Hi,

I was conducting GLM analysis using the command line. Everything seemed to work fine until I wanted to visualize the uncorrected significance map using the following command (my glmdir folder for the contrast is lh.scheme1.glmdir):

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=$SUBJECTS_DIR/qdec/lh.scheme1.glmdir/scheme1/sig.mgh:overlay_threshold=4,5 -viewport 3d

'Did not find any volume geometry information in the surface' appears in the terminal window. In freeview, only the fsaverage lh.inflated file appears.

I am wondering whether it is actually related to my experimental scheme. I want to study the relationship between cortical volume and variable X, while isolating for the effects of 4 factors (2 discrete A and B, 2 continuous C and D).

So I've created an FSGD file:

GroupDescriptorFile 1
Title xxx
Class A1B1
Class A1B2
Class A2B1
Class A2B2
Variables X C D

Input ....

And I have created a scheme1.mtx contrast matrix that goes like this:

0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 0 0 0 0

So that only the slope for X is modelled while isolating for the effect of everything else. I am however unsure of whether it is the proper way to conceptualize the issue.

I've done mris_preproc --fsgd scheme1.fsgd --cache-in volume.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.scheme1.volume.15.mgh

And then mri_glmfit --y lh.scheme1.volume.15.mgh --fsgd scheme1.fsgd dods --C scheme1.mtx --surf fsaverage lh --cortex --glmdir lh.scheme1.glmdir

I am clueless of where may be my mistake.

Thank you

Shady

Shady Rahayel
Étudiant au Ph.D. en neuropsychologie R/I
Université du Québec à Montréal

Centre d'Études Avancées en Médecine du Sommeil
Hôpital du Sacré-Coeur de Montréal