afni.nimh.nih.gov

Sorry, small misalignments are unavoidable, and it's likely you will have to use a nonlinear approach. auto_warp.py should make this relatively painless although it will still be slow. See this class documentation (slides 38 and 39) for how to invert the transformation:

http://afni.nimh.nih.gov/pub/dist/edu/latest/afni11_roi/afni11_roi.pdf