Methods for optimizing the acquisition, reconstruction and analysis of positron emission tomography (PET) images for functional brain mapping have been investigated. The scatter fraction and noise-equivalent count rate characteristics were measured for the ECAT 951/31R PET scanner operating in septa-extended two-dimensional (2-D) and septa-retracted three-dimensional (3-D) modes. The 3-D mode is shown to provide higher signal-to-noise images than the 2-D mode at specific activities less than 30 kBq/ml. To enable increased temporal resolution in dynamic 3-D PET activation studies, a parallel version of the 3-D reconstruction algorithm was developed. Implementation of the reprojection algorithm on an 88 processor 1860 supercomputer resulted in a more than tenfold increase in reconstruction speed compared to a single 1860 processor system. An investigation of the optimal duration for imaging brain activations was undertaken in 12 normal subjects using repeated H2(15)O slow infusions and a visually presented lexical decision task. The significance of change in regional cerebral blood flow (CBF) was determined using statistical parametric maps for images acquired during stimulation, immediately after stimulation, and commencing 1 min after cessation of the stimulus. Regions of CBF change were detected in all three images. Dynamic 3-D, or four-dimensional (4-D), PET activation scanning is shown to be practical and likely to further improve the sensitivity of PET for detection of subtle regional CBF changes in functional brain mapping research.