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The purpose of this study was to validate and demonstrate a method for segmenting the carotid bifurcation into the common, internal, and external carotid arteries (CCA, ICA, ECA) in contrast-enhanced MR angiography (CE-MRA) data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A segmentation pipeline utilizing a convolutional neural network (DeepMedic) was tailored and trained for multi-class segmentation of the carotid arteries in CE-MRA data from the Swedish CardioPulmonsary bioImage Study (SCAPIS). Segmentation quality was quantitatively assessed using the Dice similarity coefficient (DSC), Matthews Correlation Coefficient (MCC), F<jats:sub>2<\/jats:sub>, F<jats:sub>0.5<\/jats:sub>, and True Positive Ratio (TPR). Segmentations were also assessed qualitatively, by three observers using visual inspection. Finally, geometric descriptions of the carotid bifurcations were generated for each subject to demonstrate the utility of the proposed segmentation method.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Branch-level segmentations scored DSC\u2009=\u20090.80\u2009\u00b1\u20090.13, MCC\u2009=\u20090.80\u2009\u00b1\u20090.12, F<jats:sub>2<\/jats:sub>\u2009=\u20090.82\u2009\u00b1\u20090.14, F<jats:sub>0.5<\/jats:sub>\u2009=\u20090.78\u2009\u00b1\u20090.13, and TPR\u2009=\u20090.84\u2009\u00b1\u20090.16, on average in a testing cohort of 46 carotid bifurcations. Qualitatively, 61% of segmentations were judged to be usable for analyses without adjustments in a cohort of 336 carotid bifurcations without ground-truth. Carotid artery geometry showed wide variation within the whole cohort, with CCA diameter 8.6\u2009\u00b1\u20091.1\u00a0mm, ICA 7.5\u2009\u00b1\u20091.4\u00a0mm, ECA 5.7\u2009\u00b1\u20091.0\u00a0mm and bifurcation angle 41\u2009\u00b1\u200921\u00b0.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The proposed segmentation method automatically generates branch-level segmentations of the carotid arteries that are suitable for use in further analyses and help enable large-cohort investigations.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12880-021-00568-6","type":"journal-article","created":{"date-parts":[[2021,2,27]],"date-time":"2021-02-27T12:02:56Z","timestamp":1614427376000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Automated segmentation of the individual branches of the carotid arteries in contrast-enhanced MR angiography using DeepMedic"],"prefix":"10.1186","volume":"21","author":[{"given":"Magnus","family":"Ziegler","sequence":"first","affiliation":[]},{"given":"Jesper","family":"Alfraeus","sequence":"additional","affiliation":[]},{"given":"Mariana","family":"Bustamante","sequence":"additional","affiliation":[]},{"given":"Elin","family":"Good","sequence":"additional","affiliation":[]},{"given":"Jan","family":"Engvall","sequence":"additional","affiliation":[]},{"given":"Ebo","family":"de Muinck","sequence":"additional","affiliation":[]},{"given":"Petter","family":"Dyverfeldt","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,2,27]]},"reference":[{"key":"568_CR1","doi-asserted-by":"publisher","first-page":"1693","DOI":"10.1056\/NEJM200006083422302","volume":"342","author":"D Inzitari","year":"2000","unstructured":"Inzitari D, Eliasziw M, Gates P, Sharpe BL, Chan RKT, Meldrum HE, et al. 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All subjects and all participants gave written, informed consent. All subjects provided written informed consent for publication before participation.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"38"}}