Fiber density and fiber cross-section with b=2000

I started to work with Matrix on my some DTI acquisitions and I found it a very good and useful tool!
However, I have some doubts and I hope that you guys can help me :wink:

I am working on DTI data acquired with multi-shell acquisition. I have 1 b0 and 106 directions with 2 b values (1000 and 2000). I would like to analyze the fiber density and fiber cross-section. Is it possible to use this kind of acquisition or I need to have a b-value > 2000? Also, is it possible to calculate the FD and FC for a single-shell acquisition?

Thank you so much!

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,

Thanks Donald,
I have both acquisitions. I will try it for both.

My apologies, I’ve just noticed I’d misread what you’d written – I’d understood that you had single-shell data acquired at b=2000s/mm², which is clearly not the case! If you have multi-shell data, you should definitely just be using the multi-shell multi-tissue CSD approach, as recommended in the documentation.

Regarding the requirement for high b-value data, my previous statement still applies, with the additional caveat that the requirement for high b-values actually becomes much muddier in this case, and basically no longer applies. This does impact on interpretability, but not on the validity of the analysis itself – see discussion of the topic in e.g. this post.

Fantastic, thanks for the clarification :slightly_smiling_face: