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The aim of this work is to propose a new approach for the determination of the design matrix in fMRI experiments. The design matrix embodies all available knowledge about experimentally controlled factors and potential confounds. This knowledge is expressed through the regressors of the design matrix. However, in a particular fMRI time series some of those regressors may not be present. In order to take into account this prior information a Bayesian approach based on hierarchical prior, which expresses the sparsity of the design matrix, is used over the parameters of the generalized linear model. The proposed method automatically prunes the columns of the design matrix which are irrelevant to the generation of data. The evaluation of the proposed approach on simulated and real experiments have shown higher performance compared to the conventional t-test approach.