Hi Monica
hmmm, hard to say without seeing the dataset. You could try using expert options to change some of the intensity thresholds if this is something specific to your acquiisition. If you upload the gzipped subject dir we will take a look
cheers Bruce
On Fri, 13 Dec 2019, Monica Bondy wrote:
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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!
- FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514
- Platform: macOS Mojave (version 10.14.6)
- 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
Screen Shot 2019-12-13 at 9.56.46 AM.png