Hi Daniel,
Sorry I think I am being incredibly obtuse.
So we have my MNI template, my FA image which is in diffusion space, and my ROI which is already in MNI space (I don't have transform matrices from this, this was made from an afni atlas already in MNI space).
I guess I am getting confused on where to put what. Does my FA image serve as the input to auto_warp.py. So this will get my FA image in template space. Then I am unsure what goes with what for 3dNwarp apply.
My apologies for all of the back and forth.
Emily