Hi @BennyD,
This way you pose the question really gets at the heart of the bifurcation of how one goes about “quantifying structural connectivity”.
The documented Fixel-Based Analysis pipeline provides all of the requisite steps for performing statistical inference of quantitative parameters at the granularity of individual fixels. However you instead express the desire to quantify:
… the amount of structural connectivity between 2 regions …
This is actually a considerably different definition. This latter definition I have a manuscript I’ve been threatening to publish for the last five years; I promise we’ll get there eventually (pinging @alan-connelly…)
Once you are operating on the premise of quantifying connectivity of a specific pathway of interest, there are then two different ways of proceeding:
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Obtain quantitative estimates of connection density within the space of each individual using quantitative tractography techniques e.g. ACT / SIFT.
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Define a fixel mask in template space corresponding to the pathway of interest; within that mask, for any particular quantitative measure of interest (e.g. FD, FC, FDC), calculate the mean value within that mask for each subject.
In either case, you obtain a single scalar measure for that pathway per subject, to which any statistical analysis can then be performed. Option 2 is probably the easier of the two, and would require considerably less computation, especially given you already have spatial & fixel correspondence across all of your data.
Hope that irons out the confusion!
Rob