An apparatus, comprising: a probe, configured for insertion into a body cavity of a patient and comprising a location sensor for measuring a position of a distal end of the probe inside the body cavity; and a processor configured: to acquire, from an imaging system, an image of the body cavity, to receive first and second sets of mapping points from the probe inserted into the body cavity, to perform a first registration between the mapping points in the first set and the image, each of the mapping points in the first set having a respective first point error value, the first registration having a first cumulative error value indicating a quality of the first registration, to generate, using the first registration, a three-dimensional anatomical map comprising the mapping points in the first set whose respective first point error values are less than a point error threshold, to perform a second registration between the mapping points in the first and the second sets and the image, each of the mapping points in the first and the second sets having a respective second point error value, the second registration having a second cumulative error value lower than the first cumulative error value, and to generate an updated 3D anatomical map comprising the mapping points in the first and the second sets whose respective second point error values are less than the point error threshold. a probe, configured for insertion into a body cavity of a patient and comprising a location sensor for measuring a position of a distal end of the probe inside the body cavity; and a processor configured: to acquire, from an imaging system, an image of the body cavity, to receive first and second sets of mapping points from the probe inserted into the body cavity, to perform a first registration between the mapping points in the first set and the image, each of the mapping points in the first set having a respective first point error value, the first registration having a first cumulative error value indicating a quality of the first registration, to generate, using the first registration, a three-dimensional anatomical map comprising the mapping points in the first set whose respective first point error values are less than a point error threshold, to perform a second registration between the mapping points in the first and the second sets and the image, each of the mapping points in the first and the second sets having a respective second point error value, the second registration having a second cumulative error value lower than the first cumulative error value, and to generate an updated 3D anatomical map comprising the mapping points in the first and the second sets whose respective second point error values are less than the point error threshold. to acquire, from an imaging system, an image of the body cavity, to receive first and second sets of mapping points from the probe inserted into the body cavity, to perform a first registration between the mapping points in the first set and the image, each of the mapping points in the first set having a respective first point error value, the first registration having a first cumulative error value indicating a quality of the first registration, to generate, using the first registration, a three-dimensional anatomical map comprising the mapping points in the first set whose respective first point error values are less than a point error threshold, to perform a second registration between the mapping points in the first and the second sets and the image, each of the mapping points in the first and the second sets having a respective second point error value, the second registration having a second cumulative error value lower than the first cumulative error value, and to generate an updated 3D anatomical map comprising the mapping points in the first and the second sets whose respective second point error values are less than the point error threshold.