Dear All,

any suggestion about this type of problem? I tried control points through the middle/axis of the atrophic gyri (intensity 30-90 in T1 or brainmask), wm.mgz edits through the same (adding from brainmask by cloning those voxels; painting 110; or 255 brush), and modifying brainmask directly by painting 110 internsity voxels through the same (gyri interiors, where wm is supposed to be). Did not work, the atrophic gyri continue to remain outside the pia. Again, this is an example of an eccentric lesion with gyral atrophy, without interruption in the gray matter ribbon but very faint wm signal through the base of the affected gyri.

Thanks,

Octavian

---------- Forwarded message ----------
From: Octavian Lie <octavian.lie@gmail.com>
Date: Tue, Nov 18, 2014 at 10:50 AM
Subject: Eccentric lesions
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>

Dear All,

I am interested at getting as good pial/cortical reconstructions as possible on a series of epilepsy pt scans, some showing eccentric (cortical) lesions (focal encephalomalacias, infarcts, or after focal resections). One particularly difficult lesion type to get an accurate cortical surface is where there are prongs of grey matter bulging out (like a bag of worms), (mostly) without visible wm, see attached picture. These prongs are maintained in the brainmask.mgz and brain.finalsurfs.mgz, but not included in the pia with the default recon. Lesion voxel intensities vary from 30-90.

I tried cp, wm edits (using brainmask or T1 as referece), both, did not matter, it did not work.

Since I am not intested in wm/subcortical segmentation but just in a good pia, I was wondering if I 'create' thin wm tracts through the center of these gm prongs to help pial segmentation. If this is a valid option, should I create those in brainmask, brain.finalsurfs or wm.mgz, and should I use 110 or 255 for the brush?

Any other suggestions are appreciated. Nevertheless, I know there is a lot of tweaking of each lesion, and I try for more of a global approach to these kinds of lesions.

Thank you,

Octavian.