Analysis and interpretation of functional MRI (fMRI) data have traditionally been based on identifying areas of significance on a thresholded statistical map of the entire imaged brain volume. This form of analysis can be likened to a "fishing expedition." As we become more knowledgeable about the structure-function relationships of different brain regions, tools for a priori hypothesis testing are needed. These tools must be able to generate region of interest masks for a priori hypothesis testing consistently and with minimal effort. Current tools that generate region of interest masks required for a priori hypothesis testing can be time-consuming and are often laboratory specific. In this paper we demonstrate a method of hypothesis-driven data analysis using an automated atlas-based masking technique. We provide a powerful method of probing fMRI data using automatically generated masks based on lobar anatomy, cortical and subcortical anatomy, and Brodmann areas. Hemisphere, lobar, anatomic label, tissue type, and Brodmann area atlases were generated in MNI space based on the Talairach Daemon. Additionally, we interfaced these multivolume atlases to a widely used fMRI software package, SPM99, and demonstrate the use of the atlas tool with representative fMRI data. This tool represents a necessary evolution in fMRI data analysis for testing of more spatially complex hypotheses.