We do have this script available for alignment across two sessions.
https://afni.nimh.nih.gov/sscc/dglen/alignmentacross2sessions
The script aligns to an in-between session space. That space could be used for all time points, or the approach could be extended to combinations of in-between spaces. I'm not sure how important that is though.
There have been a few papers looking at this that might be useful. The Freesurfer folks published a method a few years ago that looks interesting.
[
www.ncbi.nlm.nih.gov]
[
surfer.nmr.mgh.harvard.edu]
