The toolbox generates lesion probability maps, which can then be used to 'fill in' the lesions, with normally appearing white matter. You could then run recon-all on these filled in T1 images. I haven't used such an approach myself, so I don't have any data regarding the validity of or accuracy of cortical measures obtained using such a method.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Granberg, Erik Tobias <EGRANBERG@mgh.harvard.edu>
Sent: Friday, January 15, 2016 1:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [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