fcc5~~15e~~f3ca3cb36f3a98c4~~·19~~48204~~·science·optional·mia-tools_2.4.7-13_amd64.deb	9	·ca7037de47fe216e16558660ec037251·1950060·science·optional·mia-tools_2.4.7-13_amd64.deb


Offset 1, 3 lines modified		Offset 1, 3 lines modified
1	-rw-r--r--···0········0········0········4·2023-08-29·09:00:00.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2023-08-29·09:00:00.000000·debian-binary
2	-rw-r--r--···0········0········0·····7564·2023-08-29·09:00:00.000000·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~~0448~~·2023-08-29·09:00:00.000000·data.tar.xz	3	-rw-r--r--···0········0········0··1942312·2023-08-29·09:00:00.000000·data.tar.xz


Offset 1, 13 lines modified		Offset 1, 13 lines modified
1	··Streams:···········1	1	··Streams:···········1
2	··Blocks:············1	2	··Blocks:············1
3	··Compressed·size:···7564·B	3	··Compressed·size:···7556·B
4	··Uncompressed·size:·30.0·KiB·(30720·B)	4	··Uncompressed·size:·30.0·KiB·(30720·B)
5	··Ratio:·············0.246	5	··Ratio:·············0.246
6	··Check:·············CRC64	6	··Check:·············CRC64
7	··Stream·Padding:····0·B	7	··Stream·Padding:····0·B
8	··Streams:	8	··Streams:
9	····Stream····Blocks······CompOffset····UncompOffset········CompSize······UncompSize··Ratio··Check······Padding	9	····Stream····Blocks······CompOffset····UncompOffset········CompSize······UncompSize··Ratio··Check······Padding
10	·········1·········1···············0···············0············7564···········30720··0.246··CRC64············0	10	·········1·········1···············0···············0············7556···········30720··0.246··CRC64············0
11	··Blocks:	11	··Blocks:
12	····Stream·····Block······CompOffset····UncompOffset·······TotalSize······UncompSize··Ratio··Check	12	····Stream·····Block······CompOffset····UncompOffset·······TotalSize······UncompSize··Ratio··Check
13	·········1·········1··············12···············0············7528···········30720··0.245··CRC64	13	·········1·········1··············12···············0············7520···········30720··0.245··CRC64


Offset 5, 18 lines modified		Offset 5, 18 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dbinarycombine·\-1·<file1>·\-2·<file2>·\-o·<out\-file>·[options]	6	.B··mia\-2dbinarycombine·\-1·<file1>·\-2·<file2>·\-o·<out\-file>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dbinarycombine	8	.B·mia\-2dbinarycombine
9	This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.	9	This·program·is·used·to·combine·two·binary·images·by·some·kind·of·operation.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-1·\-\-file1=(~~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=(output,·required);·io"	18	.IP·"\-o·\-\-out-file=(output,·required);·io"
19	output·mask·image	19	output·mask·image
20	·For·supported·file·types·see·PLUGINS:2dimage/io	20	·For·supported·file·types·see·PLUGINS:2dimage/io
21	.IP·"\-p·\-\-operation=nor"	21	.IP·"\-p·\-\-operation=nor"
22	Operation·to·be·applied	22	Operation·to·be·applied


Offset 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:2dimage/io	71	·For·supported·file·types·see·PLUGINS:2dimage/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:2dimage/io	74	·For·supported·file·types·see·PLUGINS:2dimage/io
75	.IP·"\-o·\-\-transform=(required,·output);·io"	75	.IP·"\-o·\-\-transform=(required,·output);·io"
76	output·transformation	76	output·transformation
77	·For·supported·file·types·see·PLUGINS:2dtransform/io	77	·For·supported·file·types·see·PLUGINS:2dtransform/io
78	.IP·"\-O·\-\-inverse-transform=(required,·output);·io"	78	.IP·"\-O·\-\-inverse-transform=(required,·output);·io"
79	inverse·output·transformation	79	inverse·output·transformation


