[Freesurfer] Longitudinal Subject/Base name errors

Hello Experts,

I am using fs 5.0.0. My naming convention is similar to 100001_S01 and 100001_S02 for subject, and then 100001 for the base. Now when I process the runs longitudinally, I get: ERROR: longitudinal base ID cannot be the same as a timepoint. I believe this is because of line 4845 in recon-all: grep $longbaseid ${longbasedir}/${BaseSubjsListFname} >& /dev/null. I can just as easily cut out this part of the code, or I could manipulate the base-tps file, or rename the base folder. But I do not know if there are other spots in the code that rely on the original naming conventions. Can anyone recommend one approach over the other?

Thank you very much, Jeff Sadino