It looks like there is only gray matter (int 42), similar to cortical ribbon gray, no white matter in that gyrus in aseg, both in the original recon, and after painting gyral centers in brainmask. Octavian
On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie <octavian....@gmail.com> wrote: > Dear Bruce, > > I am not sure how an ok aseg.mgz would look like for a lesion like that, > but it looks like it includes one larger gyrus excluded by the pia, see > attached, I would be happy to retrieve that one as it is the bulkiest of > all the ones left out. > Thank you, > > Octavian > > On Tue, Nov 25, 2014 at 7:38 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> Hi Octavian >> >> I wouldn't use control points since it really isn't healthy wm. The only >> thing you can do is edit the wm.mgz and possibly also the brainmask, but >> it's so abnormal looking you may not be able to get accurate surfaces. >> How does the aseg look? If it is ok there may be one other option. >> >> cheers >> Bruce >> >> >> On Tue, 25 Nov 2014, Octavian Lie wrote: >> >> > 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....@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. >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >
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