Offset 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·(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=(~~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: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 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=(requ~~ired~~,·ou~~tput~~);·io"	21	.IP·"\-o·\-\-out-file=(output,·required);·io"
22	combined·output·image	22	combined·output·image
23	·For·supported·file·types·see·PLUGINS:2dimage/io	23	·For·supported·file·types·see·PLUGINS:2dimage/io
24	.RE	24	.RE
25	.SS·Help·&·Info	25	.SS·Help·&·Info
26	.RS	26	.RS
27	.IP·"\-V·\-\-verbose=warning"	27	.IP·"\-V·\-\-verbose=warning"
28	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	28	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


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

16	·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.	16	·Note·that·for·this·nonlinear·motion·correction·a·preceding·linear·registration·step·is·usually·required.
17	.SH·OPTIONS	17	.SH·OPTIONS
18	.SS·	18	.SS·
19	File-IO	19	File-IO
20	.RS	20	.RS
21	.IP·"\-i·\-\-in-file=(~~req~~uired,·in~~put~~);·string"	21	.IP·"\-i·\-\-in-file=(input,·required);·string"
22	input·perfusion·data·set	22	input·perfusion·data·set

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

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


Offset 6, 18 lines modified		Offset 6, 18 lines modified
6	.B··mia\-2dimagefilterstack·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter>	6	.B··mia\-2dimagefilterstack·\-i·<in\-file>·\-o·<out\-file>·[options]·<PLUGINS:2dimage/filter>
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimagefilterstack	8	.B·mia\-2dimagefilterstack
9	This·program·runs·a·series·filters·on·a·series·of·consecutive·numbered·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.	9	This·program·runs·a·series·filters·on·a·series·of·consecutive·numbered·input·image.·The·filters·are·given·as·extra·parameters·on·the·command·line·and·are·run·in·the·order·in·which·they·are·given.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File·IO	11	.SS·File·IO
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-file=(~~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=(requ~~ired~~,·ou~~tput~~);·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

21	.RS·10	21	.RS·10
22	.I	22	.I
Offset 388, 15 lines modified		Offset 388, 15 lines modified
388	.TP·10	388	.TP·10
389	.B·combiner	389	.B·combiner
390	Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·	390	Combine·two·images·with·the·given·combiner·operator.·if·'reverse'·is·set·to·false,·the·first·operator·is·the·image·passed·through·the·filter·pipeline,·and·the·second·image·is·loaded·from·the·file·given·with·the·'image'·parameter·the·moment·the·filter·is·run.,·supported·parameters·are:·
391	.P	391	.P
392	.RS·14	392	.RS·14
393	.I	393	.I
394	image	394	image
395	=(~~req~~uired,·in~~put~~,·io)	395	=(input,·required,·io)
396	.RS·2	396	.RS·2
397	second·image·that·is·needed·in·the·combiner.	397	second·image·that·is·needed·in·the·combiner.
398	For·supported·file·types·see·PLUGINS:2dimage/io	398	For·supported·file·types·see·PLUGINS:2dimage/io

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

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

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

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

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

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

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

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

876	.RE	876	.RE
877	.RE	877	.RE
878	.RS·14	878	.RS·14
Offset 902, 15 lines modified		Offset 902, 15 lines modified
902	.TP·10	902	.TP·10
903	.B·medianmad	903	.B·medianmad
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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 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dimageselect	8	.B·mia\-2dimageselect
9	This·program·is·used·to·select·one·2D·images·from·a·multi-image·file.	9	This·program·is·used·to·select·one·2D·images·from·a·multi-image·file.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(required,·input);·io"	12	.IP·"\-i·\-\-in-file=(required,·input);·io"
13	input·images	13	input·images
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	15	.IP·"\-o·\-\-out-file=(output,·required);·io"
16	output·image	16	output·image
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-n·\-\-number=0"	18	.IP·"\-n·\-\-number=0"
19	image·number·to·be·selected	19	image·number·to·be·selected

