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: > > External Email - Use Caution > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
