Hello Z K, Were you able to fix the bug? Best, Paul On Fri, Mar 3, 2017 at 12:14 PM, Z K <zkauf...@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 <a...@ikem.cz > > <mailto:a...@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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the sender > > and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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