Precise localisation of cortical activation in the early development of the infant brain remains unclear. It is challenging to co-register haemodynamic responses during functional activation in infants with the underlying anatomy of the brain. We used a multispectral imaging algorithm to reconstruct 3D optical topographic images of haemodynamic responses in an infant during voice processing. In this chapter, we present a method for co-registering 3D optical topography images reconstructed from functional activation data in infants onto anatomical brain images obtained from MRI structurals of the individual infants.