Hi Patrick,
Personally I’m not a big fan of the scaling by reciprocal of the node volumes; it’s there for feature-completeness, but it considerably alters the interpretation of the connectivity measures. I’ve probably ranted on it a few times on here, but I lose track of such things. The argument I give in the discussion of this preprint regarding intracranial volume extends to individual node volumes also.
The body of that preprint also does a better job of justifying the mechanism by which one can obtain estimates of white matter connectivity that should be better quantitatively than raw streamline count.
Yep that looks fine. Note that this may be different to how such quantifications are done elsewhere, as described in this wiki post.
Personally when I constructed my own pipeline I initially used affine registration for the same reason, but found the results to be entirely lacklustre and switched to nonlinear registration. So it is indeed possible that, for tutorials at least, people stick to linear registration for simplicity, but for an actual experiment I would myself recommend going nonlinear, even with a parcellation as crude as AAL.
Cheers
Rob