Hi Xiaodong,
I am not an expert, but in case you don’t have this information already, I’ve included some suggestions and details that may be of use.
I typically and successfully use QSIprep for the DWI preprocessing (including bias correction) (GitHub - PennLINC/qsiprep: Preprocessing of diffusion MRI, which also generates some QC measures (see also their article on this: An analysis-ready and quality controlled resource for pediatric brain white-matter research | Scientific Data)
Besides the Mrtrix documentation, a good resource, with scripts, for FBA is:
Of course, there is the paper:
https://www.sciencedirect.com/science/article/pii/S1053811921006923?via%3Dihub
In the case of masks: synthstrip: synthstrip.io. Also part of Freesurfer is a very versatile tool.
Importantly, note that for “Single” data, the Single-Shell 3-Tissue CSD (SS3T-CSD) and not MSMT-CSD: Single-Shell 3-Tissue CSD (SS3T-CSD) | MRtrix3Tissue, is the recommended algorithm (see discussion: Single shell vs. "Single tissue" - #5 by araikes)
Finally, while the documentation states a threshold (e.g., -fmls_peak_value) of 0.6, 0.8 might be a better choice in many cases (see: Dhollander (FBA pipeline - quality check for several steps). Anyway, as recommended in the guidelines, it is best to check this on your own data.
Cheers
William