afni.nimh.nih.gov

This could be done with the following steps:

1. Align the twins' brain images approximately with 3dAllineate, so that they are "pretty close".
2. Use 3dQwarp -plusminus to warp the two previously aligned brain images towards each other -- to "meet in the middle".

If you want them to be close to MNI space, then in step 1 you should align them to the MNI template instead of to each other. The goal of step 1 is to get them close enough so that step 2 can work well.