It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log.
mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny > > Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or > is BA3b.thresh the only one? If you remove the .thresh do you still get an > error? > > Thanks, > a.y > > On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: > >> Hello, >> >> I ran recon-all and left it running Friday afternoon/evening. When I >> next >> checked it this morning, the script had finished with errors. Looks like >> there was a problem with the file: >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label >> >> /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is >> a >> symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage >> >> Seems like I should be able to read lh.BA3b.thresh.label. Not sure why >> the >> script couldn't open it. Thoughts? >> >> -Ronny >> >> Further info below: >> >> machine: quito >> Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 >> /usr/local/freesurfer/dev/bin/freesurfer >> SUBJECTS_DIR: >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects >> Working Directory: >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig >> >> ** the exact command line I ran >> recon-all -autorecon2-cp -autorecon3 -subjid subj004 >> >> ** The command that caused the error (which was as a part of/ within the >> recon-all script) is >> mri_label2label --srcsubject fsaverage --srclabel >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label >> --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh >> --regmethod surface >> >> ** ERROR MESSAGE RECEIVED ** >> Permission denied >> mri_label2label: could not open label file >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label >> >> srclabel = >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label >> srcsubject = fsaverage >> trgsubject = subj004 >> trglabel = ./lh.BA3b.thresh.label >> regmethod = surface >> >> srchemi = lh >> trghemi = lh >> trgsurface = white >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects >> FREESURFER_HOME /usr/local/freesurfer/dev >> Loading source label. >> Invalid argument >> ERROR reading >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label >> Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC >> 2013 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 >> >> For more details, see the log file >> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> _______________________________________________ >> 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 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.