20	.RE	20	.RE
21	.SS·Help·&·Info	21	.SS·Help·&·Info


Offset 6, 15 lines modified		Offset 6, 15 lines modified
6	.B··mia\-2dimagestack\-cmeans·\-i·<in\-file>·\-o·<out\-probmap>·[options]	6	.B··mia\-2dimagestack\-cmeans·\-i·<in\-file>·\-o·<out\-probmap>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dimagestack\-cmeans	8	.B·mia\-2dimagestack\-cmeans
9	This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram·and·then·writes·the·probability·mapping·for·thr·original·intensity·values	9	This·program·first·evaluates·a·sparse·histogram·of·an·input·image·series,·then·runs·a·c-means·classification·over·the·histogram·and·then·writes·the·probability·mapping·for·thr·original·intensity·values
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·File-IO	11	.SS·File-IO
12	.RS	12	.RS
13	.IP·"\-i·\-\-in-file=(~~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=(output,·required);·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


Offset 5, 21 lines modified		Offset 5, 21 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dlerp·\-1·<first>·\-2·<second>·\-o·<out\-file>·\-p·<positions>·[options]	6	.B··mia\-2dlerp·\-1·<first>·\-2·<second>·\-o·<out\-file>·\-p·<positions>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dlerp	8	.B·mia\-2dlerp
9	Merge·two·images·by·pixel-wise·linearly·combining·their·intensities.	9	Merge·two·images·by·pixel-wise·linearly·combining·their·intensities.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-1·\-\-first=(~~req~~uired,·in~~put~~);·io"	12	.IP·"\-1·\-\-first=(input,·required);·io"
13	first·input·image·	13	first·input·image·
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-2·\-\-second=(~~req~~uired,·in~~put~~);·io"	15	.IP·"\-2·\-\-second=(input,·required);·io"
16	second·input·image·	16	second·input·image·
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	18	.IP·"\-o·\-\-out-file=(output,·required);·io"
19	output·vector·field	19	output·vector·field
20	·For·supported·file·types·see·PLUGINS:2dimage/io	20	·For·supported·file·types·see·PLUGINS:2dimage/io
21	.IP·"\-p·\-\-positions=(required);·vfloat"	21	.IP·"\-p·\-\-positions=(required);·vfloat"
22	image·series·positions·(first,·target,·second)	22	image·series·positions·(first,·target,·second)

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


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)·····1472·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2davgmasked.1.gz	150	-rw-r--r--···0·root·········(0)·root·········(0)·····1472·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2davgmasked.1.gz
151	-rw-r--r--···0·root·········(0)·root·········(0)·····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)·····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)·····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)·····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)·····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)·····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)·····1871·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz	155	-rw-r--r--···0·root·········(0)·root·········(0)·····1871·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2deval-transformquantity.1.gz
156	-rw-r--r--···0·root·········(0)·root·········(0)·····3~~499~~·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz	156	-rw-r--r--···0·root·········(0)·root·········(0)·····3501·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz
157	-rw-r--r--···0·root·········(0)·root·········(0)·····1913·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid.1.gz	157	-rw-r--r--···0·root·········(0)·root·········(0)·····1915·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dfluid.1.gz
158	-rw-r--r--···0·root·········(0)·root·········(0)·····1548·2023-08-29·09:00:00.000000·./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)·····1590·2023-08-29·09:00:00.000000·./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)·····3462·2023-08-29·09:00:00.000000·./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)·····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)·····6177·2023-08-29·09:00:00.000000·./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)·····6370·2023-08-29·09:00:00.000000·./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)·····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)·····1491·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimageselect.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
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	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)·····1950·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz	171	-rw-r--r--···0·root·········(0)·root·········(0)·····1949·2023-08-29·09:00:00.000000·./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)·····1669·2023-08-29·09:00:00.000000·./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)·····2776·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmulti-force.1.gz	175	-rw-r--r--···0·root·········(0)·root·········(0)·····2776·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmulti-force.1.gz
176	-rw-r--r--···0·root·········(0)·root·········(0)·····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)·····5396·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageregistration.1.gz
177	-rw-r--r--···0·root·········(0)·root·········(0)·····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)·····1860·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimageto3d.1.gz
178	-rw-r--r--···0·root·········(0)·root·········(0)·····1542·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmultiimagevar.1.gz	178	-rw-r--r--···0·root·········(0)·root·········(0)·····1542·2023-08-29·09:00:00.000000·./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)·····1734·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-segment.1.gz	181	-rw-r--r--···0·root·········(0)·root·········(0)·····1731·2023-08-29·09:00:00.000000·./usr/share/man/man1/mia-2dmyocard-segment.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 5, 18 lines modified		Offset 5, 18 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dmyoseries\-compdice·\-1·<first>·\-2·<second>·[options]	6	.B··mia\-2dmyoseries\-compdice·\-1·<first>·\-2·<second>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmyoseries\-compdice	8	.B·mia\-2dmyoseries\-compdice
9	This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·two·image·series	9	This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·two·image·series
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-1·\-\-first=(~~inp~~ut,·requi~~red~~);·string"	12	.IP·"\-1·\-\-first=(required,·input);·string"
13	first·segmentation·set	13	first·segmentation·set

