When there is an alignment failure using the talairach method freesurfer reverts to mni tools. The mni tools will error out with mritotal on more modern linux platforms because mritotal references shellwords.pl which no longer ships with perl (starting around 5.14). So in order to solve this error the user either needs to manually align the data or use an older version of perl. Manually aligning the data is probably the easier route.
On 12/15/2016 08:33 AM, Aquino Domenico wrote:
Dear Freesurfer team,,
I'm trying to segment a pre-processed 3D PSIR volume.
After few minutes Freesurfer return the following error:
mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.12174/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/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/mritotal line 460.
ERROR: mritotal failed, see transforms/talairach.log
I can't understand which could be the problem.
In attachment you'll find the log file.
Could you please help me?
Thanks a lot,
Domenico
Eng. Domenico Aquino Department of Neuroradiology IRCCS Foundation Neurological Institute "Carlo Besta" Via Celoria,11-20133 Milano Phone: +39 02 23942472 Fax +39 02 23942543
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