We are pleased to announce the release of BrainSuite13, which is the first version of BrainSuite that runs natively on both Mac and Windows platforms (a Linux release is also planned). BrainSuite13 includes many new features for processing, analyzing, and visualizing MRI data. In addition to the cortical surface extraction tools upon which BrainSuite was initially developed, we have also added new functionality for performing brain image registration using SVReg (Surface/Volume Registration), which uses the surface extraction results to initialize an automated registration procedure. We are also introducing the BrainSuite Diffusion Pipeline (BDP), which provides new tools for correcting distortion in diffusion MR images and registering them to a structural T1-weighted image, computing various diffusion products including tensors and ODFs. BDP can compute ODFs using the recently developed Funk-Radon and Cosine Transform (FRACT). The results of BDP can be combined with the results of SVReg, enabling the analysis of diffusion and connectivity in the context of neuroanatomical ROIs. The software is available for download from the download page.