In M R brain images, segmentation using intensity values is severely limited owing to field inhomogeneities, susceptibility artifacts and partial volume effects. Edge based segmentation methods suffer f r o m spurious edges and gaps in boundaries. A ,method is presented which combines the advantages of edge based and region based segmentation. Farst a multiscale image representation is constructed which favors intratissue diffusion over inter-tissue diffusion by exploiting local contrast. Subsequently a multiscale linking model (the hyperstack) is used t o group voxels into a number of segments. This facilitates segmentation of grey matter, white matter and cerebrospinal fluid with minimal user interaction. Using a supervised segmentatzon technique and M R simulations of a brain phant o m as validation it is shown that the errors are in the order of or smaller than reported in literature.