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Two commonly used indices, pressure reactivity index and mean flow index, reflect different aspects of this regulation, namely changes in cerebral blood volume and blood flow velocity. However, their interchangeability, particularly in the context of traumatic brain injury (TBI), remains questionable. This study investigates the frequency and physiological basis of discordance between these indices. Using 96 simultaneous recordings of intracranial pressure (ICP) and transcranial Doppler-derived flow velocity in TBI patients, 501 non-overlapping 20-minute segments were extracted. Each segment was classified based on autoregulatory state, and physiological parameters, including ICP, CPP, end-tidal CO\u2082, cerebral compliance, critical closing pressure, and vascular dynamics, were analysed. Discordance between indices occurred in 26% of segments. Statistical and machine learning models identified vessel stability metrics (e.g. wall tension, vascular resistance, time constant) and intracranial dynamics (e.g. compliance, compensatory reserve) as the most predictive features of discordance. These findings suggest that the two indices capture distinct physiological processes and should not be used interchangeably. 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