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