A novel MR method and system is described for using MR images for planning radiotherapy treatment. The images are obtained by a scanner which generates a magnetic field with a magnetic center (isocenter). First at least one fiducial marker (4; 5) is applied to the body (1) of the patient at a predetermined distance from the isocenter. The patient is repositioned within said scanner such that an anatomical target (2) is located in close vicinity of said isocenter. A first image of said target (2) is obtained and then the patient (1) is shifted such that the fiducial marker (4; 5) is close to the isocenter. A second image is obtained at the shifted position, in which the fiducial marker has an accurate geometrical position, that is merged into said first image.