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Try setting the first element of the covariance to -1 for the unused measurement fields.

( Have a look at the IMU message description http://docs.ros.org/api/sensor_msgs/html/msg/Imu.html )

Try setting the first element of the covariance to -1 for the unused measurement fields.

# If you have no estimate for one of the data elements (e.g. your IMU doesn't produce an orientation 
#  estimate), please set element 0 of the associated covariance matrix to -1

( Have a look at (from the IMU message description http://docs.ros.org/api/sensor_msgs/html/msg/Imu.html )

But I don't know if this helps with your cartographer problem, I haven't used it yet.