14	.IP·"\-2·\-\-second=(~~inp~~ut,·requi~~red~~);·string"	14	.IP·"\-2·\-\-second=(required,·input);·string"
15	second·segmentation·set	15	second·segmentation·set

16	.IP·"\-k·\-\-skip=2"	16	.IP·"\-k·\-\-skip=2"
17	images·to·skip·atthe·begin·of·the·series	17	images·to·skip·atthe·begin·of·the·series

18	.RE	18	.RE
19	.SS·Help·&·Info	19	.SS·Help·&·Info


Offset 5, 15 lines modified		Offset 5, 15 lines modified
5	.SH·SYNOPSIS	5	.SH·SYNOPSIS
6	.B··mia\-2dmyoseries\-dice·\-i·<input>·[options]	6	.B··mia\-2dmyoseries\-dice·\-i·<input>·[options]
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmyoseries\-dice	8	.B·mia\-2dmyoseries\-dice
9	This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.	9	This·program·is·used·to·evaluate·the·per-frame·dice·index·of·segmented·regions·of·an·image·with·respect·to·the·segmentation·of·a·reference·frame·from·the·same·series.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-input=(~~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 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=(output,·required);·io"	15	.IP·"\-o·\-\-out-file=(output,·required);·io"
16	output·myocardial·mask	16	output·myocardial·mask
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-f·\-\-save-features=(output);·string"	18	.IP·"\-f·\-\-save-features=(output);·string"
19	save·ICA·features·to·files·with·this·name·base	19	save·ICA·features·to·files·with·this·name·base


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

24	.IP·"\-r·\-\-registered="	24	.IP·"\-r·\-\-registered="
25	File·name·base·for·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, 15 lines modified		Offset 14, 15 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=(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=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.


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

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

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


Offset 8, 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 46, 15 lines modified		Offset 46, 15 lines modified

46	.RE	46	.RE
47	.SS·File-IO	47	.SS·File-IO
48	.RS	48	.RS
49	.IP·"\-i·\-\-in-file=(input,·required);·string"	49	.IP·"\-i·\-\-in-file=(input,·required);·string"
50	input·perfusion·data·set	50	input·perfusion·data·set

51	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	51	.IP·"\-o·\-\-out-file=(required,·output);·string"
52	output·perfusion·data·set	52	output·perfusion·data·set

53	.IP·"\-r·\-\-registered="	53	.IP·"\-r·\-\-registered="
54	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	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.

55	.IP·"···\-\-save-cropped=(output);·string"	55	.IP·"···\-\-save-cropped=(output);·string"
56	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base	56	save·cropped·set·to·this·file,·the·image·files·will·use·the·stem·of·the·name·as·file·name·base


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=(~~req~~uired,·in~~put~~);·string"	20	.IP·"\-i·\-\-in-file=(input,·required);·string"
21	input·perfusion·data·set	21	input·perfusion·data·set

