FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/

and

 cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - 

ln: failed to create symbolic link './fsaverage': File exists

The problem is that your FREESURFER_HOME contains slash in the end. Remove it and rerun relevant part of recon-all. It should work then.

Antonin



Hello Freesurfer,
I was running recon-all in steps (recon-all -autorecon1, recon-all
-autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). However,
it exited with error during the BA_exvivo labels part of autorecon3 (please
see attached recon-all.log file). Please, how can I fix it? Thanks
Best,
Paul