Hello, I've tried a number of ways to generate pial surfaces for a monkey brain that has, to my eyes, very clear contrast. The white matter is segmented without too much pain and is mostly correct, but the pial surface never completely covers the gray matter. Instead, it either attaches to the white matter surface or meets the pial surface half way. I've tried more non-uniformity correction, and even painting in the gray matter more uniformly so that it could not possibly miss it, yet it does. Are there some secret parameters (i.e., low, hi gray values, etc. ) that one can play with it? Any guidance would be much appreciated.
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