Hi @mblesac,
Some other users have reported similar issues (see threads linked here).
- Have you tried using the most recent LTS version (20.2.7 at this time)?
- Have you confirmed that the phase encoding directions are correct for your fieldmap and BOLD files?
- Have you confirmed that fMRIPrep is using your fieldmaps and not doing the SYN-based fieldmapless method? You did not share your command, so I don’t know if you enabled it or not.
- Does fMRIPrep return any errors?
- Is this error consistent across subjects?
Best,
Steven