Brain architecture has been shown to change with different disease processes and this can be quantitatively measured using automated brain segmentation methods. FreeSurfer is a validated automated brain morphometry analysis method but requires time-consuming post-processing and is computationally complex. Fully automated prototype brain morphometry post-processing is available on our scanner, which generates brain morphology data at the end of the sequence acquisition and doesn’t require manual post-processing. This study confirms that this prototype software yields brain morphology data that is highly correlated to FreeSurfer for major brain regions. Therefore, it can be used to investigate biomarkers of brain atrophy in research and clinical research arenas.