Hi Elijah
I would try messing around with the intensity limits detected by mris_make_surfaces (and possibly also in mri_segment). There have been a number of posts on how to do this if you check the archive. It's pretty straightforward using the expert options in recon-all. Basically, look at the numbers that mris_make_surfaces prints out and see if you can constrain the allowable range of gray and white matter at the various borders to prevent what you are seeing (e.g. don't allow white matter to be as dark as the border that it finds in this example). You might also need to play with mri_normalize as the low contrast in your images looks like it is causing it to fail in some places and grow into the gray matter (you might try the -gentle switch, or -mprage).
cheers Bruce
On Sun, 16 Mar 2014, Elijah Mak wrote:
Hello Freesurfer Community, I have a basic question about pial edits.
I have a couple of subjects with very thin cortical measurements.Looking at the images, I think it could be an issue of weak intensity contrast between the GM and WM resulting in the erroneous pial surfaces? I have attached 2 screenshots in this email.
In such a scenario, what can be done to correct the pial surfaces?
Thank you very much for looking into this.
Best Regards, Elijah