I have a question about the order of pre-processing steps.
First a brief run down of what we do in our group:
Prior to acquisition of our task based runs, we collect two volumes of the brain using a spin echo EPI sequence from both phase encoding directions (A to P and P to A) to be utilized in later distortion correction (a la topup / applytop up in FSL).
During preprocessing, a popular preprocessing order prescription is to run basic motion correction (e.g., using fsl’s mcflirt) before top-up. First quick question: do folks agree that this is the correct order prescription? When we thought through the logic, that order made sense, but we saw one functional connectivity paper recommend doing it the opposite order (namely topup before mcflirt) with no rationale given. Nonetheless, it seems that many prescribe motion correction as the first step, including fMRI prep, so we are thinking this order is best?
Still, we started wondering a bit more about these two steps. Post motion correction, your functional volumes will be aligned (often to the middle volume of a run), which is great, but what about the spin echo images? Should you also apply mcflirt to those images so they align to the functional data as best as possible? Otherwise, aren’t you applying distortion correction to functional images that are in a slightly different position and thus perhaps not making the most of this step? Pragmatically, I do not know if you can even do motion correction on the spin echo data because the spin echo volumes are different sequences relative to the remaining data so maybe it is not even a good idea? Could it mess up the spin echo data with downstream consequences for the efficacy of topup?
Any insight here would be wonderful.