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 <matthieuvanhou...@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 >
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