[Freesurfer] Combining cross sectional and longitudinal analyses

Hi

I have two groups I want to compare, in total 172 scans Of these 78 got a a follow up. Groups are approximately evenly distributed.

I want to do first a cross sectional comparison and subsequently a longitudinal analysis for the 78 subjects only.

My question is: (1) Is it is valid to analyse all data using the longitudinal processing stream ( e.g. recon-all -all, recon-all -base, recon-all -long), even though I do separate cross sectional and longitudinal analyses? Or (2) should I analyse first the 175 using the cross sectional stream and then separately analyse the 78 with a follow up scan with the longitudinal stream?

Of course I would prefer option 1 as that would reduce potential editing/adjusting

many thanks in advance William