Matlab and C++ code for implementation of the Extended Kalman Filter for estimating dynamic quantities for a single rigid body with distributed force/torque measurements and distributed gyroscopes and accelerometers measurements.It also include estimation of the orientation under the quaternion representation.
https://github.com/jeljaik/extended-kalman-filter/blob/b8d2d510291bc67b503eb799f18fe459dfe6a4f7/quaternionEKF/computeNoiseCovarianceMatrix.m#L34
This line looks like it may be a typo, in the (reference?) Tools/ekf.m file you use Qd = [Q11 Q12; Q12' Q22]; You might want to check.
I also realise this project may not be in active development any more so no worries if not.