1. A method comprising: acquiring a first three-dimensional computed tomography image of a patient volume at a computed tomography scanner; acquiring projection images of the patient volume located at an isocenter of a linear accelerator; determining a first transformation between a coordinate system of the linear accelerator and a coordinate system of the first three-dimensional computed tomography image based on the projection images; acquiring a second three-dimensional computed tomography image of the patient volume; identifying a treatment isocenter in the second three-dimensional computed tomography image; determining a second transformation between the coordinate system of the first three-dimensional computed tomography image and the coordinate system of the second three-dimensional computed tomography image; determining a first position of the linac isocenter in the first three-dimensional computed tomography image based on the first transformation; determining a second position of the treatment isocenter in the first three-dimensional computed tomography image based on the second transformation; and aligning the treatment isocenter in the patient volume with the linac isocenter based on the first position and the second position.