The functional architecture of the cortex has never been mapped in vivo with the fidelity necessary to distinguish “functional unit”. Mapping the functional architecture of the cortex, reflecting the observed regional and layer differences in synaptic density and its correlate energy metabolism, has been very challenging. Here we set out to address this issue by in vivo high-resolution cerebral blood volume (CBV) mapping of the mouse cortex. Tailored software, MouseStream, was developed to reconstruct the cortical CBV data through the normalized curved cortical coordinate (NCCC). NCCC allows projection of functional architectures mapped using CBV onto the cortical surface across the whole cortex and from different cortical depths.