[Freesurfer] Longitudinal strean including more than an image per time point

Dear all,

We want to run the longitudinal FS processing pipeline for our study, which has 4 time points. The 1st one was acquired with a radiofrequency head coil of 8 channels. Then, due to unexpected problems, some subjects at the 2nd time point were acquired with a different head coil of 16 channels. At time points 3 and 4, all subjects were scanned with the first head coil and only the subjects with different head coil at time point two were acquired twice (using both head coils). My question is: is there a way to do the longitudinal processing pipeline including more than an image per time point (one with the 16ch and the other with the 8ch)? If so, which will be the best procedure to follow?

Thanks in advance for your time,

Maria