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. <DGREVE@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
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