Deconvolution kernel across the whole brain?


Hello all,

Is it assumed in “Fibre density and cross-section - Single-tissue CSD” that the deconvolution kernel is the same across the whole brain? If so, how can we extend this to the infants’ data?

Thank you,


Any thoughts?


Too many, unfortunately…

Yes. That’s a central assumption in any spherical deconvolution approach, whether in MRtrix3 or otherwise. That’s extended in multi-tissue CSD to a set of kernels, each of which is assumed the same across the whole brain.

It depends what you mean by ‘infants’ exactly. If neonates, then you can use simple approaches as suggested in this thread. See this thread for a more involved discussion of the difficulties in modelling such data (there’s a few others on the topic if you search around). Otherwise, there’s been a bit of work on this presented at the last ISMRM, but it’s still very much an open question.

If on the other hand, by ‘infants’ you mean children over 1 or 2 years of age, then I reckon the standard adult pipeline would work just fine. The kernel is estimated from the data, so should match their particular properties – it might differ from what you’d see in adults, but probably not by a great deal by that age.

If by ‘extend’ you meant how do we include infant and adult data together in the same analysis, then that’s a whole other question… But again, if ‘infant’ refers to subjects aged 1-2 or older (preferably at least 2), then you might find that you can analyse them all using the same response function(s), as we recommend for any group analysis. But this is a gut feeling: the validity of this recommendation would need to be verified somehow, and furthermore will depend heavily on the specifics of your research question…


Thanks for your elaboration.
By infants, I mean from newly born to 6 months old subjects.
Our focus is on driving the brain growth trajectories in the first 6 months of life and we were hoping the using the mrtrix tools and specifically the tools related to CSD and FOD could help us.


OK, you’re right in the range where the brain is developing fast… This is where things get really interesting, but also where the research is very much ongoing. All I can say is this is obviously an area of great interest to some of us, given our involvement in the dHCP. You might be interested in some of @maxpietsch’s latest work in this area (requires an ISMRM login unfortunately).