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In this paper, we discuss methods of channel estimation and decoding in amplify-and-forward (AF) based multiple-input multiple-output (MIMO) relay networks. We derive three different decoders, namely decoder-I, decoder-II, and decoder-III, for orthogonal space-time block codes using pilot symbol-aided channel estimation over Rayleigh fading MIMO channels in an AF based cooperative communication system. Decoder-I is a decoupled decoder which uses estimated channel gains in decoding. The other two decoders jointly process the received pilot signals and data samples through vector derivative (decoder-II) and probability density function marginalization (decoder-III). Simulation results show that decoder-II and decoder-III have almost the same performance. However, decoder-II is computationally less complex as compared to decoder-III. We also derive an expression for the moment generating function (m.g.f.) of the received signal-to-noise ratio at the destination for decoder-I and by using this m.g.f. the analytical symbol error rate is obtained.