Highlights•White matter lesion changes and brain atrophy occurred simultaneously in early MS.•Spatio-temporal correspondence involved mostly the periventricular region.•In year 1, lower lesion volume changes were related to faster pseudo-atrophy.•Pseudo-atrophy was linked to the therapy-driven and “natural” resolution of oedema.•In the untreated period, higher lesion volume changes were linked to faster atrophy.