Hi Steve,
Thanks for your response. I’m not sure how to check whether the code is checking the transforms due to my limited coding/programming knowledge…
However, I think you’re on the right track as my dwi, baseline, and brainmask have the same spacing and origin (with some floating number differences), whereas the ones I converted have very different origins. I tried centering my dwi and the converted/exported brain masks but the origin is still different from my DWI. Manually changing the origin of the masks to the dwi / baseline still gives me the error above, and visually in the viewer shifts the mask significantly AWAY from the brain from my dwi/baseline.
EDIT: I actually noticed an extra menu on the export portion of the segmentation module where I can specify the master volume. Ensuring this is the DWI seems to have fixed the problem! : )