Traditional analyses of Functional Magnetic Resonance Imaging (fMRI) use little anatomical information. The registration of the images to a template is based on the individual anatomy and ignores functional information; subsequently detected activations are not confined to gray matter (GM). In this paper, we propose a statistical model to estimate a probabilistic atlas from functional and T1 MRIs that summarizes both anatomical and functional information and the geometric variability of the population. Registration and Segmentation are performed jointly along the atlas estimation and the functional activity is constrained to the GM, increasing the accuracy of the atlas.