Segmentation of anatomical regions of the brain is one of the fundamental problems in medical image analysis. It is traditionally solved by iso-surfacing or through the use of active contours/deformable models on a gray-scale MRI data. In this paper we develop a technique that uses anisotropic di usion properties of brain tissue available from DT- MRI to segment out brain structures. We develop a computational pipeline starting from raw diffusion tensor data, through computation of invariant anisotropy measures to construction of geometric models of the brain structures. This provides an environment for user-controlled 3D segmentation of DT-MRI datasets. We use level set approach to remove noise from the data and to produce smooth, geometric models. We apply our technique to DT-MRI data of a human subject and build models of the isotropic and strongly anisotropic regions of the brain. Once geometric models have been constructed they may be combined to study spatial relationships and quantitatively analyzed to produce the volume and surface area of the segmented regions.