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Abstract: Background: For robotized transcranial magnetic stimulation (TMS), the magnetic coil is placed on the patient\'s head by a robot. As the robotized TMS system requires tracking of head movements, robot and tracking camera need to be calibrated. However, for robotized TMS in a clinical setting, such calibration is required frequently. Mounting/unmounting a marker to the end effector and moving the robot into different poses is impractical. Moreover, if either system is moved during treatment, recalibration is required. Methods: To overcome this limitation, we propose to directly track a marker at link three of the articulated arm. Using forward kinematics and a constant marker transform to link three, the calibration can be performed instantly. Results: Our experimental results indicate an accuracy similar to standard hand-eye calibration approaches. It also outperforms classical hand-held navigated TMS systems. Conclusion: This robust online calibration greatly enhances the system\'s user-friendliness and safety