[Freesurfer] longitudinal analysis 5.0 or 5.1?

Dear Freesurfers:   We have a large group of subjects (for which we have two time-points) that were run  through the recon-all stream using 5.0.  We have done no manual editing yet.   We would like to do a longitudinal analysis of these subjects using 5.1 by comparing both time-points for each subject.  Is that a possibility using 5.1?   Also, at what point should I correct for topographical defects, or make edits to the white matter or brain mask volume? Should I edit both time-points separately first and then initiate the longitudinal analysis? If so, could I do the manual editing using 5.1?

thank you very much for your help, cheers, cat