{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T09:05:12Z","timestamp":1781600712204,"version":"3.54.5"},"reference-count":39,"publisher":"Wiley","license":[{"start":{"date-parts":[[2024,2,9]],"date-time":"2024-02-09T00:00:00Z","timestamp":1707436800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1184219"],"award-info":[{"award-number":["GNT1184219"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Magnetic Resonance Imaging"],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>The brainstem is a crucial component of the central autonomic nervous (CAN) system. Functional MRI (fMRI) of the brainstem remains challenging due to a range of factors, including diverse imaging protocols, analysis, and interpretation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Purpose<\/jats:title><jats:p>To develop an fMRI protocol for establishing a functional atlas in the brainstem.<\/jats:p><\/jats:sec><jats:sec><jats:title>Study Type<\/jats:title><jats:p>Prospective cross\u2010sectional study.<\/jats:p><\/jats:sec><jats:sec><jats:title>Subjects<\/jats:title><jats:p>Ten healthy subjects (four males, six females).<\/jats:p><\/jats:sec><jats:sec><jats:title>Field Strength\/Sequence<\/jats:title><jats:p>Using a 3.0 Tesla MR scanner, we acquired T1\u2010weighted images and three different fMRI scans using fMRI protocols of the optimized functional Imaging of Brainstem (FIBS), the Human Connectome Project (HCP), and the Adolescent Brain Cognitive Development (ABCD) project.<\/jats:p><\/jats:sec><jats:sec><jats:title>Assessment<\/jats:title><jats:p>The temporal signal\u2010to\u2010noise\u2010ratio (TSNR) of fMRI data was compared between the FIBS, HCP, and ABCD protocols. Additionally, the main normalization algorithms (i.e., FSL\u2010FNIRT, SPM\u2010DARTEL, and ANTS\u2010SyN) were compared to identify the best approach to normalize brainstem data using root\u2010mean\u2010square (RMS) error computed based on manually defined reference points. Finally, a functional autonomic brainstem atlas that maps brainstem regions involved in the CAN system was defined using meta\u2010analysis and data\u2010driven approaches.<\/jats:p><\/jats:sec><jats:sec><jats:title>Statistical Tests<\/jats:title><jats:p>ANOVA was used to compare the performance of different imaging and preprocessing pipelines with multiple comparison corrections (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05). Dice coefficient estimated ROI overlap, with 50% overlap between ROIs identified in each approach considered significant.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The optimized FIBS protocol showed significantly higher brainstem TSNR than the HCP and ABCD protocols (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05). Furthermore, FSL\u2010FNIRT RMS error (2.1\u2009\u00b1\u20091.22\u2009mm; <jats:italic>P<\/jats:italic>\u2009\u2264\u20090.001) exceeded SPM (1.5\u2009\u00b1\u20090.75\u2009mm; <jats:italic>P<\/jats:italic>\u2009\u2264\u20090.01) and ANTs (1.1\u2009\u00b1\u20090.54\u2009mm). Finally, a set of 12 final brainstem ROIs with dice coefficient\u2009\u22650.50, as a step toward the development of a functional brainstem atlas.<\/jats:p><\/jats:sec><jats:sec><jats:title>Data Conclusion<\/jats:title><jats:p>The FIBS protocol yielded more robust brainstem CAN results and outperformed both the HCP and ABCD protocols.<\/jats:p><\/jats:sec><jats:sec><jats:title>Evidence Level<\/jats:title><jats:p>2<\/jats:p><\/jats:sec><jats:sec><jats:title>Technical Efficacy<\/jats:title><jats:p>Stage 1<\/jats:p><\/jats:sec>","DOI":"10.1002\/jmri.29286","type":"journal-article","created":{"date-parts":[[2024,2,10]],"date-time":"2024-02-10T06:44:05Z","timestamp":1707547445000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Functional <scp>MRI<\/scp> of the Brainstem for Assessing Its Autonomic Functions: From Imaging Parameters and Analysis to Functional Atlas"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4499-672X","authenticated-orcid":false,"given":"Abdalla Z.","family":"Mohamed","sequence":"first","affiliation":[{"name":"Thompson Institute University of the Sunshine Coast  Sunshine Coast Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Kwiatek","sequence":"additional","affiliation":[{"name":"Thompson Institute University of the Sunshine Coast  Sunshine Coast Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Del Fante","sequence":"additional","affiliation":[{"name":"Thompson Institute University of the Sunshine Coast  Sunshine Coast Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vince D.","family":"Calhoun","sequence":"additional","affiliation":[{"name":"Tri\u2010Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University  Atlanta Georgia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Lagopoulos","sequence":"additional","affiliation":[{"name":"Thompson Brain and Mind Healthcare  Birtinya Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zack Y.","family":"Shan","sequence":"additional","affiliation":[{"name":"Thompson Institute University of the Sunshine Coast  Sunshine