Dear FS experts,
I got no answer to my question. Could anyone explain me what is the problem and how to solve it ?
Best regards, Matthieu
2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte matthieuvanhoutte@gmail.com:
Dear experts,
I am confronted with some problem in the "recon-all" of a few subjects concerning Talairach space, but don't know how to manage these.
Please find below the recon-all log with errors :
#-------------------------------------------- #@# Talairach Failure Detection Fri Dec 4 15:29:38 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6911, pval=0.4932 >= threshold=0.0050)
awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
tal_QC_AZS /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
TalAviQA: 0.93027 z-score: -10 ERROR: Talairach QA check failed! z-score = -10 <= -9 = threshold atlas xform error = 0 < -60 | > 24 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 INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Fri Dec 4 15:29:39 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/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
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri /home/global//freesurfer5.3//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 wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Fri Dec 4 15:31:35 CET 2015 tmpdir is transforms/tmp.talairach.13347 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.13347/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=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (7.45058e-09, 1, 0) writing to transforms/tmp.talairach.13347/src.mnc...
mritotal -verbose -debug -clobber -modeldir /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.13347/src.mnc transforms/talairach.auto.xfm
Fri Dec 4 15:31:58 CET 2015 talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Fri Dec 4 15:31:59 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0039, 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 wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s M0_2011-02-23 exited with ERRORS at Fri Dec 4 15:32:00 CET 2015
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks in advance for helping !
Best regards, Matthieu