Fiber density and fiber cross-section with b=2000

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Hi Andrea,

All of the original fixel-based work was done using single-shell acquisition – there is no fundamental reason why you can’t use single-shell data for any of these analyses. And b=2000 s/mm² data are perfectly acceptable – going from b=1000 s/mm² to b=2000 s/mm² makes a big difference, moving beyond that to e.g. b=3000s/mm² helps a bit more in terms of angular contrast and interpretability, but I don’t think that should preclude you from performing your analysis.

There are however a number of ways to process single-shell data:

  • using the regular csd algorithm in dwi2fod;
  • using the more heavily regularised hard-constrained version of it, which requires using the msmt-csd algorithm in dwi2fod with a single shell of data and a single tissue type output (as described in our documentation);
  • using a 2-shell 2-tissue CSD to extract WM & CSF densities, using the b=0 as the additional shell (we can treat the set of b=0 volumes as a shell in their own right), as described elsewhere on this forum (this is probably what I’d recommend);
  • Use the single-shell 3-tissue CSD approach proposed by Thijs Dhollander, with the caveat that this approach is not supported by the MRtrix3 team.

All of these will provide outputs that are usable within the FBA framework.

All the best,
Donald