Hi @kay1 , it looks like there are different fields of view in your images. If the scanner re-shimmed between the two acquisitions then your distortion correction is going to be off. That’s why there’s a strict check here.
If you’re confident that there wasn’t a re-shimming between your acquisitions you can manually copy the affine from one of your images into the other (eg the affine from the dir-AP_dwi to the dir-PA_dwi).