An automated method for segmenting magnetic resonance head images into brain and non‐brain has been developed. It is very robust and accurate and has been tested on thousands of data sets from a wide variety of scanners and taken with a wide variety of MR sequences. The method, Brain Extraction Tool (BET), uses a deformable model that evolves to fit the brain's surface by the application of a set of locally adaptive model forces. The method is very fast and requires no preregistration or other pre‐processing before being applied. We describe the new method and give examples of results and the results of extensive quantitative testing against “gold‐standard” hand segmentations, and two other popular automated methods. Hum. Brain Mapping 17:143–155, 2002. © 2002 Wiley‐Liss, Inc.