In mri_segstats command line generated from autorecon, I get an error that the option "--euler" is unknown.

====================================================
== /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all
3667   if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix ) ) then
3668       set cmd = ($cmd --euler)
3669   endif
====================================================



Cut-and-paste the following info into your FreeSurfer problem report:
---------------------------------------------------------------------

FREESURFER_HOME: /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0

RedHat release: CentOS release 5.8 (Final)

Kernel info: Linux 2.6.18-308.16.1.el5 x86_64

---------------------------------------------------------------------
Please include the following additional information in your report:

  1) subject name
  2) the entire command-line executed
  3) the error message generated
  4) optionally include the subject's /script/recon-all.log

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1)Subject Name = 12126_12126_20091110_30

2) We are running on a shared cluster of computers, so we wanted to break it into 3 sections to make it more robust to failing jobs.

#!/bin/bash
export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon1
status=$?
exit $status

#!/bin/bash
export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon2
status=$?
exit $status

#!/bin/bash
export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon3
status=$?
exit $status

3)
#--------------------------------------------
#@# ASeg Stats Thu Jan 24 20:57:29 CST 2013
/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS/12126_12126_20091110_30

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/ASegStatsLUT.txt --subject 12126_12126_20091110_30 

ERROR: Option --euler unknown
Linux helium-login-0-0.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 12126_12126_20091110_30 exited with ERRORS at Thu Jan 24 20:57:30 CST 2013





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