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Preprocessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https:\/\/openneuro.org\/datasets\/ds005143\/versions\/1.3.1 and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared with other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https:\/\/github.com\/sct-pipeline\/fmri-segmentation\/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.<\/jats:p>","DOI":"10.1162\/imag.a.98","type":"journal-article","created":{"date-parts":[[2025,7,21]],"date-time":"2025-07-21T20:01:22Z","timestamp":1753128082000},"update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":7,"title":["EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data"],"prefix":"10.1162","volume":"3","author":[{"given":"Rohan","family":"Banerjee","sequence":"first","affiliation":[{"name":"Department of Computer Science, Polytechnique Montreal, Montreal, Quebec, Canada"},{"name":"Mila\u2014Quebec AI Institute, Montreal, Quebec, Canada"},{"name":"NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Merve","family":"Kaptan","sequence":"additional","affiliation":[{"name":"Division of Pain Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9646-0201","authenticated-orcid":false,"given":"Alexandra","family":"Tinnermann","sequence":"additional","affiliation":[{"name":"Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0679-0499","authenticated-orcid":false,"given":"Ali","family":"Khatibi","sequence":"additional","affiliation":[{"name":"McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada"},{"name":"Centre de recherche de l\u2019Institut Universitaire de G\u00e9riatrie de Montr\u00e9al, Montr\u00e9al, Quebec, Canada"},{"name":"Centre of Precision Rehabilitation for Spinal Pain (CPR Spine), University of Birmingham, Birmingham, United Kingdom"},{"name":"Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9515-6810","authenticated-orcid":false,"given":"Alice","family":"Dabbagh","sequence":"additional","affiliation":[{"name":"Max Planck Research Group Pain Perception, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"B\u00fcchel","sequence":"additional","affiliation":[{"name":"Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0351-6108","authenticated-orcid":false,"given":"Christian W.","family":"K\u00fcndig","sequence":"additional","affiliation":[{"name":"Spinal Cord Injury Center, Balgrist University Hospital, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0524-6029","authenticated-orcid":false,"given":"Christine S.W.","family":"Law","sequence":"additional","affiliation":[{"name":"Division of Pain Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2406-9251","authenticated-orcid":false,"given":"Dario","family":"Pfyffer","sequence":"additional","affiliation":[{"name":"Division of Pain Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States"},{"name":"Spinal Cord Injury Center, Balgrist University Hospital, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5078-9025","authenticated-orcid":false,"given":"David J.","family":"Lythgoe","sequence":"additional","affiliation":[{"name":"Department of Neuroimaging, Institute of Psychology, Psychiatry & Neuroscience, King\u2019s College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4584-0236","authenticated-orcid":false,"given":"Dimitra","family":"Tsivaka","sequence":"additional","affiliation":[{"name":"Department of Neuroimaging, Institute of Psychology, Psychiatry & Neuroscience, King\u2019s College London, London, United Kingdom"},{"name":"Medical Physics Department, Medical School, University of Thessaly, Larisa, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2879-3861","authenticated-orcid":false,"given":"Dimitri","family":"Van De Ville","sequence":"additional","affiliation":[{"name":"Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland"},{"name":"Neuro-X Institute, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3986-1719","authenticated-orcid":false,"given":"Falk","family":"Eippert","sequence":"additional","affiliation":[{"name":"Max Planck Research Group Pain Perception, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, 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Neuroimaging, Institute of Psychology, Psychiatry & Neuroscience, King\u2019s College London, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7257-9646","authenticated-orcid":false,"given":"Molly G.","family":"Bright","sequence":"additional","affiliation":[{"name":"Department of Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States"},{"name":"Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3804-0991","authenticated-orcid":false,"given":"Nawal","family":"Kinany","sequence":"additional","affiliation":[{"name":"Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland"},{"name":"Neuro-X Institute, Ecole Polytechnique F\u00e9d\u00e9rale de 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