Hi Marcel,
I am not an expert myself, but I successfully did some fixel preprocessing.The directions.nii is a specific fixel analyses format see Fixel image (directory) format — MRtrix 3.0 documentation
A very clear fixel analysis stream with easy-to-follow scripts can be found here: Meisler_Reading_FBA/fba/bash_scripts at main · smeisler/Meisler_Reading_FBA · GitHub
Regarding the peak threshold, the default 0.06 may be too liberal; 0.08 might be better (at least on my data). Best to test on your own data. See also (FBA pipeline - quality check for several steps)
Hope this helps. Cheers William