An important parameter often investigated in the characterization of cortical functional organization is the areal extent of functional modules. Because it allows the visualization of functional modules with high spatial resolution in a noninvasive way to the cortex, intrinsic signal optical imaging (ISI) can be employed for the quantification of these areal extents. The present paper describes the use of the normalized threshold analysis of areal extent quantification for the objective assessment of single-whisker functional representations in the primary somatosensory cortex of adult rats. As the success of areal extent quantification depends on the ability of ISI to allow visualization of cortical representations with minimal stimulus-dependent blood vessel representations, which are commonly encountered by ISI, the present paper also describes the further development of the intratrial analysis of visualization for minimizing these vessel representations. Both analyses are discussed with respect to their advantages as well as their inherent limitations.