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Volume-of-interest (VOI) extraction for radionuclide and anatomical measurements requires correct identification and delineation of the anatomical feature being studied. The authors have developed a toolset for specifying three dimensional (3-D) VOIs on a multislice positron emission tomography (PET) dataset. The software is particularly suited for specifying cerebral cortex VOIs which represent a particular gyrus or deep brain structure. A registered 3-D magnetic resonance image (MRI) dataset is used to provide high-resolution anatomical information, both as oblique two-dimensional (2-D) sections and as volume renderings of a segmented cortical surface. VOIs are specified indirectly in two dimensions by drawing a stack of 2-D regions on the MRI data. The regions are tiled together to form closed triangular mesh surface models, which are subsequently transformed into the observation space of the PET scanner. Quantification by this method allows calculation of radionuclide activity in the VOIs, as well as their statistical uncertainties and correlations. The methodology for this type of analysis and validation results are presented.