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.
