I am trying to preprocess an fMRI dataset collected from a single subject with 60+ runs. These runs were collected across a period of 5 days and each time the subject was in the scanner, 4-5 runs were collected. Every time the participant was put inside the scanner, a new run of blip-down sequence (for fieldmap correction) was collected.
My question is if I apply TOPUP on each dataset (before motion correction), would it be valid to align all the runs collected on different days, with different fieldmap (i.e. shimming) together, and coregister to a single T1?
Another way is to run the preprocessing separately for each group of runs where the blip-down sequence (i.e. shimming) is the same for that set of acquisitions. What would be the rationale/benefit for analysing in this way?
Relatedly, on AFNI, I do not think it is possible to indicate multiple “blip_reverse_dataset” for a list of runs (please correct me if wrong).
Thank you so much in advance.