We present an automatic technique to quantify changes in the volume of cerebral structures. The only manual step is a segmentation of the structure of interest in the first image. The image analysis comprises: i) a precise rigid co-registration of the time series of images, ii) the computation of residual deformations betweens pairs of images. Automatic quantification can be obtained either by propagation of the segmentation or by integration of the deformation field. These approaches have been applied to monitor brain atrophy in one patient and to investigate a ‘mass effect’ in tissue surrounding a brain tumour in four patients undergoing radiotherapy. Segmentation propagation gave good results for quantifying contrasted structures such as ventricles or well-circumscribed tumours; however, integration of the deformations may be more appropriate to quantify diffusive tumours.