Use of full gradient matrix with cross terms?

[andrew_yung]

Hello there, I am trying to see if MRtrix can accept the b value information as a full b matrix with gradient cross terms, as opposed to just entering in a series of b-gradient vectors and their related effective b-values. I am working with Bruker data and so have access to the full b matrix for every diffusion image set in the scan.

I assume that the full 3x3 b matrix cannot be derived fully from just the gradient vectors and effective b-values. I hope that is correct?

[ThijsDhollander]

Just for reference, this was mostly answered by:

@jdtournier

So you could do this, but bear in mind there is no support within MRtrix3 for the full b-matrix. While we do provide a tensor-fitting routine, it’s very much a low priority for us. There is no real way to handle full b-matrices within a HARDI / multi-shell HARDI framework. There is some recent research from other labs that might be able to handle this in future, but it’s certainly not implemented within MRtrix3, and we have no plans at the moment to do anything about it…

In general, you would be much better off making sure the sequence does not generate large cross-terms. That used to be a problem when the read-dephase gradient was played out at the same time as the 90° slice refocus gradient, before the DW gradients - most other gradients don’t have anywhere near the same effect. If your sequence is still doing this, it’s about 20 years out of date… Also, it’s now recommended to disable the 180° crushers for b>0 images, since the DW gradients are essentially enormous crushers anyway. If you do all of this, there’s essentially nothing but the very short 180° slice-select gradient to worry about, and that self-refocuses very quickly, so should only produce tiny cross-terms.