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We are getting an error with recon-all at the stage of Talairach slignment. The error is the one described on the known issues: Can't locate shellwords.pl in @INC. We are running
perl5.18, so I downloaded and installed perl5.12 and changed the first line of mritotal as indicated on the ReleaseNotes. We are now getting a different error (pasted below). It appears I need to do manual Talairach alignment,
but not entirely sure how to proceed with that (is there documentation available)? Any other suggestions?
#@# Talairach Failure Detection Mon Nov 16 12:48:42 EST 2015
/Users/PBCAR/neuro/TNE/freesurfer_data/309/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
recon-all -s 309 exited with ERRORS at Mon Nov 16 12:48:42 EST 2015
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