The present invention provides a Dixon method for controlling a magnetic resonance imaging system (100). Dixon magnetic resonance data, first calibration magnetic resonance data and second calibration magnetic resonance data are collected using a pulse sequence command. Have the magnetic resonance imaging system perform multiple pulse repetitions (310). The multiple pulse repetitions cause the magnetic resonance imaging system to generate a Dixon readout gradient (320) along the readout direction (402). The pulse sequence command causes the processor to execute one or more first modified pulse repetitions (306) and one or more second modified pulse repetitions (308). The one or more first modified pulse repetitions cause the magnetic resonance imaging system to generate a first modified readout gradient (324). For collecting first calibration magnetic resonance data during a first modified readout gradient during at least one of the one or more first modified pulse repetitions. The first modified readout gradient is a reduction of the amplitude of the Dixon readout gradient by a predetermined factor. The one or more second modified pulse repetitions cause the magnetic resonance imaging system to generate a second modified readout gradient (328). For collecting second calibration magnetic resonance data during a second modified readout gradient during at least one of the one or more second modified pulse repetitions. The second modified readout gradient is the Dixon readout gradient amplitude reduced by the predetermined factor. The first or second modified readout gradient has an inverted polarity with respect to the Dixon readout gradient. By Fourier transforming the first and second calibrated magnetic resonance data in the readout direction, the first and second Fourier transformed data are calculated and the position between the first and second Fourier transformed data is calculated. Calculate the corrected phase difference by calculating the phase difference,
