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....@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....@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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
