This toolbox aims to align the functional neuroanatomy of individual brains based on the patterns of neural activity while watching a movie. Instead of basing alignment on functionally defined areas, whose location is defined as the center of mass or the local maximum response, the alignment is based on patterns of response as they are distributed spatially both within and across cortical areas. The method is implemented in the two-dimensional manifold of an inflated, spherical cortical surface. The method, although developed using movie data, generalizes successfully to data obtained with another cognitive activation paradigm, viewing static images of objects and faces, and improves group statistics in that experiment as measured by a standard general linear model (GLM) analysis.