Hi @aszymanski,
Good to hear you’re enjoying using MRtrix!
As to a water compartment: multi-tissue CSD variants, with a compartment for CSF (free water), do this for you (and in contrast to NODDI, they account for the difference in T2; NODDI has a tendency to overestimate free water).
If you have multi-shell data (at least 3 distinct b-values, including b=0; i.e. same prerequisite as for NODDI), then you can use multi-shell multi-tissue CSD for this purpose. Have a read of the paper about the method. To use the method, you’ll need the dwi2fod command with the msmt_csd algorithm.
If you have single-shell data (a single, preferably high, b-value and b=0 image(s)), then there’s a new method I came up with last year, called single-shell 3-tissue CSD (abstract). This one is not publicly available yet in MRtrix though, but it will be eventually.
Both of these methods require you to obtain multi-tissue response functions from your data beforehand: typically this will be a single-fibre white matter response function, a grey matter response function and a CSF (free water) response function. To obtain these without any hassle caused by distortions, alignment of a T1w image or segmentation thereof, I’ve recently introduced an algorithm (abstract) that only requires your DWI data as input, and manages everything using just that. This algorithm can be used via the dwi2response script with the dhollander algorithm.
The result of dwi2response dhollander followed up by, e.g. dwi2fod msmt_csd (for multi-shell data) will give you WM FODs, a GM compartment image and a CSF (free water) compartment image!
Hope this helps. 
Cheers,
Thijs