Thanks. I looked at the SIENAX script and can see how to remove BET and substitute my own brain and skull masks. But now the problem is the skull mask. The one SIENAX uses is a strange beast, looks like a point cloud with vague outlines of the inner and outer skull. I can certainly make a hard brain mask using something else, or hand-edit one, but I have no idea how to make the type of skull mask used here by SIENAX.
It seems like SIENA does use a hard skull mask, but that does not help me with SIENAX.
If I cannot make my own "fuzzy" skull mask for SIENAX, I will have to go back to tweaking BET the best I can, unless you have other ideas.
-Jeff
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