Nodular heterotopia (NH) with overlying polymicrogyria can result in medically uncontrolled seizures. Most patients also exhibit deficits of function related to the location of the abnormal cortex. However, functional imaging studies show that the abnormal cortex can retain some function, making surgical planning difficult. It is not known if the connectivity of the abnormal cortex is normal. In this article, we performed an evaluation of molecular diffusion within the white matter in a patient with refractory epilepsy due to NH with overlying polymicrogyria. We observed that the white matter underlying the polymicrogyric area shows signs of microstructural abnormalities. This result suggests that the deficit of function from polymicrogyria result from both the structurally abnormal cortex and from its impaired connectivity.