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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
