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Purpose: This study aimed to investigate any cerebral function deficits in AS using functional MRI technology and its possible relationship to clinical and laboratory results. Materials and Methods: Twenty seven patients with AS and 28 control subjects were included in this study. All of them underwent structural MRI and resting state-functional MRI (rs-fMRI) scanning. Comparisons of amplitude of low frequency fluctuations (ALFF) of rs-fMRI signals between AS patients and normal controls were performed using two sample t-tests. To examine functional connectivity within the groups, one-sample t tests were performed on the individual z-value maps. The z values were compared between the two groups using two-sample t test. Partial correlations between ALFF values and functional connectivity of the brain regions which showed group difference and clinical results including the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) score, the serum high-sensitivity C-reactive protein (hsCRP), and the erythrocyte sedimentation rate (ESR) were analyzed for AS patients. Results: Compared with normal controls, the AS patients exhibited significant lower ALFF in the left medial frontal gyrus, the right precentral gyrus and the right posterior cingulate, while higher ALFF in the left cerebellum anterior lobe, the left middle temporal gyrus, the left superior occipital gyrus, the left postcentral gyrus and the right precuneus. AS patients showed widespread brain connectivity alterations. Functional connectivity strength of the left precuneus and the left middle temporal gyrus were closely correlated with the the BASDAI scores, ESR and hsCRP in AS patients. Conclusion: AS is associated with a altered cortical activity of rs-fMRI signals. Measurement of functional connectivity strength of the left precuneus and the left middle temporal gyrus may aid in the clinical detection and evaluation of AS.