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This study aims to investigate the resting state functional connectivity (rsFC) changes of the hypothalamus in fibromyalgia patients. 24 Fibromyalgia patients and 24 matched healthy controls (HCs) were recruited. Resting state fMRI data were collected from the fibromyalgia patients and HC\u2019s. Fibromyalgia patients went through a second scan after 12\u00a0weeks of Tai Chi mind\u2013body intervention. Data analysis showed that fibromyalgia patients displayed <jats:italic>less<\/jats:italic> medial hypothalamus (MH) rsFC with\u00a0the thalamus and amygdala when compared to the functional connectivity in the HCs. After the Tai Chi mind\u2013body intervention, fibromyalgia patients showed <jats:italic>increased<\/jats:italic> MH rsFC with the thalamus and amygdala accompanied by clinical improvement. Effective connectivity analysis showed disrupted MH and thalamus interaction in the\u00a0fibromyalgia\u00a0patients, which was altered by mind\u2013body exercise. Our findings suggest that fibromyalgia is associated with altered functional connectivity within the diencephalon and limbic system. Elucidating the roles of the diencephalon and limbic system in the pathophysiology and development of fibromyalgia may facilitate the development of a new biomarker and effective treatment methods for this prevalent disorder.<\/jats:p><jats:p><jats:italic>Trial Registration<\/jats:italic> ClinicalTrials.gov, NCT02407665. Registered: 3 April 2015, <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/clinicaltrials.gov\/ct2\/show\/NCT02407665?term=NCT02407665&amp;draw=2&amp;rank=1\">https:\/\/clinicaltrials.gov\/ct2\/show\/NCT02407665?term=NCT02407665&amp;draw=2&amp;rank=1<\/jats:ext-link><\/jats:p>","DOI":"10.1186\/s13041-020-00705-2","type":"journal-article","created":{"date-parts":[[2021,1,20]],"date-time":"2021-01-20T12:03:20Z","timestamp":1611144200000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Altered functional connectivity between hypothalamus and limbic system in fibromyalgia"],"prefix":"10.1186","volume":"14","author":[{"given":"Jian","family":"Kong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiting","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyi","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Ming","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgia","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William F.","family":"Harvey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenchen","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,1,20]]},"reference":[{"key":"705_CR1","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/B978-0-7020-4086-3.00033-3","volume":"119","author":"JE Sumpton","year":"2014","unstructured":"Sumpton JE, Moulin DE. 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