Probably a network glitch? I'd try restarting it and seeing if the error persists.
On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: > 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. 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