We study how the spontaneous relaxation of a qubit affects a continuous quantum non-demolition measurement of the initial state of the qubit. Given some noisy measurement record $Psi$, we seek an estimate of whether the qubit was initially in the ground or excited state. We investigate four different measurement protocols, three of which use a linear filter (with different weighting factors) and a fourth which uses a full non-linear filter that gives the theoretically optimal estimate of the initial state of the qubit. We find that relaxation of the qubit at rate $1/T_1$ strongly influences the fidelity of any measurement protocol. To avoid errors due to this decay, the measurement must be completed in a time that decrease linearly with the desired fidelity while maintaining an adequate signal to noise ratio. We find that for the non-linear filter the predicted fidelity, as expected, is always better than the linear filters and that the fidelity is a monotone increasing function of the measurement time. For example, to achieve a fidelity of 90%, the box car linear filter requires a signal to noise ratio of $sim 30$ in a time $T_1$ whereas the non-linear filter only requires a signal to noise ratio of $sim 18$.
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