Unfortunately it doesn’t seem like the explanation in your last paragraph applies, as my scanner was a “3-Tesla Siemans TIM MAGNETOM Trio MRI scanner”.
To confirm, it is not normal for b=0 images to be saved as their own .nii files (unless I used one of the two scanners you mentioned and exported as classic DICOM)?
If so, I maybe I can simply ignore/delete that .nii file with no corresponding .bvec/.bval files, because the b=0 images I’m looking for probably exist in the other .nii files that do properly have corresponding .bvec/.bval files?
(It is still mystifying that there would be a protocol named “DTI b0 1 AP” when b0 images are never collected by themselves, but if I can safely ignore it then I’m willing to.)
The other relevant information about the scan would be that two sets of whole-brain diffusion-weighted volumes (30 directions, b = 1000 s mm-2, 65 slices, voxel size = 2 x 2 x 2 mm3, TR = 9.3 s, TE = 94 ms) plus 6 volumes without diffusion-weighting (b = 0 s mm-2) were collected.
To double check, this thread you linked regarding spatial undistortion was referring to B0 fieldmaps and not b=0 diffusion images, right?
Also, I’m really glad you mentioned that sometimes a second diffusion series where the phase encoding polarity is reversed is also sometimes collected, because I now realize that that’s exactly what happened in my case. I was trying make sense of the AP and PA naming scheme I encountered, and reading up on the phase encoding polarity business made it click.