Coast Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,2,9]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","first-page":"513","DOI":"10.3389\/fnins.2015.00513","article-title":"Functional imaging of autonomic regulation: Methods and key findings","volume":"9","author":"Macey PM","year":"2016","journal-title":"Front Neurosci"},{"key":"e_1_2_9_3_1","volume-title":"Textbook of anatomy: Head, neck and brain","author":"Sing V","year":"2014"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-374236-0.10008-2"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2021.118135"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/hbm.25962"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1089\/brain.2015.0347"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1089\/brain.2020.0975"},{"key":"e_1_2_9_9_1","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1002\/mds.28895","article-title":"Disruption of brainstem structural connectivity in REM sleep behavior disorder using 7 tesla magnetic resonance imaging","volume":"37","author":"Garc\u00eda\u2010Gomar MG","year":"2021","journal-title":"Mov Disord"},{"key":"e_1_2_9_10_1","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3389\/fnins.2019.01425","article-title":"Probabilistic template of the lateral parabrachial nucleus, medial parabrachial nucleus, vestibular nuclei complex, and medullary viscero\u2010sensory\u2010motor nuclei complex in living humans from 7 tesla MRI","volume":"13","author":"Singh K","year":"2020","journal-title":"Front Neurosci"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tics.2020.01.008"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06098-1"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.13.5951"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04492-9"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2314-9"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2008.12.037"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.0485-17.2017"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2016.10.019"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2006.05.050"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1097\/NEN.0b013e3182588293"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0077089"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2011.09.006"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1635"},{"key":"e_1_2_9_24_1","doi-asserted-by":"crossref","unstructured":"BeckmannCF MackayCE FilippiniN SmithSM.Group comparison of resting\u2010state FMRI data using multi\u2010subject ICA and dual regression. Human Brain Mapping Conference2009 p 181.","DOI":"10.1016\/S1053-8119(09)71511-3"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2016.12.036"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.782"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10286-018-0577-0"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2021.117852"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0025-6196(12)62272-1"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2014.01.060"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2019.116290"},{"key":"e_1_2_9_32_1","doi-asserted-by":"crossref","first-page":"10","DOI":"10.7554\/eLife.62324","article-title":"Physiological and motion signatures in static and time\u2010varying functional connectivity and their subject identifiability","volume":"10","author":"Xifra\u2010Porxas A","year":"2021","journal-title":"Elife"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2011.01.042"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2016.09.038"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2018.12.051"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2017.12.073"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2019.00433"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1002\/hbm.25474"},{"key":"e_1_2_9_39_1","first-page":"Section 4","volume-title":"Neuroscience online: An electronic textbook for the neurosciences","author":"Dougherty P","year":"2020"},{"key":"e_1_2_9_40_1","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.neuroimage.2011.11.095","article-title":"Neuroimaging of the periaqueductal gray: State of the field","volume":"60","author":"Linnman C","year":"2013","journal-title":"Neuroimage"}],"container-title":["Journal of Magnetic Resonance Imaging"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jmri.29286","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,10]],"date-time":"2024-02-10T06:44:15Z","timestamp":1707547455000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jmri.29286"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,9]]},"references-count":39,"alternative-id":["10.1002\/jmri.29286"],"URL":"https:\/\/doi.org\/10.1002\/jmri.29286","archive":["Portico"],"relation":{},"ISSN":["1053-1807","1522-2586"],"issn-type":[{"value":"1053-1807","type":"print"},{"value":"1522-2586","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,9]]},"assertion":[{"value":"2023-07-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-01-24","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-02-09","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"jmri.29286"}}