The input is a table, so the output is a table (the sig.mgh file will just have the number of values that are in the table; this is not a "volume" you can look at in FV). Look in the sig.table.dat file for the sigs.

On 4/13/2021 8:41 AM, Griem, Julia wrote:

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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
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