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

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


Offset 7, 18 lines modified		Offset 7, 18 lines modified
7	.SH·DESCRIPTION	7	.SH·DESCRIPTION
8	.B·mia\-2dmyoset\-all2one\-nonrigid	8	.B·mia\-2dmyoset\-all2one\-nonrigid
9	This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an·image·set.·All·images·are·registered·to·one·user·defined·reference·image.	9	This·program·runs·non-rigid·registration·of·a·series·of·images·given·in·an·image·set.·All·images·are·registered·to·one·user·defined·reference·image.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.SS·	11	.SS·
12	File-IO	12	File-IO
13	.RS	13	.RS
14	.IP·"\-i·\-\-in-file=(~~inp~~ut,·requi~~red~~);·string"	14	.IP·"\-i·\-\-in-file=(required,·input);·string"
15	input·perfusion·data·set	15	input·perfusion·data·set

16	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·string"	16	.IP·"\-o·\-\-out-file=(required,·output);·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=(~~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·"\-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	=(~~req~~uired,·in~~put~~,·io)	381	=(input,·required,·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	=(~~req~~uired,·in~~put~~,·string)	725	=(input,·required,·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	=(~~req~~uired,·in~~put~~,·io)	751	=(input,·required,·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	=(~~req~~uired,·in~~put~~,·io)	789	=(input,·required,·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	=(~~req~~uired,·in~~put~~,·io)	813	=(input,·required,·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	=(~~req~~uired,·in~~put~~,·io)	822	=(input,·required,·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	=(requ~~ired~~,·ou~~tput~~,·io)	858	=(output,·required,·io)
859	.RS·2	859	.RS·2
860	name·of·the·output·file·to·save·the·variation·image·too..	860	name·of·the·output·file·to·save·the·variation·image·too..
861	For·supported·file·types·see·PLUGINS:2dimage/io	861	For·supported·file·types·see·PLUGINS:2dimage/io

862	.RE	862	.RE
863	.RE	863	.RE
864	.RS·14	864	.RS·14
Offset 888, 15 lines modified		Offset 888, 15 lines modified
888	.TP·10	888	.TP·10
889	.B·medianmad	889	.B·medianmad
890	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·	890	Filter·that·evaluates·simultaniously·the·pixel·wise·median·and·the·median·absolute·deviation·(MAD)·of·an·image·in·a·given·window.·Pixel·intensities·below·the·given·threshold·will·be·ignored·and·at·their·loctions·the·output·median·and·MAD·are·set·to·zero.·The·median·intensity·image·is·directly·passed·to·the·pipeline,·the·variation·image·is·saved·to·a·file·given·with·the·varfile·parameter.·Both·output·images·have·the·same·pixel·type·like·the·input·image.,·supported·parameters·are:·
891	.P	891	.P
892	.RS·14	892	.RS·14
Max diff block lines reached; 1357/4902 bytes (27.68%) of diff not shown.


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, 18 lines modified		Offset 6, 18 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=(ou~~tput~~,·requ~~ired~~);·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
21	.RS	21	.RS
22	.IP·"\-V·\-\-verbose=warning"	22	.IP·"\-V·\-\-verbose=warning"
23	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:	23	verbosity·of·output,·print·messages·of·given·level·and·higher·priorities.·Supported·priorities·starting·at·lowest·level·are:


Offset 11, 15 lines modified		Offset 11, 15 lines modified
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(input,·required);·string"	12	.IP·"\-i·\-\-in-file=(input,·required);·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 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dseries\-mincorr	8	.B·mia\-2dseries\-mincorr
9	Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal·correlation·of·the·time-intensity·curve·between·neighboring·pixels.	9	Given·a·set·of·images·of·temporal·sucession,·this·program·evaluates·the·minimal·correlation·of·the·time-intensity·curve·between·neighboring·pixels.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-set=(input,·required);·string"	12	.IP·"\-i·\-\-in-set=(input,·required);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-set=(requ~~ired~~,·ou~~tput~~);·io"	14	.IP·"\-o·\-\-out-set=(output,·required);·io"
15	output·image·of·minimal·correlation	15	output·image·of·minimal·correlation
16	·For·supported·file·types·see·PLUGINS:2dimage/io	16	·For·supported·file·types·see·PLUGINS:2dimage/io
17	.IP·"\-k·\-\-skip=2"	17	.IP·"\-k·\-\-skip=2"
18	skip·images·at·beginning·of·series	18	skip·images·at·beginning·of·series

