This looks like a problem we had with an older version. What version of
freesurfer are you running?
Martin Kavec wrote:
Hi,
I am trying to mask a non-brain tissue left by watershed based on the cortical
surfaces. I found that all what I need to be left is in aparc+aseg.mgz, so I
converted it to nifiti, along with brainmask.mgz and used FSL to binarize
aparc+aseg and mask the brainmask. I found that at many places the results is
too conservative and too much of the GM is missing, see the attached images,
and particularly the temporal lobes.
Is there a better approach to what I am trying to do and what could be the
explanation to the results I get.
Thanks,
Martin
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