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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