3D Magnetic Resonance (MR) and Diffusion Tensor Imaging (DTI) have become important noninvasive tools for the study of animal models of brain development and neuropathologies. Fully automated analysis methods adapted to rodent scale for these images will allow highthroughput studies. A fundamental first step for most quantitative analysis algorithms is skullstripping, which refers to the segmentation of the image into two tissue categories, brain and non-brain. In this manuscript, we present a fully automatic skull-stripping algorithm in an atlasbased manner. We also demonstrate how to either modify an external atlas or to build an atlas from the population itself to present a self-contained approach. We applied our method to three datasets of rat brain scans, at different ages (PND5, PND14 and adult), different study groups (control, ethanol exposed, intrauterine cocaine exposed), as well as different image acquisition parameters. We validated our method by comparing the automated skull-strip results to manual delineations performed by our expert, which showed a discrepancy of less than a single voxel on average. We thus demonstrate that our algorithm can robustly and accurately perform the skull-stripping within one voxel of the manual delineation, and in a fraction of the time it takes a human expert.© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.