It’s not per se a “have to” for
dwi2response, it’s just what those algorithms give you automatically (WM, GM and CSF response functions). But from an “interface” point of view, yes, you’ll always get all 3 response functions returned. For
dwi2fod with the current
msmt_csd algorithm, yes, 2 b-values (i.e. single-shell data with b=0 images) will only give you 2 tissue types. In that scenario, the natural thing to do is 2-tissue CSD with WM and CSF; to at least cover a wider range of diffusivities (compared to e.g. using a WM-GM model without CSF; which I definitely wouldn’t recommend).
Yep, exactly. That would be “single-shell 3-tissue CSD”, or SS3T-CSD for short. We’re using it over here on all our single-shell data (which is, mostly, all our data) and in several collaborations with people in the same scenario because of a range of reasons. At the moment it’s only an internal prototype; but a full version will be released at some point in MRtrix3, and along with it, or eventually after it, a further range of tools to deal with many “3-tissue” things. I’ve had successful results using lower b-values as well, and in a range of applications. See some links to ResearchGate stuff in this post as well (at the end of it): Low b-values with increasing and decreasing response function magnitude .
Yep, depending on your response functions, you’ll almost certainly get just a WM-CSF fit, with the GM inherently not being used in the fit. So you’d probably describe that just as well as 2-tissue CSD. Be careful though: if you just keep on using the “3” outputs from this (including the GM which is, apart from numerical inaccuracies, essentially zero), you can easily run into other problems. That would for instance be the case if you perform
mtnormalise on this output: the close-to-zero GM image may/will cause issues there.
mtnormalise works reasonably well on 2-tissue results, but you’ll have to explicitly only feed it the 2 tissue types (WM and CSF). Hence, to avoid these kinds of issues even getting an (accidental) chance of happening, I’d recommend to simply also perform the
dwi2fod with only 2 tissue types; for the sake of clarity and self-documentation of your pipeline.