This report proposes a double simulated annealing (DSA) for functional magnetic resonance image (fMRI) analysis. The first simulated annealing (SA) is used to disconnect the brain from the skull. The second SA is applied to locate the activation area of the fMRIs. The performance evaluation of this approach includes receiver-operating characteristic (ROC) analysis, similarity analysis, and comparisons with other analytical methods such as classical SA (CSA), a t-Test, cross-correlation (CCR), and a general linear model (GLM). Experimental results show that the proposed algorithm can get better solutions than other approaches.