You should edit the wm.mgz. In these places, the WM will be labeled as non-WM. Just erase the mislabeled voxels.
On 8/6/19 6:31 PM, Caroline Chwiesko wrote:
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Hello Freesurfer experts,
I wrote a previous email about my issue that in many of my subjects I have spots where the ? h.white is extending too much into the gray matter after running recon-all.
As I understood from a conversation from somebody else, [[Freesurfer] WM surface including too much gray matter], you are currently looking into whether default parameter adjustments in recon-all can fix this problem. Until then, it was recommended to edit those errors manually.
My question is what editing technique should I use if I want to manually edit thesis type of errors? Removing the voxels that I think are gray matter from the white matter file using recon edit? I am a little confused about this because I noticed that the ?h.white boundary does not necessarily follow the wm boundary (see attached image), so I am wondering, if changes to the wm will fix the problem that I have.
Thank you very much in advance! Carolin
Screen Shot 2019-08-06 at 1.32.16 PM.png
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