First of all an important distinction: the output
-noise produces the noise level, which is not the same as the residuals. See the user guide for details on how to calculate those.
That said, your noise map certainly doesn't look as expected. Can you check if the image value in the black voxels are NaN (not a number)? That would be a numerical issue I have seen before in fMRI data, but not yet in DWI data. Can you also try if a larger window size, e.g.,
-extent 7,7,7 or
-extent 9,9,9, does produce a homogeneous noise map?
As a way forward, I have been working on improving numerical stability in the GitHub branch
denoising_updates. Can you check if this works for you?
cd [your mrtrix folder]
git checkout denoising_updates
dwidenoise ... (as you did before)
If that still doesn't help, try adding option
-datatype float64 to test in double precision. Afterwards, you can reset your default mrtrix install with
git checkout master && ./build.