1. A method performed in a radiotherapy system, the radiotherapy system comprising a source for producing a beam of radiation, a first imaging device for imaging from the beam, the source and the first imaging device mounted so as to be rotatable about an axis perpendicular to the direction of the beam, and a second imaging device having a volume within which imaging takes place, the method aligning the beam using a fiducial phantom including a plurality of markers, the fiducial phantom being located between the source and the first imaging device, the method comprising: rotating the source and the first imaging device in a trajectory about the axis while obtaining a plurality of images of the fiducial phantom from a plurality of different angles, wherein at least one image of the plurality of images includes a first feature of the second imaging device; adjusting the trajectory of the source relative to the first feature so as to position the isocenter substantially in the center of the volume; determining, from the locations of the markers in each image of the fiducial phantom, a position of the source at the rotational position the image was obtained; and calculating the center of rotation of the positions of the source to define the isocenter of the radiotherapy system.