I think the version of 5.2 that Nick cut was a little out of synch with some changes I made. Try using this version of mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos4
doug
On 1/24/13 10:14 PM, Johnson, Hans J wrote:
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 = ($cmd --euler) 3669 endif ====================================================
Cut-and-paste the following info into your FreeSurfer problem report:
FREESURFER_HOME: /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
RedHat release: CentOS release 5.8 (Final)
Kernel info: Linux 2.6.18-308.16.1.el5 x86_64
Please include the following additional information in your report:
- subject name
- the entire command-line executed
- the error message generated
- optionally include the subject's /script/recon-all.log
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
1)Subject Name = 12126_12126_20091110_30
- We are running on a shared cluster of computers, so we wanted to
break it into 3 sections to make it more robust to failing jobs.
#!/bin/bash export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon1 status=$? 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
#-------------------------------------------- #@# 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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