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Chronic pain diseases are characterised by an ongoing and fluctuating endogenous pain, yet it remains to be elucidated how this is reflected by the dynamics of ongoing functional cortical connections. In this study, we investigated the cortical encoding of 20 patients with chronic back pain and 20 chronic migraineurs in 4 repeated fMRI sessions. A brain parcellation approach subdivided the whole brain into 408 regions. Linear mixed-effects models were fitted for each pair of brain regions to explore the relationship between the dynamic