Interesting questions you raise here…
This is true, but applies primarily to single-shell CSD, since in this case there is no mechanism for handling contamination with CSF. Using high b-values attenuates the free water / extracellular signal to a sufficient extent that it can to all intents and purposes be ignored.
However, given that you have multi-shell data, you’d be using multi-tissue CSD. In this framework, the free water signal and GM signals are explicitly assigned to different outputs, so there is much less contamination of the white matter signal. I’m not sure whether the use of multi-tissue CSD will sidestep the free-water contamination issue completely when your raw data don’t contain sufficiently high b-values, but I reckon it’ll at least do a decent job. I’d be interested in hearing what the others have to say about this, it’s slightly unclear to me how to reason about it…
There is a mild divergence of opinion on this topic… Yes, it will mean that the signal will be affected by the extracellular signal to some extent. However, whether this therefore means that any differences in AFD cannot be meaningfully interpreted in terms of actual fibre density… Well personally I’m not sure it’s necessarily such a big issue: If you detect a 20% drop in AFD, it’s very difficult to see how that could possibly be due to the extracellular signal, given that it makes up ~20% by volume (in healthy parenchyma), and has much lower signal than the WM signal, even at lower b-values. Nonetheless, it does muddy the waters slightly in that it is no longer possible to rule out some involvement of the extracellular space - some of the change may be due to differences in there, although it’s IMO very unlikely to account for the whole difference…
Note the above applies to single-shell CSD - as I mentioned above, it’s not entirely clear to me how that translates to the multi-tissue CSD…
Yes, I’d agree with that - as per my previous comment. If you find a reduction is AFD (for example), by far the most likely explanation will be a genuine reduction in fibre density, even using lower b-values than optimal. So while the AFD measured at lower b-values might not be one-to-one with the intra-axonal space, but it’s still likely to correlate very strongly with the fibre density.
Not one that we’ve come up with, no… But you could always cover yourself by talking about changes in the FOD / fODF or something like that?
Good question. Personally, I can’t see any reasons why it would - these should be unaffected. Again, no doubt the others will have their own take on this…