We propose a method for brain atlas deformation in presence of large space-occupying tumors or lesions, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its central point. Atlas-based methods have been of limited use for segmenting brains that have been drastically altered by the presence of large space-occupying lesions. Our approach involves four steps. First, an affine registration brings the atlas and the patient into global correspondence. Secondly, a local registration warps the atlas onto the patient volume. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery and radiotherapy.