External Email - Use Caution Sorry for the very late reply and not explaining the problem well in the first place. I would still appreciate your assistance if possible. Like some other threads that are on the archive, I was experiencing the problem where the pial surface wasn't getting all of the gray matter. None of the threads have seem to been resolved so I hope I could get some help. Would it be alright if I sent the subject directory for you to take a look? Thank you.
On Fri, Dec 13, 2019 at 4:56 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Can you be clearer as to what the problem is? If it is that the cortical > segmentation (red voxels) don't seem to follow the white/pial surfaces, > then there is nothing to worry about because the aseg is not expected to > have a good cortical segmentation (see aparc+aseg.mgz instead). > > On 12/13/2019 12:12 PM, Monica Bondy wrote: > > External Email - Use Caution > Hello FreeSurfer experts, > > I am trying to figure out how to fix the segmentation so that the cortex > is properly included. > I have had this problem with several subjects, especially in the temporal > lobe regions. > > I have tried tkmregister but it unfortunately didn't change anything. I am > in the middle of using control points to try to fix this problem but it > hasn't been ideal as it is requiring a lot of control points. Do you have > any ideas on how to fix this? > > I have attached an image of what the problem looks like below. Please let > me know if you need anything else. > > Thank you! > > 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 > 2. Platform: macOS Mojave (version 10.14.6) > 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat > Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64 > > [image: Screen Shot 2019-12-13 at 9.56.46 AM.png] > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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