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" fischl@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" fischl@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
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