Dear Freesurfer team, 

I am comparing subcortical volumes (aseg table) in 2 groups with no other variables. Based on the GLM lecture slides from the course I attended, I ran the following glmfit command: 

mri_glmfit 

--table aseg_table.txt 

--fsgd FSGD/DemographicsSubcortBinaryGroup.fsgd 

--C Contrasts/HC-ASPD.mtx 

--C Contrasts/ASPD-HC.mtx 

--glmdir roi.binarygroup.glmdir

It created all the correct output and subdirectories. 

I then used 

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=ASPD-HC/sig.mgh

but an error saying "failed to load surface overlay" comes up and the terminal error message is "number of vertices in overlay data does not match with surface". I assume this is because I am trying to load a 'whole-brain' sig.mgh onto a lh surface? Do I have to change the glmfit command to specify hemispheres, and if so, how do I do that since I do not want to look at cortical but subcortical data? Or alternatively, can I load both hemispheres into freeview so the overlay sig.mgh fits? 

Thank you so much,
Julia