Hello Z K, Thank you. I will do it later and update you. Best, Paul On Mon, Mar 6, 2017 at 9:07 AM, Z K <[email protected]> wrote:
> 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 <[email protected]> wrote: > > Hello Z K, > Were you able to fix the bug? > Best, > Paul > > On Fri, Mar 3, 2017 at 12:14 PM, Z K <[email protected]> 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 <[email protected] >> > <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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/proce >> ssing/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 >> > [email protected] <mailto:[email protected] >> vard.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 >> > [email protected] >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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 . 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. > >
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