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

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

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


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dseries2dordermedian	8	.B·mia\-2dseries2dordermedian
9	This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the·gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In·addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given·pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving·additional·filters·as·free·parameters·(filter/2dimage).	9	This·program·evaluates·the·pixel-wise·median·of·the·absolute·values·of·the·gauss·filtered·2nd·order·temporal·derivative·of·a·series·of·images.·In·addition,·it·can·be·used·to·output·the·time-intensity·curve·of·a·given·pixel.The·program·supports·slice-wise·spacial·pre-filtering·by·giving·additional·filters·as·free·parameters·(filter/2dimage).
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(input,·required);·string"	12	.IP·"\-i·\-\-in-file=(input,·required);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(requ~~ired~~,·ou~~tput~~);·io"	14	.IP·"\-o·\-\-out-file=(output,·required);·io"
15	output·image·name	15	output·image·name
16	·For·supported·file·types·see·PLUGINS:2dimage/io	16	·For·supported·file·types·see·PLUGINS:2dimage/io
17	.IP·"\-k·\-\-skip=0"	17	.IP·"\-k·\-\-skip=0"
18	Skip·files·at·the·beginning	18	Skip·files·at·the·beginning

19	.IP·"\-e·\-\-enlarge-boundary=5"	19	.IP·"\-e·\-\-enlarge-boundary=5"
20	Enlarge·cropbox·by·number·of·pixels	20	Enlarge·cropbox·by·number·of·pixels
Offset 842, 15 lines modified		Offset 842, 15 lines modified
842	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.	842	Intensity·thresholding·parameter:·Pixels·with·intensities·below·this·threshold·will·be·set·to·zero,·and·also·not·used·when·evaluating·mean·and·variation.

843	.RE	843	.RE
844	.RE	844	.RE
845	.RS·14	845	.RS·14
846	.I	846	.I
847	varfile	847	varfile
848	=(requ~~ired~~,·ou~~tput~~,·io)	848	=(output,·required,·io)
849	.RS·2	849	.RS·2
850	name·of·the·output·file·to·save·the·variation·image·too..	850	name·of·the·output·file·to·save·the·variation·image·too..
851	For·supported·file·types·see·PLUGINS:2dimage/io	851	For·supported·file·types·see·PLUGINS:2dimage/io

852	.RE	852	.RE
853	.RE	853	.RE
854	.RS·14	854	.RS·14
Offset 878, 15 lines modified		Offset 878, 15 lines modified
878	.TP·10	878	.TP·10
879	.B·medianmad	879	.B·medianmad
880	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:·	880	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:·
881	.P	881	.P
882	.RS·14	882	.RS·14
883	.I	883	.I
884	madfile	884	madfile
885	=(requ~~ired~~,·ou~~tput~~,·io)	885	=(output,·required,·io)
886	.RS·2	886	.RS·2
887	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..	887	name·of·the·output·file·to·save·the·median·absolute·deviation·image·too..
888	For·supported·file·types·see·PLUGINS:2dimage/io	888	For·supported·file·types·see·PLUGINS:2dimage/io

889	.RE	889	.RE
890	.RE	890	.RE
891	.RS·14	891	.RS·14
Offset 1197, 15 lines modified		Offset 1197, 15 lines modified
1197	.TP·10	1197	.TP·10
1198	.B·tee	1198	.B·tee
1199	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·	1199	Save·the·input·image·to·a·file·and·also·pass·it·through·to·the·next·filter,·supported·parameters·are:·
1200	.P	1200	.P
1201	.RS·14	1201	.RS·14
1202	.I	1202	.I
1203	file	1203	file
1204	=(requ~~ired~~,·ou~~tput~~,·io)	1204	=(output,·required,·io)
1205	.RS·2	1205	.RS·2
1206	name·of·the·output·file·to·save·the·image·too..	1206	name·of·the·output·file·to·save·the·image·too..
1207	For·supported·file·types·see·PLUGINS:2dimage/io	1207	For·supported·file·types·see·PLUGINS:2dimage/io

