Re: [Freesurfer] Talairach Failure Detection

Hi,

I did recon-all -i <dicoms> -s <id>

and then what Nick posted.

2012/10/18 Bruce Fischl fischl@nmr.mgh.harvard.edu

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 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<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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
  >
  >
  >
  >

...

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