A system (11) includes a medical probe (36) for insertion into a cavity of an organ, which includes a position and direction sensor (60) and a camera (45), both operating in a sensor coordinate system (62). The system further includes a processor (44) configured to: receive, from an imaging system (21) operating in an image coordinate system (28), a three-dimensional image of the cavity including open space and tissue； receive, from the medical probe, signals indicating positions and respective directions of the medical probe inside the cavity； receive, from the camera, respective visualized locations inside the cavity； register the image coordinate system with the sensor coordinate system so as to identify one or more voxels in the image at the visualized locations, and when the identified voxels have density values in the received image that do not correspond to the open space, to update the density values of the identified voxels to correspond to the open space.
