Cooperative communication systems can effectively be used to combat fading. A cooperative protocol that can be used with half-duplex terminals is the Quantize and Forward (QF) protocol, in which the relay quantizes the information received from the source before forwarding it to the destination. While the outage behavior and error performance of the QF protocol have been investigated extensively, only few research has been performed on the effects of channel parameter estimation. In this contribution, estimates are derived for all communication channels involved, while keeping the complexity of the relay terminal unaltered. First, channel estimates are calculated using known pilot symbols sent by the source and relay. Thereafter, these pilot-based channel estimates are refined using a code-aided Expectation Maximization (EM) approach, yielding an error performance that is very close to that of a system in which the channel parameters are assumed to be known.