In that case it may be better to apply some form of GM lesion filling. Studies have shown that (at least in FAST and SPM) WM lesions affect the GM
segmentation throughout the brain (i.e. Chard et al, Gelinau-Morel et al, Battaglini et al) – and I have the feeling that the same is true for FreeSurfer. The reason is that the WM (and so the GM) distribution is slightly different as a result of the lesions,
thereby the border of the GM is drawn slightly different compared to the normal situation. So I would try to fill the WM (and GM) lesions before running FreeSurfer. Note that estimating the proper local GM intensity may be challenging as there is a lot of
intensity variation in the GM.
Best, Martijn
Hi Martijn,
Thank you for the response! I believe you are right that it is a complex problem. It is true that the GM/WM border can sometimes by hard to identify in type I (leukocortical) lesions, but in in purely intracortical lesions, it is still readily identifiable.
We also have corresponding 7T scans to help guide our edits. In this case we are specifically interested in looking at the relationship of cortical pathology and cortical thickness and are therefore still looking for a possible workaround.
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.
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
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