Dear Experts,
I ran the wm.mgz corrections and pial corrections using the command:
-autorecon2 –autorecon3 –subjid sub2
However, Freesurfer exited the program with the following message:
SUBJECTS_DIR /Users/subdir FREESURFER_HOME Applications/freesurfer Loading source label. No such file or directory fsaverage/label/lh.BA1.label ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label Darwin mso00820bg.rush.eduhttp://mso00820bg.rush.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
Can someone please explain what this error message means regarding whether I need to rerun the autorecon processes with the fsaverage folder within my current subjects folder? I copied fsaverage/ from freesurfer/ to my designated SUBJECTS_DIR but have not run the recon. It seems that the pial surfaces were regenerated while the white matter segment was not corrected for this one subject. I ran other subjects within this SUBJECTS_DIR (before I copied the fsaverage folder) but the white matter segment and pial surfaces were regenerated for them. Looking forward to your responses.
Thank you,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edumailto:Vy_dinh@rush.edu