force each run to the same affine in realign4d

This PR addresses an issue raised by Anisha and Satra regarding multi-session space-time realignment when runs have different affines. The simple fix I propose here is to re-define each run's affine as the affine of the first run. This is done at the very beginning of the algorithm (not just at save time) to make sure that the same coordinate systems are used all the way through.