Dear experts,
We have recently encountered processing errors (during recon-all and -autorecon2&3) due to the creation of symbolic links within our SUBJECTS_DIR. Since our data were located on a data mount, the system somehow could not source the linked file. We have addressed this issue by directly copying fsaverage and th *EC_average files directly to our current SUBJECTS_DIR so that the symbolic links did not need to be created.
However, this brings to light some another concern. The subjects for our study were processed on a local computer and then copied to the server so that they could be processed on multiple computers. Since we wanted to keep a copy of the "raw" reconned data, we copied these subjects to another directory and proceeded to do manual edits. Are there other symbolic links created within the subjects directories or SUBJECTS_DIR that would become defunct with these copies? I read a post in the Freesurfer forum that the link to fsaverage (and other folders) were only created during recon-all for display purposes. However, when running group analyses, these folders/files will need to be accessed, so does that mean that we would have to change the path info in these links? Would you caution against moving the subject directories after recon-all has been run? Rather than all the steps in run recon-all again, are there specific functions that will recreate these links?
Thanks,
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