Hi all,

I am working on some difficult NHP T2s that I need to align to NMT. They are difficult because some are not exactly complete (the rear and sometimes the very front of the brain is cut off), they have an implant artifact, and crucially in the most important area they have both a local change of tissue shape and a hypersignal. (my ultimate goal is to threshold that hypersignal or it's difference from normal brain, and refer it to the atlas)

If the T2s were acquired along with a T1 things would be easier (such T1 would have that local change of shape but no hypersignal, so it should warp nicely to NMT, and I could apply the warp to the T2), but most weren't.

Can you offer any hints as to strategy? So far I have had most luck with 3dAllineate followed by 3dQWarp both on inverted T2s (via 3dUnifize -T2 -T2), both using either hel or lpa. Though none is as a good as I would like, and also if hel works on some cases it fails on others, and vice versa for lpa. I may have to accept that but I am still hoping for a more universal solution. Even the better cases are not perfect, the main problem (as far as I can tell) seems to be confusing the gm/csf boundary with either the wm/gm boundary or csf/skull boundary along the dorsal surface,

One area in which I have been failing completely is skull stripping. I am aligning non-stripped T2 to non-stripped NMT. I have a feeling that stripped T2 to stripped NMT would align better, but is there a good way to strip such T2 before alignment? I tried 3dAutomask and it basically thinks that almost the entire volume is brain. 3dSkullStrip creates a blob that more resembles the brain but still it deviates from the actual brain by a lot. Maybe I can't figure out how to tune them to a monkey T2. Any suggestions, please?