so the GM is properly labeled by the aseg there? What about the faint wm? On Tue, 25 Nov 2014, Octavian Lie 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
