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Atlas\u2010based segmentation methods using single templates have emerged as a practical approach to automate the process for brain or head and neck anatomy, but pose significant challenges in regions where large interpatient variations are present. We show that significant changes are needed to autosegment thoracic and abdominal datasets by combining multi\u2010atlas deformable registration with a level set\u2010based local search. Segmentation is hierarchical, with a first stage detecting bulk organ location, and a second step adapting the segmentation to fine details present in the patient scan. The first stage is based on warping multiple presegmented templates to the new patient anatomy using a multimodality deformable registration algorithm able to cope with changes in scanning conditions and artifacts. These segmentations are compacted in a probabilistic map of organ shape using the STAPLE algorithm. Final segmentation is obtained by adjusting the probability map for each organ type, using customized combinations of delineation filters exploiting prior knowledge of organ characteristics. Validation is performed by comparing automated and manual segmentation using the Dice coefficient, measured at an average of 0.971 for the aorta, 0.869 for the trachea, 0.958 for the lungs, 0.788 for the heart, 0.912 for the liver, 0.884 for the kidneys, 0.888 for the vertebrae, 0.863 for the spleen, and 0.740 for the spinal cord. Accurate atlas segmentation for abdominal and thoracic regions can be achieved with the usage of a multi\u2010atlas and perstructure refinement strategy. To improve clinical workflow and efficiency, the algorithm was embedded in a software service, applying the algorithm automatically on acquired scans without any user interaction.<\/jats:p><jats:p>PACS numbers: 87.57.nm, 87.57.N\u2010, 87.57.Q\u2010<\/jats:p>","DOI":"10.1120\/jacmp.v15i4.4468","type":"journal-article","created":{"date-parts":[[2017,2,27]],"date-time":"2017-02-27T23:34:21Z","timestamp":1488238461000},"page":"22-38","source":"Crossref","is-referenced-by-count":37,"title":["Multiatlas segmentation of thoracic and abdominal anatomy with level set\u2010based local search"],"prefix":"10.1002","volume":"15","author":[{"given":"Eduard","family":"Schreibmann","sequence":"first","affiliation":[{"name":"Department of Radiation Oncology and Winship Cancer Institute of Emory University  Atlanta GA USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Marcus","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology and 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