Greetings experts,

I have a scan protocol in which a single set of forward/reverse spin echo field maps was obtained towards the start of the scan session, followed by about 45min of different tasks that all use the same acquisition sequence (which are each fed to a separate afni_proc.py pipeline). I have noticed that, due to minor movements in between tasks, etc., the forward direction field map is not always perfectly aligned with the functional scan that is used as the volreg base (in our case, TR=2 of each task). If I am understanding the scripts correctly, I also noticed it appears when using the standard -blip commands in conjunction with afni_proc.py, the script seems to assume that the blip forward/reverse fieldmaps are already registered to the functional/EPI data and does not apply any type of registration prior to applying the blip warp. My question is two-fold:

1. Would it make sense in this scenario to linearly align the forward field map to the EPI volreg base (and apply the same transformation to the reverse field map)? If so, what would be the best way to accomplish this (e.g., run some separate alignment command(s) prior to running the main afni_proc.py step and then pass in the pre-registered versions as the -blip images?)
2. Alternatively, is it simply a bad idea to apply distortion correction when the participant may have moved a bit from the exact head position they were in for the field map acquisitions? Might this do more harm than good? We were advised to collect a fresh set of field maps whenever there is any shimming done or whenever the participant has been completely removed from the scanner, but I wasn't sure of the impact of more minor head adjustments in the space of one scan session.

Thank you!!