Hi Gianpaolo,
I’m not sure what’s going on exactly, but the first thing to note is that you’re not using a supported version of MRtrix3:
As I’d stated elsewhere, the code you’re using is an external, independent fork of our own code, and as such is not endorsed in any way by the MRtrix3 team. I’d recommend you use an official version of MRtrix3 (preferably the latest), and try to reproduce the problem there – there’s a good chance it’s already been fixed in the official version.