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A fundamental challenge in neuroscience is accurately defining brain states and predicting how and where to perturb the brain to force a transition. Here, we investigated resting-state fMRI data of patients suffering from disorders of consciousness (DoC) after coma (minimally conscious and unresponsive wakefulness states) and healthy controls. We applied model-free and model-based approaches to help elucidate the underlying brain mechanisms of patients with DoC. The model-free approach allowed us to characterize brain states in DoC and healthy controls as a probabilistic metastable substate (PMS) space. The PMS of each group was defined by a repertoire of unique patterns (i.e., metastable substates) with different probabilities of occurrence. In the model-based approach, we adjusted the PMS of each DoC group to a causal whole-brain model. This allowed us to explore optimal strategies for promoting transitions by applying off-line in silico probing. Furthermore, this approach enabled us to evaluate the impact of local perturbations in terms of their global effects and sensitivity to stimulation, which is a model-based biomarker providing a deeper understanding of the mechanisms underlying DoC. Our results show that transitions were obtained in a synchronous protocol, in which the somatomotor network, thalamus, precuneus and insula were the most sensitive areas to perturbation. This motivates further work to continue understanding brain function and treatments of disorders of consciousness. Author summary: We studied disorders of consciousness (DoC) by defining a brain state as a repertoire of metastable substates with different probabilities of occurrence. We created whole-brain computational models of DoC to uncover the causal mechanisms underlying recovery. These models allowed us to simulate transitions by studying the effects of artificial individual local perturbations under different protocol regimes. We demonstrated successful transitions in the synchronization protocol and showed that the most sensitive areas were located in the somatomotor network, thalamus, precuneus and insula. In the long-term, this could bring valuable insights for understanding DoC and open new avenues for future clinical therapies. [ABSTRACT FROM AUTHOR]