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
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