1. A magnetic resonance imaging system comprising: a prep scan section for performing a prep of scan acquiring plural sets of echo signals of a plurality of cardiac time phases which are mutually different from each other for each slice; a prep image generating section for generating a plurality of prep images corresponding to the plurality of cardiac time phases on the basis of the plural sets of echo signals, respectively; a reference information acquiring section for acquiring reference information for determining a first cardiac time phase and a second cardiac time phase on the basis of the plurality of prep images; a reference information display section for displaying the reference information; a cardiac time phase setting section for setting the first cardiac time phase and the second cardiac time phase in response to an operator's specification; an imaging scan section for acquiring imaging echo signals by performing an imaging scan upon each of the first cardiac time phase and the second cardiac time phase which are set by the cardiac time phase setting section; and an imaging image generating section for generating a first image based on an echo signal of the first cardiac time phase obtained by the imaging scan section, generating a second image based on an echo signal of the second cardiac time phase obtained by the imaging scan section, and acquiring a differential image by calculating a difference between the first image and the second image.