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
What exactly is the problem? You only specified the lh.inflated, so it is not unusual that that is the only thing you see. If it is that you were expecting some activation (colors) on the surface, then try reducing the threshold (4 is pretty high)
On 12/06/2016 05:41 PM, Shady Rahayel wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Shady Rahayel