Dear Freesurfer experts,

I wanted to run the Freesurfer's longitudinal processing pipeline (described here https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a series of MRI scans from a single patient. However, after looking at the scans, i realized that for most time points, the patient doesn't have a "simple/normal" T1 MPRAGE sequence available. Instead, they have a T1 sequence with a contrast agent, as well as T1 mp2rage sequences.

Is it possible/advisable to run recon-all in general or this pipeline in particular on T1 MPRAGE scans that have a contrast agent, or that are mp2rage instead of MPRAGE?

Thanks in advance!

Best,

Darko