Freesurfer Group Analysis(FSGD)
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.
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
Data
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:
mri_concat T1_ces.nii.gz T2_ces.nii.gz --o T1T2_ces.nii.gz
FSGD File
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 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.