The present invention relates to the field of radiation therapy. In particular, the invention concerns a method of calibrating a positioning system in a radiation therapy system comprising a radiation therapy unit having a fixed radiation focus point. The method comprises the steps of: -releasably attaching a calibration tool to the fixation arrangement; -performing an image scanning procedure with the imaging system; -determining a position of the calibration tool in a coordinate system related to the imaging system; and -calculating a position difference between the determined position of the calibration tool in the coordinate system related to the imaging system and a position of the calibration tool in the stereotactic fixation unit coordinate system, thereby determining a relationship between the coordinate system related to the imaging system and the position of the calibration tool in the stereotactic fixation unit coordinate system.