Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
