Background In multiple sclerosis (MS), both lesion accrual and brain atrophy predict clinical outcomes. However, it is unclear whether these prognostic features are equally relevant throughout the course of MS. Among 103 participants recruited following a clinically isolated syndrome (CIS) and followed up over 30 years, we explored (1) whether white matter lesions were prognostically more relevant earlier and brain atrophy later in the disease course towards development of secondary progressive (SP) disease; (2) if so, when the balance in prognostic contribution shifts and (3) whether optimised prognostic models predicting SP disease should include different features dependent on disease duration.

Methods Binary logistic regression models were built using age, gender, brain lesion counts and locations, and linear atrophy measures (third ventricular width and medullary width) at each time point up to 20 years, using either single time point data alone or adjusted for baseline measures.

Results By 30 years, 27 participants remained CIS while 60 had MS (26 SPMS and 16 MS-related death). Lesions counts were prognostically significant from baseline and at all later time points while linear atrophy measure models reached significance from 5 years. When adjusted for baseline, in combined MRI models including lesion count and linear atrophy measures, only lesion counts were significant predictors. In combined models including relapse measures, Expanded Disability Status Scale scores and MRI measures, only infratentorial lesions were significant predictors throughout.

Conclusions While SPMS progression is associated with brain atrophy, in predictive models only infratentorial lesions were consistently prognostically significant.