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BACKGROUND Quantitative imaging such as Diffusion-Weighted MRI (DW-MRI) can be exploited to non-invasively derive patient-specific tumour microstructure information for tumour characterization and local recurrence risk prediction in radiotherapy. PURPOSE To characterize tumour microstructure according to proliferative capacity and predict local recurrence through microstructural markers derived from pre-treatment conventional DW-MRI, in skull-base chordoma (SBC) patients treated with proton (PT) and carbon ion (CIRT) radiotherapy. METHODS Forty-eight patients affected by SBC, who underwent conventional DW-MRI before treatment and were enrolled for CIRT (n = 25) or PT (n = 23), were retrospectively selected. Clinically verified local recurrence information (LR) and histological information (Ki-67, proliferation index) were collected. Apparent diffusion coefficient (ADC) maps were calculated from pre-treatment DW-MRI and, from these, a set of microstructural parameters (cellular radius R, volume fraction vf, diffusion D) were derived by applying a fine-tuning procedure to a framework employing Monte Carlo simulations on synthetic cell substrates. In addition, apparent cellularity (ρapp ) was estimated from vf and R for an easier clinical interpretation. Histogram-based metrics (mean, median, variance, entropy) from estimated parameters were considered to investigate differences (Mann-Whitney U-test, α = 0.05) in estimated tumour microstructure in SBCs characterized by low or high cell proliferation (Ki-67). Recurrence-free survival analyses were also performed to assess the ability of the microstructural parameters to stratify patients according to the risk of local recurrence (Kaplan-Meier curves, log-rank test α = 0.05). RESULTS Refined microstructural markers revealed optimal capabilities in discriminating patients according to cell proliferation, achieving best results with mean values (p-values were 0.0383, 0.0284, 0.0284, 0.0468 and 0.0088 for ADC, R, vf, D, and ρapp, respectively). Recurrence-free survival analyses showed significant differences between populations at high and low risk of local recurrence as stratified by entropy values of estimated microstructural parameters (p = 0.0110). CONCLUSION Patient-specific microstructural information was non-invasively derived providing potentially useful tools for SBC treatment personalization and optimization in particle therapy. This article is protected by copyright. All rights reserved.