Dear freeSurfer,
I have problems with defining new labels for my brain scan or even of fsaverage. I need to define a new label (ROI) to be able to find the grey matter thickness for that specific region.
My first problem is that when I define a new label on fsaverage, it does not save it for me and it gives me the following error:
mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz, -1): could not open file /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could not open label file /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label
I intend to define a new label (ROI) on fsaverage and then use the mri_labe2label command to copy it on my desired structural MRI image. But it does not work for me.
My second problem is that when I define a new label on my subject's MRI image and I run the mri_anatomical_stats with the label of my subject, it does not give me any output and this is what I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh limiting computations to label anon/label/lh.test.label. reading volume /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz... reading input surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... reading input pial surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial... reading input white surface /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
and the error is that it could not find the file lh.test.label, however I can see it in the label folder.
Please guide me with this issue.
Best Regards, Mahtab.