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
