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.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.edu