Dear Freesurfer experts,
I'm involved in the infant research (less than 1 year of age).
I tried running the recon-all command, however it fails and I got the error below at the end. Could anybody please let me know how to fix it?
other error message please see attached file below.
#@# Talairach Wed Feb 17 16:07:00 CST 2016
/Volumes/YangLab/S001/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n
\n talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
/Volumes/YangLab/S001/mri
/Applications/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
Darwin MRI2deiMac.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
Wed Feb 17 16:07:21 CST 2016
tmpdir is transforms/tmp.talairach.45862
/Volumes/YangLab/S001/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.45862/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.45862/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=10.34, TE=5.09, TI=0.00, flip angle=12.00
i_ras = (-1, 1.32713e-08, 0)
j_ras = (-7.45058e-09, -7.45058e-09, -1)
k_ras = (-5.82077e-09, 1, 0)
writing to transforms/tmp.talairach.45862/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.45862/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 MRI2deiMac.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
recon-all -s S001 exited with ERRORS at Wed Feb 17 16:07:23 CST 2016
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