An error in the co-registration of a coordinate system used to represent a head of a subject in image data with a coordinate system used to represent the location of trackers affixed to the scalp surface of the head and a tracked device, such as a transcranial magnetic stimulation (“TMS”) induction coil device, is corrected using information representative of the actual distance between the tracked device and the scalp of the subject, such that representations of the tracked device and the subject's head are accurately shown on a display of a navigated brain stimulation (“NBS”) system tracking movement of the tracked device in relation to the subject's head. The correction of the error in the co-registration is performed without collecting additional tracking information from trackers on a tracked TMS coil device and the head, which avoids interrupting NBS using the TMS coil device.