{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T14:57:13Z","timestamp":1788274633328,"version":"build-2803163510"},"reference-count":29,"publisher":"Wiley","issue":"14","license":[{"start":{"date-parts":[[2019,6,17]],"date-time":"2019-06-17T00:00:00Z","timestamp":1560729600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100008486","name":"Schweizerische Multiple Sklerose Gesellschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008486","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["MHV program; PMPDP3 171391"],"award-info":[{"award-number":["MHV program; PMPDP3 171391"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Human Brain Mapping"],"published-print":{"date-parts":[[2019,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Neurodegenerative disorders, such as Alzheimer's disease (AD) and progressive forms of multiple sclerosis (MS), can affect the brainstem and are associated with atrophy that can be visualized by MRI. Anatomically accurate, large\u2010scale assessments of brainstem atrophy are challenging due to lack of automated, accurate segmentation methods. We present a novel method for brainstem volumetry using a fully\u2010automated segmentation approach based on multi\u2010dimensional gated recurrent units (MD\u2010GRU), a deep learning based semantic segmentation approach employing a convolutional adaptation of gated recurrent units. The neural network was trained on 67 3D\u2010high resolution T1\u2010weighted MRI scans from MS patients and healthy controls (HC) and refined using segmentations of 20 independent MS patients' scans. Reproducibility was assessed in MR test\u2013retest experiments in 33 HC. Accuracy and robustness were examined by Dice scores comparing MD\u2010GRU to FreeSurfer and manual brainstem segmentations in independent MS and AD datasets. The mean %\u2010change\/<jats:italic>SD<\/jats:italic> between test\u2013retest brainstem volumes were 0.45%\/0.005 (MD\u2010GRU), 0.95%\/0.009 (FreeSurfer), 0.86%\/0.007 (manually edited segmentations). Comparing MD\u2010GRU to manually edited segmentations the mean Dice scores\/<jats:italic>SD<\/jats:italic> were: 0.97\/0.005 (brainstem), 0.95\/0.013 (mesencephalon), 0.98\/0.006 (pons), 0.95\/0.015 (medulla oblongata). Compared to the manual gold standard, MD\u2010GRU brainstem segmentations were more accurate than FreeSurfer segmentations (<jats:italic>p<\/jats:italic> &lt;\u2009.001). In the multi\u2010centric acquired AD data, the mean Dice score\/<jats:italic>SD<\/jats:italic> for the MD\u2010GRU\u2010manual segmentation comparison was 0.97\/0.006. The fully automated brainstem segmentation method MD\u2010GRU provides accurate, highly reproducible, and robust segmentations in HC and patients with MS and AD in 200 s\/scan on an Nvidia GeForce GTX 1080 GPU and shows potential for application in large and longitudinal datasets.<\/jats:p>","DOI":"10.1002\/hbm.24687","type":"journal-article","created":{"date-parts":[[2019,6,17]],"date-time":"2019-06-17T17:14:13Z","timestamp":1560791653000},"page":"4091-4104","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Accurate, rapid and reliable, fully automated MRI brainstem segmentation for application in multiple sclerosis and neurodegenerative diseases"],"prefix":"10.1002","volume":"40","author":[{"given":"Laura","family":"Sander","sequence":"first","affiliation":[{"name":"Neurology Clinic and Policlinic, Departments of Medicine, Clinical Research and Biomedical Engineering University Hospital Basel and University of Basel  Basel Switzerland"},{"name":"Translational Imaging in Neurology (ThINK) Basel, Department of Medicine and Biomedical Engineering University Hospital Basel and University of Basel  Basel Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Pezold","sequence":"additional","affiliation":[{"name":"Center for medical Image Analysis &amp; 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