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My apologies, it ends up that this swap was because my initial registration .lta file wasn't referencing the correct source and destination files. Once I figured out how to export the correct initial transfrom from freeview, everything works.

Thanks! Dylan

On Feb 23, 2022, at 9:15 AM, Tisdall, Dylan mtisdall@pennmedicine.upenn.edu wrote:

Thanks for the help with my previous question on formatting the bbregister command line. Now that I've got it running, I'm seeing that 1 of my two subjects ends up with a 90 degree rotation (swapping SI and AP axes) when I try to register my 7T T1 or T2 scan to the surfaces from my 3T T1 scan.

I've so far tried to analyze similar datasets from two subjects, and I'm only having this SI/AP swap in one of them (the second subject works great once I apply an initial transform to get it close)

What steps should I take to try to understand what's going wrong?

I've loaded the moving image into freeview, applying the initial transform as part of the load, and the result seems to align pretty closely with the surfaces when I load those as well... so I'd expect bbregister should align these well.

Thanks again, Dylan