The invention provides for a method of operating a magnetic resonance system for acquiring magnetic resonance data (152) from a phantom (124) within a measurement (zone 108). The phantom comprises a known volume of at least one predetermined substance ((128), 130). The method comprises the step of acquiring (300) the magnetic resonance data by controlling the magnetic resonance system with pulse sequence instructions (150). The pulse sequence instructions cause the magnetic resonance system to acquire the magnetic resonance data according to a magnetic resonance fingerprinting technique. The pulse sequence instructions specify a train of pulse sequence repetitions. Each pulse sequence repetition has a repetition time chosen from a distribution of repetition times. Each pulse sequence repetition comprises a radio frequency pulse chosen from a distribution of radio frequency pulses. The distribution of radio frequency pulses cause magnetic spins to rotate to a distribution of flip angles. Each pulse sequence repetition comprises a sampling event where the magnetic resonance signal is sampled for a predetermined duration at a sampling time before the end of the pulse sequence repetition. The method further comprises determining (302) one or more performance degradation conditions of the magnetic resonance system by comparing the magnetic resonance data with a magnetic resonance fingerprinting dictionary (154). The magnetic resonance fingerprinting dictionary contains a listing of magnetic resonance signals for a set of system states in response to execution of the pulse sequence instructions for each of the at least one predetermined substance.