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Background Functional neuroimaging study has opened an avenue for exploring the pathophysiology of cluster headache (CH).The aim of our study was to assess the changes in brain activity in CH patients by the regional homogeneity method using resting-state functional magnetic resonance imaging technique.Methods The functional magnetic resonance imaging scans were obtained for 12 male CH patients with spontaneous right-sided headache attacks during “in attack” and “out of attack” periods and 12 age- and sex-matched normal controls.The data were analyzed to detect the altered brain activity by the regional homogeneity method using statistical parametric mapping software.Results Altered regional homogeneity was detected in the anterior cingulate cortex,the posterior cingulate cortex,the prefrontal cortex,insular cortex,and other brain regions involved in pain processing and modulation among different groups.Conclusion It is referred that these brain regions with altered regional homogeneity might be related to the pain processing and modulation of CH.