I have cruised the mailing list for 5.3 specific causes. Some runs work and some hit this error.recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1
We are crunching a set of over 300 and I have checked the obvious. This is what I downloaded: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
We are running scientific linux 6.3 in our cluster and the one machine I checked did indeed have perl in /usr/bin and we are all x86_64.
I recently upgraded our pipeline from 5.1 to 5.3 but this is the first time running with these exact options.
I am not the one doing the research, I only automated it to run in our HTCondor cluster.
If it helps stdout for that one job is:
Linux glow-c112.cs.wisc.edu 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Fri Jun 13 19:00:45 CDT 2014 Found 1 runs /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig/001.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz
/var/lib/condor/execute/slot1/dir_4596/1217_1
mri_convert /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz --conform
mri_convert /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz...
mri_add_xform_to_header -c /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/transforms/talairach.xfm /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Jun 13 19:01:08 CDT 2014 /var/lib/condor/execute/slot1/dir_4596/1217_1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux glow-c112.cs.wisc.edu 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 1217_1 exited with ERRORS at Fri Jun 13 19:01:11 CDT 2014
For more details, see the log file /var/lib/condor/execute/slot1/dir_4596/1217_1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Command requested is <recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1 > finished with result<256> Non-zero recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1 Changing to 1217_1 to read scripts/recon-all.log ................................................................................................................................... Finished WITH freesurfer errors<<<<To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%3E%3E%3E%3E Tar up subject directory before leaving 1217_1/ 1217_1/mri/ 1217_1/mri/orig/ 1217_1/mri/orig/001.mgz 1217_1/mri/transforms/ 1217_1/mri/transforms/bak/ 1217_1/mri/rawavg.mgz 1217_1/mri/orig.mgz 1217_1/mri/orig_nu.log 1217_1/mri/mri_nu_correct.mni.log 1217_1/mri/tmp.mri_nu_correct.mni.5252/ 1217_1/mri/tmp.mri_nu_correct.mni.5252/nu0.mnc 1217_1/scripts/ 1217_1/scripts/build-stamp.txt 1217_1/scripts/recon-all.env 1217_1/scripts/recon-all.log 1217_1/scripts/csurfdir 1217_1/scripts/recon-all-status.log 1217_1/scripts/recon-all.local-copy 1217_1/scripts/recon-all.cmd 1217_1/scripts/recon-all.error 1217_1/surf/ 1217_1/tmp/ 1217_1/label/ 1217_1/touch/ 1217_1/touch/conform.touch 1217_1/stats/ 1217_1/src/ 1217_1/trash/ 1217_1/bem/ total 152