Give information on the output files in the documentation

[civier]

There is no information (that I can easily see in Readme or help) about what are the files that are generated by the pipeline as output. Often, it is not clear by their names.
Especially, I think it is important to document what is the orientation of the output files (the dwi orientation, the T1 orientation, other?)

[Lestropie]

I'm doing something similar right now for the outputs of statistical inference in MRtrix3. I suppose I haven't really considered doing similar for this tool given that I'd still like to be making quite large changes (including taking the preproc analysis level and parting it off into its own BIDS App), and BIDS DWI derivatives is still in a very elementary form so the form that those data should take is still somewhat ambiguous.