A method for fully automated localization and channel identification of electroencephalography (EEG) electrodes. The electrode locations are automatically identified from three dimensional images stored in an electronic format, wherein the images may be derived from magnetic resonance imaging (MRI) that render the electrodes visible and object shapes and properties are used to locate the electrodes in the three dimensional images. The three dimensional images also show the brain in detail, such that the relationship of the electrodes to the brain is available, thereby making it possible to better identify electrical sources within the brain that create the EEG signals.