Hello Paul,

I've been trying to replicate it the issue on my Mac without any success. But I do have what might be a potential solution ide like you to try. Could you please

source freesurfer, then run the following command.

 $> sudo -E fs_update

(This will update a freesurfer file on your machine). Then retry the subject with the parallel flag. Please let me know how it goes. Thanks.

-Zeke

On Mar 6, 2017, at 8:56 AM, miracle ozzoude <miracooloz@gmail.com> wrote:

Hello Z K, 

Were you able to fix the bug?

Best, 

Paul

On Fri, Mar 3, 2017 at 12:14 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Im looking into this now, but I think their might be a bug when using
the -parallel flag on Mac platforms. I should have a fix shortly. I will
let you know.

On 03/03/2017 12:10 PM, miracle ozzoude wrote:
> Thanks Antonin. I also have different error when running another
> subject. Recon fails in the smooth stage of recon-all (please see the
> attached screenshot). How can i fix this?
> Best,
> Paul
>
>
> On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch <ansk@ikem.cz
> <mailto:ansk@ikem.cz>> wrote:
>
>     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 <mailto: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 <mailto: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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