One object of the present invention is to perform compartmental analysis of the dynamics of a tracer in the brain, and the present invention provides a compartmental analysis system including a measurement apparatus that measures the strength of an electromagnetic wave from a tracer and a compartmental analyzer that performs compartmental analysis of the dynamics of the tracer in the brain on the basis of the strength of the electromagnetic wave, wherein the compartmental analyzer includes a rate constant calculation unit that calculates a rate constant when the tracer moves between compartments on the basis of the strength of an electromagnetic wave in a first compartment corresponding to the cerebral blood vessel in the brain or an input function in the first compartment, the strength of an electromagnetic wave in a second compartment corresponding to the brain tissue in the brain, and the strength of an electromagnetic wave in a third compartment corresponding to the cerebral sulcus or cerebral ventricle in the brain.
