[ENH] Mrtrix3-based pipeline

[GalKepler]

Discussed in #186

^{Originally posted by GalBenZvi November 22, 2021}
Hi all,

I've been using mrtrix3 to process my diffusion data for the past few months and it seems to provide good results.

I was wondering if it might be beneficial to provide a mrtrix3-based pipeline in dMRIPrep?

I know that several functions of mrtrix3 actually serve as wrappers for FSL functions (like dwifslpreproc), but some preprocessing tools that are available in mrtrix3 aren't in FSL (like MP-PCA denoising, Gibbs de-ringing, etc.).

Would love your input on this matter!

Over the past few months, I've learned that mrtrix has an internal procedure for handling the rotation of b-vectors when applying such rotations and transformations to the DWI images (as part of many processes during preprocessing).

Additionally, I've implemented a pre-processing pipeline that is suitable for handling sophisticated fieldmap schemes (DWI+EPI) as this is the scheme we're using in my lab.
It is currently located in my fork of dMRIPrep but I would love to merge it into nipreps's original tool.
As mentioned, my pipeline utilizes mrtrix, but if this poses a problem in terms of integration with nipreps, I would be happy to explore alternatives.

Looking forward to your thoughts! (: