Thanks Nick very much for your suggestion.
Unfortunately it did not fix the error.
I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached.
What can be happening here? Any idea to fix it?
thanks
Daniel
2012/10/17 Nick Schmansky nicks@nmr.mgh.harvard.edu
Daniel,
See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
Nick
On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote:
Dear experts,
Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below).
I tried to follow the tutorial to fix a bad Talairach with:
- tkregister2 --mgz -s <id> --fstal --> not green lines appear, I
attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file.
- Anyway, I tried also -notal-check to see if something changed in
spite Talairach failed, but it fails also (off course).
- I used -use-mritotal but I still get the same. However, this time
processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck.
Please, any idea?
Thanks a lot
Daniel
#@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 /home/daniel/FreeSurfer/subjects/N001511_d2/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 siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC 2011 x86_64 GNU/Linux
recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST 2012
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