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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