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

Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Granberg, Erik Tobias
Verzonden: vrijdag 15 januari 2016 21:15
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] Cortical MS lesions - correcting pial surfaces

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? 

Thank you for the help! 

Kind regards,
Tobias

Post-doctoral research fellow 
Multiple Sclerosis Imaging Group 
MGH/HMS/MIT Athinoula A. Martinos Center for Biomedical Imaging 
149 13th St Charlestown, MA 02129