Thank you so much for your patient guidance and insightful suggestions. Your detailed explanations and pipeline recommendations have been tremendously helpful to my study.
Through carefully reviewing the official MRtrix3 documentation (particularly the dwi2fod section), I’ve identified the key technical rationale: When using the msmt_csd algorithm with datasets containing only two distinct b-values (e.g., my current data with 1×b=0 and 55×b=1000 volumes), it’s only feasible to reliably estimate fiber orientation distributions (FODs) for white matter and CSF, whereas grey matter FOD estimation becomes mathematically underdetermined or invalid.
Best regards,
Xiaodong Chen
The Seventh Affiliated Hospital, Sun Yat-sen University