Diffuse Optical Tomography (DOT) has recently emerged as a methodology for non-invasive brain imaging. The time-of-flight variant (ToF-DOT), with added dimensionality and depth selectivity, is capable of imaging deeper with centimeter-scale resolution. However, for decoding neural activity in the brain, a greater spatial resolution is needed (millimeter-scale) at a depth that has not been well studied (5-10 millimeters deep). We have demonstrated that imaging through the skull can be improved to millimeter-scale resolution using a higher density of sampled measurements than what has been traditionally employed. We have shown these results both with confocally captured and time-gated measurements to reduce experimental runtime, reconstruction runtime, and hardware needed for an integrated chip. We have also demonstrated this procedure with fluorescent markers in a mouse, achieving millimeter-scale spatial resolution and stimulus-triggered dynamic reconstruction through a human skull phantom. Our ToF-DOT system can distinguish between different stimuli applied to the mouse by localizing activity to different regions of the brain. We finally illustrate an extension to human use by demonstrating the potential of a high-density, fiber-based ToF-DOT system for hemodynamic monitoring. These studies highlight the potential of high-density ToF-DOT as a high-accuracy, non-invasive, optical brain-computer-interface.