Multiple sclerosis(MS) is characterized by white matter(WM) lesions and grey matter(GM) atrophy in the central nervous system. Software to measure GM atrophy is severely hindered by the presence of lesions. In order to facilitate development of accurate GM segmentation software in the presence of WM lesions, we present a novel, robust, flexible and open-source lesion simulation tool: LESIM. Initial analysis with 25 LESIM lesion simulated images shows natural-looking lesions in the correct locations, with correct signal-to-noise ratio and intensity compared to the rest of the image. Analysis with FSL-SIENAX confirms that GM segmentation is affected in HCs with simulated lesions.