As I understand it, even monozygotic twins do not have very similar cortical folding patterns. You could try using the same-subject methods suggested in the README.registration file, but they may not work that well. Alternatively, you could put both subjects into AC-PC aligned space, which would not involve any stretching/shrinking of the brains, but would align them somewhat. At that point, you'd have to judge whether to use Talairach to try to further align their results (e.g., by flipping back and forth between their SPGRs to see how well the structures of interest overlap), or just leave them at the same orientation.