It is an object of the invention to improve MRI based treatment, especially MRI based radiotherapy. This object is achieved by a method for calibrating a magnetic resonance imaging (MRI) phantom having an expected geometry and comprising at least one MRI detectable part with a position within the geometry which is known with a geometric inaccuracy. The method comprises the following steps: step 1: placing the phantom at a predetermined location in a magnetic resonance system such that the MRI detectable part is within a symmetry plane of a gradient system of the magnetic resonance imaging system and; step 2: acquiring an MRI image of the MRI detectable part of the phantom by means of a first sequence, wherein the MRI image comprises multiple slices; step 3: determining the geometric inaccuracy of the MRI detectable part of the MRI phantom based on the position and the representation of the part in the MRI image.