A method of operating a surgical system. The method includes obtaining a magnetic resonance imaging (MRI) scan in which magnetic resonance (MR) visible targets are located; registering a robotic arm to the MRI scan using a digitizing tool, the robotic arm including: multiple joints and multiple degrees of freedom; an MR-compatible structural material; multiple MR-compatible joint motors; multiple MR-compatible joint encoders; and an end effector holding an MR-compatible surgical tool having a tool tip; and displaying a location of the tool tip relative to an image from the MRI scan.