The resting state dynamics of the brain shows robust features of spatiotemporal pattern formation but the actual nature of its time evolution remains unclear. Computational models propose specific state space organization which defines the dynamic repertoire of the resting brain. Nevertheless, methods devoted to the characterization of the organization of brain state space from empirical data still lack and thus preclude comparison of the hypothetical dynamical repertoire of the brain with the actual one. We propose here an algorithm based on set oriented approach of dynamical system to extract a coarse-grained organization of brain state space on the basis of EEG signals. We use it for comparing the organization of the state space of large-scale simulation of brain dynamics with actual brain dynamics of resting activity in healthy subjects. The dynamical skeleton obtained for both simulated brain dynamics and EEG data depicts similar structures. The skeleton comprised chains of macro-states that are compatible with current interpretations of brain functioning as series of metastable states. Moreover, macro-scale dynamics depicts correlation features that differentiate them from random dynamics. We here propose a procedure for the extraction and characterization of brain dynamics at a macro-scale level. It allows for the comparison between models of brain dynamics and empirical measurements and leads to the definition of an effective coarse-grained dynamical skeleton of spatiotemporal brain dynamics.