ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those.
thanks -robert On 6/4/13 8:59 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: Hi Robert I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2 cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote: > Hi, > > We were re-processing a subject to test the fix for 5.2 to 5.3. The >initial recon-all and subsequent autrecon2 > and autorecon3 were run a few days ago under 5.2. Yesterday I installed >5.3 and we ran the following: > > export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer > recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3 > > It ran for about 4.5 hours and then gave this error: > > >-------------------------------------------------------------------------- >----------------------------- > [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log > SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer > FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 > Loading source label. > Invalid argument > ERROR reading >/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh. >label > Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 >19:32:05 EDT 2008 x86_64 x86_64 x86_64 > GNU/Linux > > recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013 > > To report a problem, see >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >-------------------------------------------------------------------------- >----------------------------- > > Some help would be appreciated. There is a file lh.BA1.label but not >lh.BA1.thresh.label, indeed there are no > files with "thresh" in their name under that subject. > > Thanks! > > -Robert > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not >be used for urgent or sensitive issues > > > 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. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
