Hi Daniel
what was your original data format? Did you start with dicoms?
Bruce
On Thu, 18
Oct 2012, Daniel Ferreira wrote:
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 <ni...@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:
>
>
> 1) 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.
>
>
> 2) Anyway, I tried also -notal-check to see if something
changed in
> spite Talairach failed, but it fails also (off course).
>
>
> 3) 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
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
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