Here we used the rat brainstem coma model and rs-fMRI to systematically study the network dynamics during recovery from coma. Using whole brain connectivity analysis we obtained connectivity slope maps from the comatose animals, which revealed the brain regions with higher connectivity changes. In parallel, we performed a seed-based analysis to specify the strengthened connections between ROIs. Both methods indicated an increase in the connectivity between basal forebrain, basal ganglia and thalamus, along the acute phase of recovery from coma. These parallel analyses applied to comatose rats provided new insights into the regulations occurring during recovery of consciousness.