Highlights • White matter tracts that overlap with the thalamus and the putamen (hub+ tracts) have a lower degree of lesional and non-lesional tissue injury than white matter tracts that do not overlap or pass through these structures (hub- tracts), suggesting a protective role of the hubs against MS pathology. • Disease in both hub+ and hub- tracts was associated with measures of disability, however, disease in hub- tracts, retained slightly stronger correlation coefficients.