I have been trying to implement fmriprep for preprocessing of my experiments.
Initially there were problems with the distortion correction via TOPUP method, in the pipeline, resulting in bizarre appearing images, even with swapped anterior and posterior directions. The dataset was an angulated one (-45 or 30 degress from the true axial plane). When I tried correction with the TOPUP routine in FSL, everything went well.
I had a hard trying to figure out what went wrong, but recently I tried it on a data that was aligned to the AC-PC line which worked well. I still can’t figure out what was the problem, but presume that it has something to do with the registration, or angulation.
I didn’t know where to start, so I can provide additional details, as probably needed.