Oops! In whatever case I'm back from my situation-with-effectively-only-mobile-internet-access and have the paper now.

The repeated scans were indeed fMRIs measuring correlation of metabolic activity (a good proxy for activity) under various conditions. They made one diffusion tensor map from all their diffusion data (multiple scans). They saw correlations between a fiber-tract map they generated from the diffusion data (you plop down seed points in the cortex and other places and let fibers follow the main directions of diffusion) and their various activity correlation maps, and correlation was strongest for areas very close to each other on the brain and weak for longer fibers, especially inter-hemisphere fibers quite possibly because the tractography has a harder time getting those. The diffusion data also tended to show denser connections for stronger functional correlations, though as we see the instantaneous state can change the activity correlation quite a bit even though the white matter fiber tracts are not going to change that much on fast timescales. The fact that correlations are different in different activities illustrates that you dont need to have day to day changes entirely in the gross physical structure that shows up on scans of this type.

The actual layout of fibers at this coarse layer of detail is one thing of several that would contribute to activity correlations, including chemistry and actual engagement of said tract fibers for that particular activity and in that particular state, and all the fine molecular twiddling and potentiation at synapse scales.