Hi Octavian,
If you have an OK aseg volume, you could try to fit a surface over it using mris_make_surfaces with the -cover_seg flag.
Lilla
On Tue, 25 Nov 2014, Bruce Fischl wrote:
---------- Forwarded message ---------- Date: Tue, 25 Nov 2014 08:05:55 -0600 From: Octavian Lie octavian.lie@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: Eccentric lesions
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.lie@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 fischl@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.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. > > >
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