Dear Paul,
the slash problem prevents to properly create symbolic link to fsaverage in your SUBJECTS_DIR.
Then, the mri_label2label could not find the fsaverage label file since symbolic link for fsaverage does not exist, hence produces the error.log you are attaching.
Regards,
Antonin
Thanks Antonin. Also, I got this error.log file in my label folder. Do you think it is due to the slash problem? Best, PaulOn Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch a...@ikem.cz wrote:
Dear Paul,
I suppose the clue is following messages from your recon-all.log file:
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