The thalamus plays a major role in regulating the transfer of information through the brain and is also implicated in many neurodegenerative diseases. It is therefore crucial to improve our understanding of this key brain structure. Structural differentiation of thalamic nuclei in post-mortem 7T MRI was investigated. Thalamic sub-regions were identified in magnitude, R2*, R1 and magnetisation transfer ratio maps from six post-mortem brains. Edge detection, k-means clustering algorithms and thin-plate spline warping to the Morel atlas were used to systematically identify thalamic nuclei. These data showed good correlation with stained histological sections and in vivo MRI data.