A system (100) is provided for performing a model-based segmentation of an anatomical structure in a medical image. The system comprises a processor (140) configured for performing a model-based segmentation of the anatomical structure by applying a deformable model to image data (042). Moreover, definition data (220) is provided which defines a geometric relation between a first part and a second part of the deformable model of which a corresponding first part of the anatomical structure is presumed to be better visible in the image data than a corresponding second part of the anatomical structure. The definition data is then used to adjust a fit of the second part of the deformable model. As a result, a better fit of the second part of the deformable model to the second part of the anatomical structure is obtained despite said part being relatively poorly visible in the image data.