Abstract Magnetic Resonance Imaging (MRI) is a flexible and powerful technology for quantifying the effects of many conditions, including numerous neurological disorders, on human brain anatomy, connectivity, vasculature, chemical composition, physiology and function. In the past 15 years, several open source tools have been developed that accurately and automatically segment an array of brain structures. In this project, we seek the resources to extend this set to enable the quantification of neuroanatomical changes that are critical to diagnosing, staging and assessing the efficacy of potential therapeutic interventions in diseases such as Alzheimer’s and Parkinson’s. This includes the acquisition of datasets to enable manual labeling of structures of interest, the generation of documentation, tutorials, unit tests, regression tests and system tests to harden the tools and make them usable by clinicians and neuroscientists, and finally the distribution and support of the data, manual labelings and tools to the more than 32,000 researchers that use FreeSurfer through our existing open source mechanism.