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Introduces a computer-aided atlas-based functional neurosurgery methodology and describes NeuroPlanner, a software system which supports it. NeuroPlanner provides four groups of functions: (1) data-related for data reading, interpolation, reformatting, and image processing; (2) atlas-related for multiple atlases reading, atlas-to-data global and local registrations, two way anatomical indexing, and multiple labeling in two and three dimensions; (3) atlas data exploration-related for three-dimensional (3 D) display and real-time manipulation of cerebral structures, continuous navigation, two-dimensional (2-D), triplanar, 3-D presentations, and 2-D interaction in four views; and (4) neurosurgery-related for targeting, trajectory planning, mensuration, simulating the insertion of microelectrode, and simulating therapeutic lesioning. All operations, excluding atlas and data reading, are real time. The combined anatomical index of the multiple brain atlas database containing complementary 2-D and 3-D atlases has about 1000 structures per hemisphere, and over 400 sulcal patterns. Neurosurgical planning with mutually preregistered multiple brain atlases in all three orthogonal orientations is novel. The approach is validated with 24 intraoperative and postoperative datasets for thalamotomies, thalamic stimulations, pallidotomies, and pallidal stimulations. Its potential benefits include increased accuracy of target definition, reduced time of the surgical procedure by decreasing the number of tracts, facilitated planning of more sophisticated trajectories, lowered cost by reducing the number of microelectrodes used, reduced surgical complications, and the extra degree of confidence given to the neurosurgeon.