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MNI coordinates determined using SPM2 and FSL/FLIRT with the ICBM‐152 template were compared to Talairach coordinates determined using a landmark‐based Talairach registration method (TAL). Analysis revealed a clear‐cut bias in reference frames (origin, orientation) and scaling (brain size). Accordingly, ICBM‐152 fitted brains were consistently larger, oriented more nose down, and translated slightly down relative to TAL fitted brains. Whole brain analysis of MNI/Talairach coordinate disparity revealed an ellipsoidal pattern with disparity ranging from zero at a point deep within the left hemisphere to greater than 1‐cm for some anterior brain areas. MNI/Talairach coordinate disparity was generally less for brains fitted using FSL. The mni2tal transform generally reduced MNI/Talairach coordinate disparity for inferior brain areas but increased disparity for anterior, posterior, and superior areas. Coordinate …