It is now recognized that important information can be extracted from the brain spontaneous activity, as exposed by recent analysis using a repertoire of computational methods. In this context a novel method, based on a blind deconvolution technique, is used to analyze potential changes due to chronic pain in the brain pain matrix's effective connectivity. The approach is able to deconvolve the hemodynamic response function from spontaneous neural events, i.e., in the absence of explicit onset timings, and to evaluate information transfer between two regions as a joint probability of the occurrence of such spontaneous events. The method revealed that the chronic pain patients exhibit important changes in the insula's effective connectivity which can be relevant to understand the overall impact of chronic pain on brain function.