Hi, I have a bunch of scans from patients with mulitple sclerosis. Since they all have substantial t2w hyperintensities I would like to automate the process of WM filling and re-running. Looking through the emails and the wiki, however, I am a bit confused.
http://www.freesurfer.net/fswiki/FsTutorial/ControlPoints says I should NOT use control points for white matter lesions: "Control points should NOT be used to try and normalize a brain lesion to 110. Such defects should be fixed with white matter edits"
BUT, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes says I should: "mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp."
I'm assuming that the guidance in the release notes supersedes the other wiki page but I wanted to make sure.
thanks, mishkin