Infrared thermography has been used to study the fast ion impact areas in the Co and Counter NBI ducts of TJ-II. Statistical results of the distribution of accumulated impacts on the walls of the duct have been obtained with an ion trajectory code. A more realistic description is obtained by coupling a beam simulation code to produce the ion birth point distribution. In this way, the main interception areas for both injectors have been found. Those areas constitute the Regions of Interest (ROI's) for the IR thermography system. The up-graded IR system, with its high definition MIR camera, enlarged window, and precision support and displacement mechanisms for camera and mirror, allows such ROI's to be captured. The optimal alignment parameters of the camera and mirror have been obtained with the optical simulation code ZEMAX, and the feasibility of the mechanical configuration in the crowded window environment has been checked with a CAD program, also used to simulate the field of view inside the ducts. Finally, infrared images of the ducts during beam pulses without magnetic field and with magnetic field have been compared, to obtain highlighted images of the fast ion impact areas in both ducts, showing the expected stellarator symmetry.