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In order to reduce fluoroscope usage in endovascular surgery there is a need to develop autonomous catheter insertion systems. We propose a system for tracking the position of the catheter using a magnetic motion capture sensor to provide feedback to a catheter driving mechanism to perform autonomous catheter insertion in major vasculature. Catheter insertion path reconstruction experiments were performed with the system inside silicone model of major vasculature to simulate surgery. As result the system reproduced a path inside the silicone blood vessel phantom with less than 7 mm of error. We found that error in path reconstruction depends on the model's cross-section diameter, the properties of the catheter insertion mechanism, the magnetic sensor and the system guidance technique.