Re: [Freesurfer] Extending pial surface to include excluded cortex

I agree that it looks like a topological defect that is fixed incorrectly. We can't tell from looking at the image of one slice though. If you gzip, tar and ftp the subject to us we will take a look

cheers Bruce

On Thu, 8 Feb 2018, Arsenije Subotic wrote:

  Hi Doug,

  I’ve noticed that in my right hemisphere on top (I’m only using this hemisphere as the
  other hemisphere has tissue loss due to ischemia) there is also some atrophy. However,
  I’ve noticed that the surface can still probably be extended. It seems that there are
  some wm voxels which connect and disconnect after a couple of slices when I have wm.mgz
  on top of brain mask and when I use the heat colormap. In this case, is it ok to add wm
  voxels to connect them to the wm.mgz volume? This is what the tutorial says I should do,
  but I am worried since the wm intensity is sometimes 0 between these detached wm voxels
  and the main wm voxel. You can see it on the top left corner. And in general if there is
  no white matter sometimes and the pial surface does not extend and there is no defect,
  what is the general protocol? Thank you for your help!

  Arsenije