From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Maria A Infante [minfante@ucsd.edu]
Sent: Friday, May 12, 2017 3:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] 2 stage model longitudinal data analysis

Hi, 
I am interested in looking at groups differences (3 groups) in percent thickness change. I want to use mri_glmfit to analyze but I am unclear on what  I should include on my fsgd file. Can you please provide an example? 

Also The example provided on the fswiki  under Option mri_glmfit doesn't call for an fsgd file. 

long_mris_slopes --qdec long.testretest.qdec \
      --meas thickness \
      --hemi lh \
      --sd $SUBJECTS_DIR \
      --do-pc1 --do-label \
      --generic-time \
      --fwhm 15 \
      --qcache fsaverage \
      --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \
      --isec-labels lh.testretest.fsaverage.cortex.label

mri_glmfit --osgm \
           --glmdir lh.testretest.thickness-pc1.fwhm15 \
           --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \
           --label lh.testretest.fsaverage.cortex.label \
           --surf fsaverage lh