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 $status
3) #-------------------------------------------- #@# ASeg Stats Thu Jan 24 20:57:29 CST 2013 /nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS/12126_12126_20091110_30
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/ASegStatsLUT.txt --subject 12126_12126_20091110_30
ERROR: Option --euler unknown Linux helium-login-0-0.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 12126_12126_20091110_30 exited with ERRORS at Thu Jan 24 20:57:30 CST 2013
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I think the version of 5.2 that Nick cut was a little out of synch with some changes I made. Try using this version of mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos4
doug
On 1/24/13 10:14 PM, Johnson, Hans J wrote:
In mri_segstats command line generated from autorecon, I get an error that the option "--euler" is unknown.
==================================================== == /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all 3667 if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix ) ) then 3668 set cmd = ($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
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.
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Douglas Greve -
Johnson, Hans J