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:Freesurfer@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
