Single shell vs. "Single tissue"

[araikes]

Hi @ThijsDhollander

Thank you for clarifying all of this. It is, I think, what I was looking for. I do think that there can be some confusion because of the various ways of talking about it. I do have a few follow-up questions that I think would be beneficial not only to me but hopefully others reading/looking for this specific information (especially since you note that there is some outdated advice).

@ThijsDhollander

Minor error in there: using the “single-tissue” approach, you’d use dwi2response tournier and dwi2fod csd. What this does is (using your b=1000 dataset as an example): dwi2response tournier uses only your b=1000 data (i.e. not b=0) and extracts a single-fibre white matter response function for the b=1000 signal. Then dwi2fod csd uses only your b=1000 data, and deconvolves your b=1000 single-fibre white matter response function form that data, resulting in an FOD.

In the tutorial for the single tissue CSD (https://mrtrix.readthedocs.io/en/3.0.3/fixel_based_analysis/st_fibre_density_cross-section.html) uses dwi2response tournier and then states the following:

When performing fixel-based analysis, constrained spherical deconvolution (CSD) should be performed using the unique (average) white matter response function obtained before. Note that dwi2fod csd can be used, however here we use dwi2fod msmt_csd (even with single shell data) to benefit from the hard non-negativity constraint, which has been observed to lead to more robust outcomes

So is the recommendation for dwi2fod msmt_csd not an “across the board” recommendation but rather just for purposes of the tutorial or is there something that I’m missing in it? The tutorial does obviously only output the white matter FOD but the explanation isn’t clear.

And thanks for the link to the review paper. I did read it prior but again, it seems like the various “single xxx” that get discussed here in the community forum often seem to be used somewhat interchangeably so a clear definition of what can/cannot be used for a single shell (always assuming that single shell means b0 + some b shell) is very helpful.