Systems and method for producing functional brain organization maps are provided. The method includes providing functional connectivity magnetic resonance image (fcMRI) data, a population atlas, a variation map indicative of inter-subject variability in the atlas. The method also includes initializing a subject map using the atlas, determining a reference signal for each functional connectivity network in the subject map using signals derived from the fcMRI data, computing correlations between the signals and reference signal of each functional connectivity network, and iteratively updating the subject map by reassigning locations in the subject brain when correlating with a functional connectivity network, updating at each iteration the reference signal using the subject map, the population atlas, the variation map, and the set of fcMRI data. The method further includes generating a report indicative of a functional brain organization for the brain of the subject using the subject map.
