The detection of brain activity with fMRI relies on focal increases in blood flow mediated by the neurovascular response. However, fMRI is also sensitive to potentially confounding and more widespread effects from autonomic variability. The latter may lead to blood flow changes through vascular reactivity in response to changes in intravascular CO2 or trough sympathetic vasoconstriction. These autonomically mediated changes may be co-occur or even be elicited by changes in brain activity. For example, arousal state changes across the sleep wake cycle are accompanied by changes in autonomic activity that have a distinct effect on the fMRI signal. These joint changes in arousal state and autonomic activity are attributed to a set of brain stem nuclei that have serve both functions and are selectively active during specific arousal states.
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