when I tun the recon-all -sub -hippo-subfields. I get a crash at line 17 in
kvlSegmentHippocampalSubfields.sh:. Should I edit the line to prevent kvlSegmentHippocampalSubfields.sh from bailing out by changin exit -1 to #exit -1. I run recon-all -hippo-subfields with 3 gb ram on the cluster and I have set the wall time to 48 hours. The cluster use PBS on Rock centos distribution.
Knut J
On 08/18/2012 07:55 PM, Knut J Bjuland wrote:
When I run recon-all for subfield segmentation I get a segmentation error? I get the error message below. Cheers
Knut J
Bad trial move (maximal deformation: 278.205, lambda: 12.021) Cost going from 433597 to 1.79769e+308 Transforming mesh Done transforming mesh Increasing lambda from 12.021 to 24.0421 and trying again. Transforming mesh Done transforming mesh Calculating Levenberg-Marquardt step with lambda 24.0421... Time taken to solve the Levenberg-Marquardt system of equations: 0.621659 ...done! maximalDeformation: 348.155 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt...
Done transforming mesh Rasterizing Levenberg-Marquardt... /global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh: line 18: 21317 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt Linux c4-1.local 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subject_id exited with ERRORS at Sat Aug 18 19:00:37 CEST 2012
For more details, see the log file /home/kjbjuland/freesurfer/20_ucsd_automatic/023/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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