Hi Koji,
The msmt_5tt
method estimates the average signal response in a WM-GM-CSF segmentation of a T1-weighted image. In and of itself, it will thus work in single-shell as well as multi-shell data. But as the warning highlights, the result (3 single-shell response functions) will not be very useful in resolving three tissues using MSMT-CSD, since it leaves you with an underdetermined problem: estimating 3 tissue volume fractions from only 2 b-values (b=0 and b=X).
Our implementation of Multi-Shell Multi-Tissue Global Tractography is not really designed for single-shell data. However, the question has come up a number of times and you can have a look at my earlier comments on the topic here. In summary, if you insist on working with single-shell (b=0 + b=X) data I recommend using a 2-tissue WM-CSF model within a white matter mask.
Hope this helps,
Daan