Hi Octavian,
Interesting topic, especially in the case where no reversed phase encoded data is available (else, an affine registration should be sufficient).
Maybe this thread can already give you some information of what you could try: Distortion correction using T1
In the past I have experimented by using ANTS with registering the FA image to a WM mask, combined with the registration between the average DWI and the T1 brain image (see Fig. 1 in this paper: https://www.ncbi.nlm.nih.gov/pubmed/25840837). Although it worked well and results seemed very nice, I was told that using the WM mask (which has very strong intensity gradients) can potentially introduce strong local deformations, so perhaps there exist better ways (see the thread I linked above). After that I haven’t experimented with it again.
N.B. I wasn’t yet using mrtrix back then, but ANTS registrations are easily importable into mrtrix (see the transformconvert command). So any other intra-subject registration approach based on ANTS can be integrated in your mrtrix pipeline.
Kind regards,
Thibo