GLM - FREESURFER
(linux - ubuntu)

#1
### Create the FSGD file and the contrast file(s) ###

vi cortisol_CSF.fsgd 
vi cortisol_CSF_intercept.mtx (1 0)
vi cortisol_CSF_slope.mtx (0 1)


#2
### Resample each subject's data into a common space and concatenate all the subjects' into a single file ###
#### One command for each hemisphere ####

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

mris_preproc --fsgd cortisol_CSF.fsgd \
  --target fsaverage \
  --hemi rh \
  --meas thickness \
  --out rh.cortisol_CSF.thickness.00.mgh


#3
### Spatial smoothing ###
#### One command for each hemisphere ####

mri_surf2surf --hemi lh \
  --s fsaverage \
  --sval lh.cortisol_CSF.thickness.00.mgh \
  --fwhm 10 \
  --cortex \
  --tval lh.cortisol_CSF.thickness.10.mgh

mri_surf2surf --hemi rh \
  --s fsaverage \
  --sval rh.cortisol_CSF.thickness.00.mgh \
  --fwhm 10 \
  --cortex \
  --tval rh.cortisol_CSF.thickness.10.mgh


#4
### GLM Analysis ###
#### One command for each hemisphere ####

mri_glmfit \
  --y lh.cortisol_CSF.thickness.10.mgh \
  --fsgd cortisol_CSF.fsgd \
  --C cortisol_CSF_intercept.mtx \
  --C cortisol_CSF_slope.mtx \
  --surf fsaverage lh \
  --cortex \ 
  --glmdir lh.cortisol_CSF.glmdir \
  --eres-save

mri_glmfit \
  --y rh.cortisol_CSF.thickness.10.mgh \
  --fsgd cortisol_CSF.fsgd \
  --C cortisol_CSF_intercept.mtx \
  --C cortisol_CSF_slope.mtx \
  --surf fsaverage rh \
  --cortex \ 
  --glmdir rh.cortisol_CSF.glmdir \
  --eres-save


##### View the uncorrected significance map in freeview #####

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.cortisol_CSF.glmdir/cortisol_CSF_intercept/sig.mgh:overlay_threshold=2,5 -viewport 3d -layout 1 

freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:annot_outline=1:overlay=rh.cortisol_CSF.glmdir/cortisol_CSF_intercept/sig.mgh:overlay_threshold=2,5 -viewport 3d -layout 1 

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.cortisol_CSF.glmdir/cortisol_CSF_slope/sig.mgh:overlay_threshold=2,5 -viewport 3d -layout 1 

freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:annot_outline=1:overlay=rh.cortisol_CSF.glmdir/cortisol_CSF_slope/sig.mgh:overlay_threshold=2,5 -viewport 3d -layout 1 


#5
### Correction for multiple comparisons - cluster + permutation ###
#### One command for each hemisphere ####

mri_glmfit-sim \
  --glmdir lh.cortisol_CSF.glmdir \
  --perm 10000 2.0 pos \
  --cwp 0.05\
  --2spaces \
  --bg 2

mri_glmfit-sim \
  --glmdir rh.cortisol_CSF.glmdir \
  --perm 10000 2.0 pos \
  --cwp 0.05\
  --2spaces \
  --bg 2


##### View the cluster summary #####

cd $SUBJECTS_DIR/lh.cortisol_CSF.glmdir/cortisol_CSF_intercept
less perm.th20.pos.sig.cluster.summary

cd $SUBJECTS_DIR/rh.cortisol_CSF.glmdir/cortisol_CSF_intercept
less perm.th20.pos.sig.cluster.summary

cd $SUBJECTS_DIR/lh.cortisol_CSF.glmdir/cortisol_CSF_slope
less perm.th20.pos.sig.cluster.summary

cd $SUBJECTS_DIR/rh.cortisol_CSF.glmdir/cortisol_CSF_slope
less perm.th20.pos.sig.cluster.summary
 

##### View the cluster annotation in freeview #####

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.cortisol_CSF.glmdir/cortisol_CSF_intercept/perm.th20.pos.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.cortisol_CSF.glmdir/cortisol_CSF_intercept/perm.th20.pos.sig.ocn.annot -viewport 3d -layout 1


freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=rh.cortisol_CSF.glmdir/cortisol_CSF_intercept/perm.th20.pos.sig.cluster.mgh:overlay_threshold=2,5:annot=rh.cortisol_CSF.glmdir/cortisol_CSF_intercept/perm.th20.pos.sig.ocn.annot -viewport 3d -layout 1


freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay= lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.pos.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.pos.sig.ocn.annot -viewport 3d -layout 1


freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=rh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.pos.sig.cluster.mgh:overlay_threshold=2,5:annot=rh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.pos.sig.ocn.annot -viewport 3d -layout 1


##### View the correlation map in freeview #####

cd $SUBJECTS_DIR/lh.cortisol_CSF.glmdir/cortisol_CSF_intercept
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=pcc.mgh

cd $SUBJECTS_DIR/rh.cortisol_CSF.glmdir/cortisol_CSF_intercept
freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=pcc.mgh

cd $SUBJECTS_DIR/lh.cortisol_CSF.glmdir/cortisol_CSF_slope
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=pcc.mgh

cd $SUBJECTS_DIR/rh.cortisol_CSF.glmdir/cortisol_CSF_slope
freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=pcc.mgh