OK, not something I’ve come across before… Just to confirm, the mrstats output you’re showing is for the dwi_den_preproc.mif image, but the dwi_den.mif image is OK?
Assuming that’s the case, does the b0_pair.mif image look sensible, for all volumes? Can I also check that the image you’ve provided to the -se_epi option of dwifslpreproc (b0_pair.mif) matches all the requirements stated in the docs:
Note that with the -rpe_pair option used here, which indicates that the SE-EPI image series contains one or more pairs of b=0 images with reversed phase encoding, the FIRST HALF of the volumes in the SE-EPI series must possess the same phase encoding as the input DWI series, while the second half are assumed to contain the opposite phase encoding direction but identical total readout time.
Finally, could the issue be related to running out of storage space…?
Also, what’s the purpose of that first mrconvert b0_AP.nii.gz b0_AP.mif command? As far as I can tell, that output is unused.
Hopefully some of this will provide a clue as to what’s going on…