Hi Juergen,
This looks like an error very early in the hippocampal subfield segmentation routines. Could you please send me the file hippo-subfields.log (found in the "scripts" subdirectory of the subject in question), and ideally the files nu.mgz, aseg.mgz, and transforms/talairach.xfm files (found in the "mri" subdirectory)?
Thanks,
Koen
2011/6/24 Jürgen Hänggi j.haenggi@psychologie.uzh.ch:
Dear FS experts
We have some problems with the segmentation of hippocampal subfields. The recon-all finished without problems, but when using GEMS the following error occured:
nan nan nan nan nan nan nan nan nan Singular: 0 m_BoundingBoxSize: [94, 66,144] minimalMappedCoordinate: [3.40282e+38, 3.40282e+38,3.40282e+38] maximalMappedCoordinate: [1.17549e-38, 1.17549e-38,1.17549e-38] Cropping with min [-1932735280 -1932735280 -1932735280] and max [-214748367 -214748367 -214748367] /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 58718 Segmentation fault kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt failed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt Darwin Reinhard-Drobetzs-iMac.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386
recon-all -s 13716099 exited with ERRORS at Fri Jun 24 00:12:30 CEST 2011
I guess the problem occurred due to the NANs in the matrix, isn't it? Thanks in advance Regards Jürgen
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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