This study investigates brain functional network dynamics of freely behaving but head-fixed mice using functional ultrasound (fUS). Unlike traditional fMRI, fUS allows recording brain activity in awake, behaving mice without anesthesia. We established a pipeline for processing fUS data and applied it to behavioral mouse data from a preclinical model of autism carrying a Shank2 gene knockout mutation. The pipeline includes several pre-processing stages, a deconvolution-based method for investigating neuronal activity underlying the fUS signal, and an analysis using hidden Markov models (HMM) to gain insight into neuronal brain states and transition dynamics. Our results reveal that brain dynamics in Shank2-/- mice are altered compared to wild-type mice, suggesting that Shank2-/- mice are more likely to remain in a state comprising motor and somatosensory cortices involvement, which is also less likely to transition to a state in which motor, somatosensory, and anterior cingulate cortices are all activated. Furthermore, we show that state brain transition alterations are also accompanied by atypical behavior performance while on the wheel. This study demonstrates that fUS combined with the proposed pipeline can effectively identify brain network alterations in preclinical mouse models of neurodevelopmental disorders, shedding light on how clinically relevant mutations impact brain networks.