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LONI Brain Parser software segments regions of interest based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retained to work with your desired regions of interest. Brain Parser specifically includes skull and scalp removal, image nonuniformity compensation, voxel-based tissue classification, topological correction, rendering, and editing functions. The collection of tools is designed to require minimal user interaction to produce cortical representations. Surface representations of the human cerebral cortex are important for visualization and analysis of neuroimaging data (Thompson et al., 1997) and as constraints for localizing functional activation from magneto-encephalography (MEG) and electro-encephalography (EEG) data (Dale and Baillet). MR imaging offers neuroanatomical detail, but extraction of cortical surfaces from MR imagery faces several problems, including measurement noise, partial volume effects, and image nonuniformity do to magnetic field inhomogeneities.