Hello all, I have 2 subjects that failed autorecon-all at the same Talairach step. Both subjects successfully completed autorecon-all in version 5.2. Here is the output from one of the subjects.
Any suggestions?
Corinna
#-------------------------------------------- #@# Talairach Fri Feb 28 12:39:50 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
/home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri /usr/local/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 $ Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri Feb 28 12:41:10 EST 2014 tmpdir is transforms/tmp.talairach.30730 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30730/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30730/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=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.13732e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.45519e-11, -1) k_ras = (2.6057e-10, 1, 1.45519e-11) writing to transforms/tmp.talairach.30730/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30730/src.mnc transforms/talairach.auto.xfm
Fri Feb 28 12:41:27 EST 2014 talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Fri Feb 28 12:41:28 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0012, 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 Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s MWP_04182013 exited with ERRORS