In imageâguided radiotherapy (IGRT) of prostate cancer, delineation of the clinical target volume (CTV) often relies on magnetic resonance (MR) because of its good softâtissue visualization. Registration of MR and computed tomography (CT) is required in order to add this accurate delineation to the dose planning CT. An automatic approach for local MRâCT registration of the prostate has previously been developed using a voxel propertyâbased registration as an alternative to a manual landmarkâbased registration. The aim of this study is to compare the two registration approaches and to investigate the clinical potential for replacing the manual registration with the automatic registration. Registrations and analysis were performed for 30 prostate cancer patients treated with IGRT using a NiâTi prostate stent as a fiducial marker. The comparison included computing translational and rotational differences between the approaches, visual inspection, and computing the overlap of the CTV. The computed mean translational difference was 1.65, 1.60, and 1.80 mm and the computed mean rotational difference was 1.51°, 3.93°, and 2.09° in the superior/inferior, anterior/posterior, and medial/lateral direction, respectively. The sensitivity of overlap was 87%. The results demonstrate that the automatic registration approach performs registrations comparable to the manual registration.PACS number(s): 87.57.nj, 87.61.âc, 87.57.Qâ, 87.56.Jâ