During brain surgery, location of lesions can change in real-time due to leakage of cerebrospinal fluid. Therefore, navigating an MR-Endoscope probe with real-time intraoperative MRI is important in clinical application. However, conventional tracking system attached to the endoscope probe induces severe artifacts and is expensive and bulky. In this study, we propose a technique for navigating the endoscope probe without additional tracking system through segmentation of signals from tunable lens filled with gadolinium contrast agents. We also demonstrated tunable liquid-filled lens endoscope for intraoperative MRI. The proposed system/approach would be a good alternative as a tracking system for intraoperative MRI.