Although we don't have a premade pipeline for this, it is certainly possible with AFNI tools. You can align all your anatomical datasets to a specific time point or to an "in-between" time point. You can use this reference anatomy instead of a standard MNI or Talairach template or use a standard space template as an additional step. For an example with just two time points, see this link:
https://sscc.nimh.nih.gov/sscc/dglen/alignmentacross2sessions