Hi @BennyD,
Well, anything that relies on an accurate alignment between a T1w (or other anatomical) image and the dMRI data can’t work well if they don’t align. If you’re unable to correct for EPI distortions in the dMRI data, which are often quite significant, the non-corrected dMRI data can’t align well to the (not EPI distorted) T1w image.
So the problem exists if EPI distortions can’t be corrected. The most common, and arguably most reliable, way to correct for EPI distortions is to use reverse phase encoded scans.
However, that said, take a look at this thread, in particular this post and all others following below that one. In short, there are alternatives to using reverse phase encoded scans, which still allow you to correct EPI distortions. If successful and accurate, that would solve the problem!
Cheers,
Thijs