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Stroke patients may present an altered hemodynamic response compared to healthy subjects. The magnitude of the BOLD fMRI response may considerably differ from the hemodynamic response function (hrf) commonly used in the analysis of the fMRI data, and, as a consequence, a BOLD signal may fail to be detected in stroke patients. The aim of the work is to develop a new method for the fMRl data analysis, suitable for the detection of cerebral activated areas in stroke patients. An analysis of the signal variance is used in order to calculate, for the anatomic areas of interest, the average BOLD signal time-course, to be used in turn as the reference function (hrf) in a correlation analysis. This way of analyzing fMRI data allows the detection of activation in the cortical sensorimotor areas not detected by a statistical analysis that uses a standard hrf as reference function.