Hi Andrea, You can use the contour tool in the voxel edit mode to quickly and roughly fill in wm. Use the tool with the wm.mgz selected in the volume layer list but set the brainmask (or T1) as the reference. Set brush value to 255, and then do crtl+alt+leftbutton while dragging the mouse to adjust the contour, and then crtl+leftclick to fill in selected regions. Note that the cerebellar white matter may be outlined by the contour as well, but if it doesn't connect with the cortical wm then it won't be filled in. -Louis
On Thu, 6 Mar 2014, Andrea Grant wrote: > Hello, > > I'm working with T1 weighted scans obtained at 7T and have a problem with a > subject. I preprocess the images to deal > with the B1 inhomogeneity (normalize to PD and mask noisy pixels), and have > successfully segmented about 20 scans. I > often need to use control points, but they normally work just as I expect. > However, I have one subject where large > areas of the brain are completely excluded from the segmentation (basically > the entire occipital lobe). I added control > points and re-ran, to no effect. > > I'm attaching a screenshot of the brainmask with surfaces, my control points, > and the white matter mask. Clearly, the > skull stripping wasn't very successful (I adjusted the watershed threshold > manually, but at one value I got the current > result and at a single integer lower I lost half the brain). I have > successfully segmented other subjects with equally > poor skull strips, though, so I don't believe this has any bearing on the > current issue. > > Is editing the white matter mask the only way to fix this? If so, do I need > to carefully fill in on every slice, or can > I just brush in here and there to sort of "goose" the white matter into that > region? I can do the slice by slice fix, > but if there's a way to avoid the several hours it will take me, I would love > to know! > > Thanks, > > Andrea > > ----- > Andrea Grant > Visual Neuroimaging Technologist > Center for Magnetic Resonance Research, University of Minnesota > 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 > gran0...@umn.edu > umn.edu/~gran0260 > > _______________________________________________ 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.
