Hi Mark
if you upload a subject that failed and the gca I'll take a look
Bruce
On Mon, 12
May 2014, Mark Plantz wrote:
Yes, I created my own atlas for use with 1-2 year olds. It seems to be
happening for all of
the subjects. I am wondering if changing the recon-all code to load the manual
t
Yes, I created my own atlas for use with 1-2 year olds. It seems to be
happening for all of the subjects. I am wondering if changing the recon-all
code to load the manual talairach.lta
file for the EM_registration and CA_normalization would possibly fix the
problem. It seems strange that the wm/gm
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 m
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
p
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
