Hi Katica
what format was the input image to recon-all? Can you verify that tkmedit
has the directions correct (that is what it labels as anterior is actually
anatomically anterior, etc...). If so, then the talairach just failed and
you will need to either try an alternative (like the MNI or SPM talairachs)
or generate it manually.
cheers
Bruce
On Thu, 2 Jan 2014, Boric, Katica A.
wrote:
Happy New Year freesuerfers!
I run into this error while doing recon-all :
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.
I would really appreciate if someone could give me some advice on how to fix
this error.
Thank you very much!
Katica Boric,
ps: Here is the error log:
#@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014
/home/XX/XXX/subjects/XXX_SurferOutput/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 Thu Jan 2 14:20:33 EST 2014
/home/XX/XXX/subjects/XXX_SurferOutput/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/XX/XXX/subjects/XXX_SurferOutput/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 localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Thu Jan 2 14:21:30 EST 2014
tmpdir is transforms/tmp.talairach.34005
/home/XX/XXX/subjects/XXX_SurferOutput/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.34005/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=8.23, TE=3.22, TI=450.00, flip angle=12.00
i_ras = (-1, -9.03383e-08, 0)
j_ras = (-1.3411e-07, 2.66591e-08, -1)
k_ras = (1.59256e-07, 1, -5.93718e-09)
writing to transforms/tmp.talairach.34005/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm
Legacy library shellwords.pl will be removed from the Perl core distribution
in the next major release. Please install it from the CPAN distribution
Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal,
line 460.
Thu Jan 2 14:21:43 EST 2014
talairach done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014
/home/XX/XXX/subjects/XXX_SurferOutput/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)
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 localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan 2 14:21:45 EST
2014
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