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Aims Multiple system atrophy(MSA)and idiopathic Parkinsons disease(IPD)show overlapping clinical manifestations while difference in prognosis and treatment; however,it is unclear about their underlying neural substrates.This study aimed at investigating the changed patterns of spontaneous brain activity between MSA and IPD.Methods Twenty-one patients with MSA(13MSA-P/8MSA-C),nine PD,and twenty-one healthy gender-and age-matched controls were recruited.Resting-state functional magnetic resonance imaging data,a neuropsychological test battery contained cognitive and depression assessments and UPDRS-Ⅲ scores were collected.Amplitude of low-frequency fluctuations(ALFF)and regional homogeneity(Reho)were measured to investigate the intensity and synchronization of local spontaneous neuronal activity among three groups.Correlations of clinical variables(e.g.,movement,cognitive and depression)with ALFF/Reho values were examined.Results Compared with controls,we observed that similar ALFF changed patterns were shared between MSA and IPD,while more widespread in MSA: decreased ALFF in bilateral frontal areal,right insular,right putamen and anterior cingulate; increased ALFF in bilateral visual cortex,bilateral temporal and parietal lobe.Compared with controls,Reho decrease in left cerebellum,increased in left prefrontal of MSA patients and decreased in right frontal of IPD patients.When a comparison was conducted between MSA and IPD,the main different regions were ALFF decreased in left frontal,left parietal,ALFF increased in right visual cortex and Reho decreased in right cerebellum and increased in bilateral frontal.In MSA patients,ALFF values in right putamen positively correlated with UPDRS-Ⅲ score and negatively correlated with MOCa scores,left visual cortex positively correlated with MOCa and MMSE scores; Reho values in left supplementary motor areas negatively correlated with H-Y stage.Conclusion The changed intensity of spontaneous brain activity between MSA and IPD were similar while MSA were much widespread.Their different patterns of decreased and incoherent neuronal activity respectively in the right frontal and right cerebellum may contribute to the different neural substrate of MSA and IPD.