I do not think it is easy to solve the problem, because often it is unknown were the exact GM/WM border is in the lesion. Manual editing may introduce
a bias to the CT, so probably it is better to leave it as a limitation of the method.
Best, Martijn
Dear FreeSurfer colleagues,
We’re working with MS data and wanted your input on how we could best handle patients with extensive cortical pathology causing inaccurate reconstructions of the surfaces. In short the pial surfaces “dips” in too deep towards the WM surface due to the T1-hypointensity.
A lot of the problems can be mediated by doing wm.mgz edits and actually including the lesioned tissues, which pushes out both surfaces to an accurate position. Sometimes though, the cortical lesion affects the whole depth of the surface and this trick does
not help.
Is there any way to directly push out or “anchor” the pial surface?
Post-doctoral research fellow
Multiple Sclerosis Imaging Group
MGH/HMS/MIT Athinoula A. Martinos Center for Biomedical Imaging
149 13th St Charlestown, MA 02129