Freesurfer Group Analysis(FSGD) - Revision history

Greg at 22:36, 30 May 2018

2018-05-30T22:36:24Z

← Older revision		Revision as of 18:36, 30 May 2018
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	=Freesurfer Group Differences Analysis=		=Freesurfer Group Differences Analysis=
	Kinda cool method that can be used to compare groups and/or regress out nuisance variables from BOLD data within Freesurfer.		Kinda cool method that can be used to compare groups and/or regress out nuisance variables from BOLD data within Freesurfer. This method can potentially be used in place of the other GLM group analysis discussed on this wiki using output from selexavg (or prior to since can specify contrasts here in one step).

	Some sources:		Some sources:

Greg: /* Correct for multi comparisons */

2018-05-30T22:30:30Z

Correct for multi comparisons

← Older revision		Revision as of 18:30, 30 May 2018
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	mri_glmfit --surface fsaverage rh --glmdir g2v0 --y T1T2_ces.nii.gz --fsgd g2v0.fsgd --C GroupDiff.mtx --C GroupT1.mtx --C GroupT2.mtx --C GroupT1T2.intercept.mtx		mri_glmfit --surface fsaverage rh --glmdir g2v0 --y T1T2_ces.nii.gz --fsgd g2v0.fsgd --C GroupDiff.mtx --C GroupT1.mtx --C GroupT2.mtx --C GroupT1T2.intercept.mtx

	=Correct for ~~multi comparisons~~=		=Correct for Multiple Comparisons=
	Next:		Next:
	mri_glmfit-sim --glmdir g2v0 --cache 3 abs --cwpvalthresh .05		mri_glmfit-sim --glmdir g2v0 --cache 3 abs --cwpvalthresh .05

Greg: /* glm */

2018-05-30T22:29:50Z

glm

← Older revision		Revision as of 18:29, 30 May 2018
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	0.5 0.5		0.5 0.5

	=~~glm~~=		=GLM=
			Run new GLM for each hemi.
	Command:		Command:
	mri_glmfit --surface fsaverage rh --glmdir g2v0 --y T1T2_ces.nii.gz --fsgd g2v0.fsgd --C GroupDiff.mtx --C GroupT1.mtx --C GroupT2.mtx --C GroupT1T2.intercept.mtx		mri_glmfit --surface fsaverage rh --glmdir g2v0 --y T1T2_ces.nii.gz --fsgd g2v0.fsgd --C GroupDiff.mtx --C GroupT1.mtx --C GroupT2.mtx --C GroupT1T2.intercept.mtx

	=Correct for multi comparisons=		=Correct for multi comparisons=

Greg: /* 'DODS' contrast files */

2018-05-30T22:28:56Z

'DODS' contrast files

← Older revision		Revision as of 18:28, 30 May 2018
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	1 0		1 0
	T2.mtx		T2.mtx
	01		0 1
	T1T2intercept.mtx		T1T2intercept.mtx
	0.5 0.5		0.5 0.5

Greg: /* FSGD */

2018-05-30T22:28:10Z

FSGD

← Older revision		Revision as of 18:28, 30 May 2018
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	mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz		mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz

	=FSGD=		=FSGD File=
	For T1 vs. T2 ~~Data~~, first line needs to stay the same. ~~(g2v0.fsgd) -- 2 groups no covariates~~		For T1 vs. T2 booth data analysis, for example, with 2 groups and no covariates (g2v0.fsgd).

			The first line needs to stay the same 'GroupDescriptorFile 1'.
	GroupDescriptorFile 1		GroupDescriptorFile 1
	Title OSGM_T1T2		Title OSGM_T1T2
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	Input FS_T2_587 GroupT2		Input FS_T2_587 GroupT2
	Input FS_T2_589 GroupT2		Input FS_T2_589 GroupT2



	='DODS' contrast files=		='DODS' contrast files=

Greg: /* Data */

2018-05-30T22:26:06Z

Data

← Older revision		Revision as of 18:26, 30 May 2018
Line 11:		Line 11:

