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Hi Doug,

I ran mri_glmfit --table aseg.txt --fsgd newCH_deblank3.fsgd dods --C groupdiff.mtx --glmdir aseg.glmdir

this created a folder aseg.glmdir which contains another folder groupdiff, where sig.ghm is,

I then tried to visualise results using

freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d

Many thanks in advance!

Francisca

On Tue, Jun 1, 2021 at 1:40 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

How did you create the sig.mgh that you are trying to overlay?

On 5/28/2021 11:16 AM, Francisca Ferreira wrote:

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Dear Experts,

I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I ran mri_glmfit using the following command

mri_glmfit --table aseg.txt --fsgd newCH_deblank3.fsgd dods --C groupdiff.mtx --glmdir aseg.glmdir

this seems to have worked. I am now trying to visualise my results adapting the recommended wiki command

freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d

Freeview crashes and I'm getting the following error

Number of vertices in overlay data (64 or 64) does not match with surface (163842). Number of vertices in overlay data (64 or 64) does not match with surface (163842).

Is there something wrong with the commands priot to this step?

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