As the printout says, the surface file does not contain any volume information in the header, so it may not be aligned properly with the volume. But I’m not sure why it doesn’t have it. Would it be possible to send me one of the volume files and the surface files you used in the command?
Ruopeng
On Feb 18, 2025, at 5:02 AM, Paola Di Filippo <paola.difilippo@unifg.itmailto:paola.difilippo@unifg.it> wrote:
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Hi again everyone. I am using freesurfer 7.4.1. on ubuntu 22 with a virtual machine. I performed my first recon-all, without hard failures as the .log ended with "recon-all completed with no errors". Then, I have tried to launch freeview to visualize both volumes and surfaces for my subject, with the following command:
freeview -v angcher.02.04.91.12.09.22/mri/T1.mgz angcher.02.04.91.12.09.22/mri/wm.mgz angcher.02.04.91.12.09.22/mri/brainmask.mgz angcher.02.04.91.12.09.22/mri/aseg.mgz:colormap=lut:opacity=0.2 -f angcher.02.04.91.12.09.22/surf/lh.white:edgecolor=blue angcher.02.04.91.12.09.22/surf/lh.pial:edgecolor=red angcher.02.04.91.12.09.22/surf/rh.white:edgecolor=blue angcher.02.04.91.12.09.22/surf/rh.pial:edgecolor=red
but in freeview, surfaces are completely misaligned with volumes. This is an image to give you an idea of the problem (sorry for the quality, i'm controlling the computer on which i work remotely from home):
<image.png>
this is what i see in the terminal after launching the command: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info
when i first tried freeview after downloading the program, i had the same problem with bert; when i launch this command:
freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
this is what I get: <image.png> again, this is what I see in the terminal: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info
The only time when i didn't experience this problem is after downloading tutorial data and trying this command: freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.white:edgecolor=blue good_output/surf/lh.pial:edgecolor=red good_output/surf/rh.white:edgecolor=blue good_output/surf/rh.pial:edgecolor=red
that gave me this outoput in freeview: <image.png>
but still I get this in the terminal: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info.
any ideas on how could I fix this problem? many thanks in advance.
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