Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on them using GLM. Thanks a lot

CREATE MASK USING MRI_BINARIZE

setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri

cd users/paul/desktop/ims/fsaverage/mri

mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz

MERGE TO LABELS

cd users/paul/desktop/ims/fsaverage/label

mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label

MRIS_PREPROC

cd users/paul/desktop/ims

mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas thickness --out lh.filename.thickness.00.mgh

MRI_SURF2SURF

mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh --fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh

GLM

mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C contrastmatrix.mtx --surf fsaverage lh --label fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir

CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations

mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces

On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

I think there is an example on the wiki in the ROI analysis section. See

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values

On 7/30/16 5:33 PM, miracle ozzoude wrote:
Hey FreeSurfer experts,
Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much.

Best,

Paul
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