The self-organising global dynamics underlying brain states emerge from complex recursive nonlinear interactions between interconnected brain regions. Until now, all efforts of capturing the causal mechanistic generating principles have proven elusive, since they have been unable to describe the non-stationarity of brain dynamics, i.e. time-dependent changes. Here, we present a novel framework able to characterise brain states with high specificity, precisely by modelling the time-dependent dynamics. Through describing the topological structure of the brain at each moment in time (its ‘information structure’), we are able to classify different brain states by using the statistics across time of these exact ‘information structures’ hitherto hidden in the neuroimaging dynamics. Proving the strong potential of this framework, we were able to classify the neuroimaging data from two classes of comatose patients (minimally conscious state and unresponsive wakefulness syndrome) compared with healthy controls with very high precision.