This thesis combines a Conscious Self-Organizing Map (SOM) with an interactive clustering method to analyze functional Magnetic Resonance Imaging (fMRI) data to produce improved brain maps compared to maps produced at The Methodist Hospital and in the literature focusing on similar problems. My new maps exhibit an increased level of symmetry, contiguity, coincidence with functional region, and more complete mapping of functional regions. The examined fMRI data contains brain activations of a subject repeatedly executing willed motion in response to a visual stimulus. Clustering the data from this experiment first determines the optimal preprocessing steps for cluster extraction, and second proves that the Conscious SOM provides a valid brain map that identifies interacting brain regions during the sequence of willed motion. I determined that the geometric rectification, motion correction, temporal smoothing, and normalization preprocessing steps facilitate the best clustering.