Just to follow up on this, I’ve run the preprocessing steps (dwidenoise & mrdegibbs) on;
- the concatenated data, including b0s in both phase-encoded directions
- the main data, including b0s in the phase-encoded direction only
The residuals look better when the steps are run on the main data only. I’ve seen other threads where concatenating is advised e.g. here
I’m struggling to see why though. Would the distortions not be in the opposite directions and could this not result in anatomical details being mapped differently?
Hanne