Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh).
Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch <a...@ikem.cz> wrote: > 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, > Paul > > On 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
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