Hi Michael,
the longitudinal  image processing pipeline does not care which one is baseline and which are follow ups. It only cares what images belong to the same subject.
So, yes you can process this one with only two tone points instead of three.

Best Martin

On Apr 12, 2016 5:09 PM, Mihaela Stefan <mikaelastephan@gmail.com> wrote:
Hello FreeSurfers,

We are conducting a longitudinal analysis and we have a subject who is missing the structural at baseline (it has fMRI data though). That subject returned for the 1st and the 2nd follow-up. Can we process the longitudinal pipeline the usual way and account for the missing baseline in the LME analysis? 

The other option would be to treat the 1st follow-up as baseline but we would like to be consistent with the fMRI analyses and keep the baseline time point.

Thanks!
Mihaela