Analyzing and interpreting of thermograms have been increasingly employed in the diagnosis and monitoring of diseases thanks to its non-invasive, non-harmful nature and low cost. This paper presents a thermal image analysis system based on image registration for morphoea disease diagnosis. A novel system is proposed to improve the diagnosis and monitoring of morphoea based on integration with the published lines of Blaschko. In this application, image registration based on global and local registration methods are found inevitable. A modified normalized gradient cross-correlation (NGC) method to reduce large geometrical differences between two multimodal images of different subjects that are represented by smooth gray edge maps is proposed for the global registration approach. It is shown in this paper that the NGC method outperforms phase correlation (PC) method by a lower rate of misregistration. This demonstrates that by using the gradients of the gray edge maps, the performance of the PC based image registration method can be greatly improved. © International Federation for Medical and Biological Engineering 2016.