HI William，
Thanks for your comments.
I think the MSMT-CSD can be used with single-shell data, according to Fibre density and cross-section - Single-tissue CSD — MRtrix3 3.0 documentation, specifically subsection 9 supports it. But I am not sure whether using SS3T-CSD will output better results or not.
I can only doubt that there is a problem with the preprocessing steps. Referring to the paper you mentioned, I found that my previous misunderstanding was that the denoising and Gibbs ringing processes are optional rather than necessary. It seems that eddy correction alone is still not sufficient. Next, I plan to start from the denoising step, reprocess the data, and then proceed with tractography.
Many thanks
Yaqin