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.
