hi bruce, thanks. from the reading of "recon-all" it looks like this is a failure is occurring in the latter part of autorecon3 so I'm just rerunning that set and skipping autorecon2 on the subjects that failed.
correct? best, -robert On 6/4/13 9:38 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: p.s. you can check to see if those labels exist in your fsaverage/label dir On Tue, 4 Jun 2013, Welsh, Robert wrote: > 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 > > > > ********************************************************** 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