	=Data=		=Data=
	If ~~caomparing~~ T1 and T2 data, grab the files used for original GLMs (e.g. ces.nii.gz).		If comparing T1 and T2 data, grab the files used for original GLMs (e.g. ces.nii.gz).
	Rename and cat them for each hemi:		Rename and cat them for each hemi:
	mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz		mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz

Greg: /* Data */

2018-05-30T22:25:40Z

Data

← Older revision		Revision as of 18:25, 30 May 2018
Line 11:		Line 11:

	=Data=		=Data=
	~~Grab~~ the files used for original ~~glms~~ (e.g. ces.nii.gz)		If caomparing T1 and T2 data, grab the files used for original GLMs (e.g. ces.nii.gz).
	Rename and cat them for each hemi		Rename and cat them for each hemi:
	mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz		mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz


	=FSGD=		=FSGD=

Greg at 22:24, 30 May 2018

2018-05-30T22:24:36Z

← Older revision		Revision as of 18:24, 30 May 2018
Line 1:		Line 1:
	https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples		=Freesurfer Group Differences Analysis=
	https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat		Kinda cool method that can be used to compare groups and/or regress out nuisance variables from BOLD data within Freesurfer.
	https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
			Some sources:
			https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

			https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat

			https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

Greg: Created page with "https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V =Data= Grab t..."

2018-05-29T20:26:43Z

Created page with "https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V =Data= Grab t..."

New page

https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

=Data=
Grab the files used for original glms (e.g. ces.nii.gz)
Rename and cat them for each hemi
mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz

=FSGD=
For T1 vs. T2 Data, first line needs to stay the same. (g2v0.fsgd) -- 2 groups no covariates
GroupDescriptorFile 1
Title OSGM_T1T2
Class GroupT1
Class GroupT2
Input FS_T1_501 GroupT1
Input FS_T1_505 GroupT1
Input FS_T1_506 GroupT1
Input FS_T1_508 GroupT1
Input FS_T1_513 GroupT1
Input FS_T1_515 GroupT1
Input FS_T1_529 GroupT1
Input FS_T1_531 GroupT1
Input FS_T1_534 GroupT1
Input FS_T1_542 GroupT1
Input FS_T1_546 GroupT1
Input FS_T1_557 GroupT1
Input FS_T1_564 GroupT1
Input FS_T1_575 GroupT1
Input FS_T1_576 GroupT1
Input FS_T1_579 GroupT1
Input FS_T1_580 GroupT1
Input FS_T1_587 GroupT1
Input FS_T1_589 GroupT1
Input FS_T2_501 GroupT2
Input FS_T2_505 GroupT2
Input FS_T2_506 GroupT2
Input FS_T2_508 GroupT2
Input FS_T2_513 GroupT2
Input FS_T2_515 GroupT2
Input FS_T2_529 GroupT2
Input FS_T2_531 GroupT2
Input FS_T2_534 GroupT2
Input FS_T2_542 GroupT2
Input FS_T2_546 GroupT2
Input FS_T2_557 GroupT2
Input FS_T2_564 GroupT2
Input FS_T2_575 GroupT2
Input FS_T2_576 GroupT2
Input FS_T2_579 GroupT2
Input FS_T2_580 GroupT2
Input FS_T2_587 GroupT2
Input FS_T2_589 GroupT2

='DODS' contrast files=
groupdiff.mtx
1 -1
T1.mtx
1 0
T2.mtx
01
T1T2intercept.mtx
0.5 0.5

=glm=
Command:
mri_glmfit --surface fsaverage rh --glmdir g2v0 --y T1T2_ces.nii.gz --fsgd g2v0.fsgd --C GroupDiff.mtx --C GroupT1.mtx --C GroupT2.mtx --C GroupT1T2.intercept.mtx

=Correct for multi comparisons=
Next:
mri_glmfit-sim --glmdir g2v0 --cache 3 abs --cwpvalthresh .05

Now you've got clusters and .annot files to load up and get sizes/means etc.

Overlay
tksurfer fsaverage lh pial
load overlay -> cache.th30.abs.sig.cluster.mgh

cache.th30.abs.sig.cluster.summary contains cluster info.

Alternatively, you can segment the cache.th30.abs.sig.cluster.annot file into desired clusters.