Hi Yaqin.
I am not an MRtrix expert. It seems you are missing some preprocessing steps (see for some information and links: Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging | Nature Protocols, Questions about FOD abnormalities and bias correction in single-shell FBA pipeline - #2 by WilliamFCB)
Also, when using single shell data you should use Single-Shell 3-Tissue CSD (SS3T-CSD) and not MSMT-CSD.
Cheers
William