In this study, we developed a correction method for coordinate transformation errors that are produced in combination with the ExacTrac X-ray system (BrainLAB) and HexaPOD (Elekta) in image guided radiation therapy (IGRT). The positional accuracy of the correction method was compared between the ExacTrac Robotics (BrainLAB) and no correction. We tried to correct iBeam evo couch top (Elekta) by operating two steps drive like ExacTrac Robotics. No correction for HexaPOD showed a maximal error of 4.52 mm, and the couch did not move to the correct position. However, our correction method for HexaPOD showed the positional accuracy within 1 mm. Our method has no significant difference with ExacTrac Robotics (paired t-test, P>0.1). But, when the correction values for the rotatory directions were large, the positional accuracy tended to be poor. The smallest setup errors for the rotatory directions are important for IGRT.