can you send us an example that works in 5.0 and fails in 5.1?
thanks
Bruce
On Wed, 2 Nov
2011, Joshua Lee wrote:
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of
5.1. However, since I am keenly interested in the hippocampal-subfield
segmentation capabilities of the most recent version, I am loathe to regress
to an earlier version of FreeSurfer
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee <jki...@ucdavis.edu> wrote:
#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011
/home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
I am receiving the error (pasted below) on about half of my
scans, despite all cans using same protocol. I detect no obvious
issue with the quality of the images. I have original dicoms,
and am using mri_convert to save into a single .mgz (or .nii,
doesn't neem to make a difference), and the unpredictability of
the error makes diagnosis problematic. TKMedit2 reveals
absolutely wacky registrations. I am processing on Freesurfer
5.1, and have replicated issue on two different installations. I
am designing a new longitudinal study inheriting the same
imaging protocol and I do not want to get in a situation
demanding manual editing of the talairach. Can anyone help me
out? Thanks, Joshua
ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32
EDT 2011
For more details, see the log file
/home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
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