Deuterium metabolic imaging (DMI) is a novel method to obtain images of dynamic metabolism in the living human brain. While DMI is generally simple and robust, small signals from deuterated skull lipids can distort the metabolic information within the brain. Here, we use MRI-based information on brain and skull locations to remove lipid signals from DMI data. With an average 90 % lipid removal, DMI is used to generate distinct and artifact-free metabolic maps on patients with brain tumors.