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 means were OK for skull stripping, but then suddenly null for the other steps.

On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 <markplantz2016@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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