FreeSurfer outside fmriprep: longitudinal?

I need to run freesurfer 7.1.1 on my mri data, therefore I will need to run FreeSurfer outside of fmriprep.

I have longitudinal data that is approximately 1 year apart for each timepoint. In order to make the FreeSurfer results compatible with fmriprep, how should I run the recon-all command? Comments from previous threads seem somewhat inconclusive.

I was thinking of merging the two T1w images together and running freesurfer on the combined T1, though this may not be ideal, since I would want separate structural measures for each timepoint.

Any help would be greatly appreciated!