Hello. FreeSurfer newbie here. I have a data set of 14 subjects. I’ve successfully run recon-all on 12 subjects but 2 are giving me the same error message: ERROR: mritotal failed, see transforms/talairach.log
Beneath that it says: For more details, see the log file /Users/kathleen/Documents/subjects/9304/scripts/recon-all.log And the recon-all.log says, for mritotal: mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.45457/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /Applications/freesurfer/mni/bin/../lib/mni_autoreg /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0 /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at /Applications/freesurfer/mni/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log Darwin Kathleens-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Dec 17 19:05:52 PST 2014; root:xnu-2422.115.10~1/RELEASE_X86_64 x86_64 recon-all -s 9304 exited with ERRORS at Thu Feb 19 09:49:28 EST 2015 All of this is fairly opaque to me. Any ideas how to fix the problem? Thank you in advance for your help. Kathleen J. Durkin, M.S. Director, Data Analysis and Training, MRI Research Program New York State Psychiatric Institute 1051 Riverside Drive New York, NY 10032
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