I am thinking that that's possible. Same command with same type of parameters executed successfully before the failure, and now previously failed command is working. I will try it again...
Thanks for the input. -Ronny > > 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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