@mattcieslak mentioned today that the preps use RAS+, while FSL typically uses LAS+, and FSL isn't great at checking that orientations match. It's possible that prep preprocessing could force the orientation is RAS+, but the raw data might still be in LAS+ and any FSL-specific steps that use both images could ignore the orientation mismatch.
ASLPrep might already have a step that does this. I'll need to dig into the code to make sure.
Summary
@mattcieslak mentioned today that the preps use RAS+, while FSL typically uses LAS+, and FSL isn't great at checking that orientations match. It's possible that prep preprocessing could force the orientation is RAS+, but the raw data might still be in LAS+ and any FSL-specific steps that use both images could ignore the orientation mismatch.
ASLPrep might already have a step that does this. I'll need to dig into the code to make sure.
Additional details
Next steps