1208	.RE	1208	.RE
1209	.RE	1209	.RE
1210	.TP·10	1210	.TP·10


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dseriescorr	8	.B·mia\-2dseriescorr
9	Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent·the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as·average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be·of·the·same·pixel·type·and·size.	9	Given·a·set·of·images·of·temporal·sucession,·evaluates·images·that·represent·the·time-intensity·correlation·in·horizontal·and·vertical·direction·as·well·as·average·correlation·of·each·pixel·with·its·neighbors.·All·input·images·must·be·of·the·same·pixel·type·and·size.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-base=(input,·required);·io"	12	.IP·"\-i·\-\-in-base=(input,·required);·io"
13	input·file·name·base	13	input·file·name·base
14	·For·supported·file·types·see·PLUGINS:2dimage/io	14	·For·supported·file·types·see·PLUGINS:2dimage/io
15	.IP·"\-o·\-\-outname=(ou~~tput~~,·requ~~ired~~);·io"	15	.IP·"\-o·\-\-outname=(required,·output);·io"
16	output·file·name·to·save·the·avarage·per\-pixel·correlation	16	output·file·name·to·save·the·avarage·per\-pixel·correlation
17	·For·supported·file·types·see·PLUGINS:2dimage/io	17	·For·supported·file·types·see·PLUGINS:2dimage/io
18	.IP·"\-z·\-\-horizontal=(output);·io"	18	.IP·"\-z·\-\-horizontal=(output);·io"
19	horiZontal·correlation·output·file·name	19	horiZontal·correlation·output·file·name
20	·For·supported·file·types·see·PLUGINS:2dimage/io	20	·For·supported·file·types·see·PLUGINS:2dimage/io
21	.IP·"\-t·\-\-vertical=(output);·io"	21	.IP·"\-t·\-\-vertical=(output);·io"
22	verTical··correlation·output·file·name	22	verTical··correlation·output·file·name


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=(ou~~tput~~,·requ~~ired~~);·io"	14	.IP·"\-o·\-\-out-file=(required,·output);·io"
15	output·file·name	15	output·file·name
16	·For·supported·file·types·see·PLUGINS:2dimage/io	16	·For·supported·file·types·see·PLUGINS:2dimage/io
17	.IP·"\-k·\-\-skip=0"	17	.IP·"\-k·\-\-skip=0"
18	Skip·files·at·the·beginning	18	Skip·files·at·the·beginning

19	.IP·"\-e·\-\-enlarge-boundary=5"	19	.IP·"\-e·\-\-enlarge-boundary=5"
20	Enlarge·cropbox·by·number·of·pixels	20	Enlarge·cropbox·by·number·of·pixels


Offset 8, 15 lines modified		Offset 8, 15 lines modified
8	.B·mia\-2dseriestovolume	8	.B·mia\-2dseriestovolume
9	Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.	9	Obtaines·a·3D·volume·image·by·combining·the·images·of·the·segmentation·set.
10	.SH·OPTIONS	10	.SH·OPTIONS
11	.RS	11	.RS
12	.IP·"\-i·\-\-in-file=(input,·required);·string"	12	.IP·"\-i·\-\-in-file=(input,·required);·string"
13	input·segmentation·set	13	input·segmentation·set

14	.IP·"\-o·\-\-out-file=(ou~~tput~~,·requ~~ired~~);·io"	14	.IP·"\-o·\-\-out-file=(required,·output);·io"
15	output·3D·image·	15	output·3D·image·
16	·For·supported·file·types·see·PLUGINS:3dimage/io	16	·For·supported·file·types·see·PLUGINS:3dimage/io
17	.IP·"\-k·\-\-skip=0"	17	.IP·"\-k·\-\-skip=0"
18	number·of·frames·to·skip·at·the·beginning·of·the·series.	18	number·of·frames·to·skip·at·the·beginning·of·the·series.

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