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 > > 1463859753944_LogoWhite.jpg > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
