Hi Mark
did you create your own .gca file? If so, why? Does it happen for all your
subjects?
Bruce
On Mon, 12 May 2014, Mark Plantz wrote:
As a quick update to this problem, it looks like the wm_mean and gm_mean are
reasonable
during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm
mean = 0 for the
#CA_normalize and #EM_registration steps.
Could this have anything to do with using a manual talairach alignment in
previous steps? I
did include the -nogcareg flag with the recon-all command.
On Mon, May 12, 2014 at 4:36 PM, Mark Plantz
<markplantz2...@u.northwestern.edu> wrote:
Hi Freesurfers,
Does anyone know if it is possible to manually set the brain centroid during
the EM
Registration step of the recon-all pipeline. I am using a non-default atlas,
and have
discovered that many of my difficulties have resulted from the brain centroid
being
incorrectly assigned to a region of black space. Thank you for the help!
Best,
MP
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