recon-all is supposed to create a symlink from the fsaverage in your /opt/freesurfer/subjects dir to you subjects dir, but sometimes this doesnt seem to work for some people. so first goto your subjects dir and check if that link is there (could be a broken link). if it isnt, then just copy the fsaverage dir from /opt/freesurer/subjects to your subjects dir (dont create a symlink).
nick On Wed, 2012-05-09 at 20:47 +0000, Rashmi Singh wrote: > Hello, > I ran recon –all on my scans and the output files reported the > following error: > > > SUBJECTS_DIR > > /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer > FREESURFER_HOME /opt/freesurfer > Loading source label. > Invalid argument > ERROR > reading > /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage/label/lh.BA1.label > Linux dale 2.6.32-40-server #87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012 > x86_64 GNU/Linux > > > recon-all -s AA435.C1 exited with ERRORS at Wed May 9 01:37:19 CDT > 2012. > > > I couldn't locate the folder fsaverage: > > /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage > > > Please advise. > Rashmi. > > > > > ______________________________________________________________________ > > This document may contain information covered under the Privacy Act, 5 > USC 552(a), and/or the Health Insurance Portability and Accountability > Act (PL 104-191) and its various implementing regulations and must be > protected in accordance with those provisions. Healthcare information > is personal and sensitive and must be treated accordingly. If this > correspondence contains healthcare information it is being provided to > you after appropriate authorization from the patient or under > circumstances that don't require patient authorization. You, the > recipient, are obligated to maintain it in a safe, secure and > confidential manner. Redisclosure without additional patient consent > or as permitted by law is prohibited. Unauthorized redisclosure or > failure to maintain confidentiality subjects you to application of > appropriate sanction. If you have received this correspondence in > error, please notify the sender at once and destroy any copies you > have made. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
