The recipe is as follows for
Define:
T_ct = translation that brings our CT coordinate system into your CT coordinate system
T_mr = translation that brings our MR coordinate system into your MR coordinate system
R_ctmr = transformation that registers CT to MR in your coordinate systems
To transform <x, y, z> for a point measured in our CT coordinate system into its registered position, <new_x, new_y, new_z> measured in our MR coordinate system
1) Apply T_ct to <x, y, z>.
2) Apply R_ctmr to the result of step 1.
3) Apply the inverse of T_mr (n.b., NOT the inverse of T_ct) to the result of step 2.