Abstract: A method for mapping functionally related brain regions of a subject. The method includes receiving a structural brain image and a dataset of resting-state functional MRI (rs-fMR1) three-dimensional (3D) image frames of a brain of the subject includes 3D image frames of the subject's brain over time. A functional connectivity map identifying groupings of functionally connected voxels is overlaid on the structural brain image. Spontaneous brain activations associated with each voxel in a grouping of functionally connected voxels are time-correlated with spontaneous brain activations in one or more other voxels in the grouping of functionally connected voxels. A reference location map for a pre-defined resting state network is generated, including reference information output. The reference location map includes brain reference locations that are informative of the one or more resting-state networks to assist a user in identifying the resting state network of the functional connectivity map.