ArticleRadiology. Artificial intelligence2025
SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans.
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18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The application of artificial intelligence in the acute and sub-acute phases of spinal cord injury- a systematic review.Spinal cord · 2026Pooled it
- Magnetic Resonance Imaging Preprocessing for Robust Spinal Cord Segmentation in Cervical Myelopathy.Journal of imaging · 2026Article
- Enhancing Spinal Cord and Canal Segmentation in Degenerative Cervical Myelopathy : The Role of Interactive Learning Models with manual Click.Journal of Korean Neurosurgical Society · 2026Article
- Accurate Segmentation and Three-dimensional Reconstruction Algorithm of Spinal Cord Injury Lesions Based on Multimodal Magnetic Resonance Imaging.Current medical imaging · 2026Article
- Building a library of acute traumatic spinal cord injury images across Canada: a retrospective cohort study protocol.BMJ open · 2025Article
- Fully Automated Segmentation of Cervical Spinal Cord in Sagittal MR Images Using Swin-Unet Architectures.Journal of clinical medicine · 2025Article
- Determination of Diagnosis and Prognosis in Spinal Cord Injury Using Machine Learning.Korean journal of neurotrauma · 2025Review
- Magnetization transfer MRI (MT-MRI) detects white matter damage beyond the primary site of compression in degenerative cervical myelopathy using a novel semi-automated analysis.Computers in biology and medicine · 2025Article
- Lesion characteristics are associated with bowel, bladder, and overall independence following cervical spinal cord injury.The journal of spinal cord medicine · 2025Article
- Deep Learning-Based Segmentation in Musculoskeletal Imaging: A Review of Research Trends.Journal of the Korean Society of Radiology · 2025Review
- 3D MRI Tract-Specific Spinal Cord Lesion Pattern Improves Prediction of Distinct Neurological Recovery.Annals of clinical and translational neurology · 2025Article
- Metabolic and Structural Alterations in the Motor System Following Spinal Cord Injury: An In-VivoJournal of neuroscience research · 2025Article
- Semiautomated Pipeline Effectively Assesses Severity and Monitor Disease Progression in Compressed Spinal Cord of Degenerative Cervical Myelopathy Patients.Neurosurgery practice · 2025Article
- EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Automatic segmentation of spinal cord lesions in MS: A robust tool for axial T2-weighted MRI scans.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Reliability of SCIseg Automated Measurement of Midsagittal Tissue Bridges in Spinal Cord Injuries Using an External Dataset.Topics in spinal cord injury rehabilitation · 2025Article
- Automatic segmentation of the spinal cord nerve rootlets.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Monitoring morphometric drift in lifelong learning segmentation of the spinal cord.Imaging neuroscience (Cambridge, Mass.)Article
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Authors and funding
9 authors.
Enamundram Naga Karthik *From the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).ORCID 0000-0003-2940-5514
Jan Valošek *From the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).ORCID 0000-0002-7398-4990
Andrew C SmithFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).ORCID 0000-0001-5020-8094
Dario PfyfferFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).ORCID 0000-0002-2406-9251
Simon Schading-SassenhausenFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).
Lynn FarnerFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).ORCID 0009-0004-8252-5448
Kenneth A WeberFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).ORCID 0000-0002-0916-9174
Patrick FreundFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).
Julien Cohen-AdadFrom the NeuroPoly Laboratory, Institute of Biomedical Engineering, Polytechnique Montréal, 2500 Chemin de Polytechnique, Montréal, Québec, Canada H3T 1J4 (E.N.K., J.V., J.C.A.); Mila-Quebec AI Institute, Montréal, Québec, Canada (E.N.K., J.V., J.C.A.); Department of Neurosurgery and Department of Neurology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia (J.V.); Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine, Aurora, Colo (A.C.S.); Spinal Cord Injury Center, Balgrist University Hospital, University of Zürich, Zürich, Switzerland (D.P., S.S.S., L.F., P.F.); Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, Calif (D.P., K.A.W.); Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (P.F.); and Functional Neuroimaging Unit, CRIUGM and Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada (J.C.A.).
Funding
Characterization of central pain mechanisms using simultaneous spinal cord-brain functional imagingR01NS109450 · NINDS · STANFORD UNIVERSITY · PI GLOVER, GARY H, MACKEY, SEAN C · 2018 to 2022
$2.9MMRI-Derived Neuromuscular Signatures to Predict Surgical Response in Degenerative Cervical MyelopathyR01NS128478 · NINDS · STANFORD UNIVERSITY · PI Kenneth Arnold Weber · 2023 to 2026
$2.2MNeuroimaging-Based Brain and Spinal Cord Biomarkers for Cervical RadiculopathyK23NS104211 · NINDS · STANFORD UNIVERSITY · PI WEBER, KENNETH ARNOLD · 2018 to 2022
$875kImproving mechanistic understanding of responsiveness to spinal cord stimulation after spinal cord injuryK01HD106928 · NICHD · UNIVERSITY OF COLORADO DENVER · PI SMITH, ANDREW CRAIG · 2022 to 2025
$508kMRI and machine learning to improve early prognosis and clinical management after spinal cord injuryR03HD094577 · NICHD · UNIVERSITY OF COLORADO DENVER · PI SMITH, ANDREW CRAIG · 2019 to 2020
$195kNICHD NIH HHS K01 HD106928NICHD NIH HHS R03 HD094577NINDS NIH HHS K23 NS104211NINDS NIH HHS L30 NS108301NINDS NIH HHS R01 NS109450NINDS NIH HHS R01 NS128478
Abstract
Purpose To develop a deep learning tool for the automatic segmentation of the spinal cord and intramedullary lesions in spinal cord injury (SCI) on T2-weighted MRI scans. Materials and Methods This retrospective study included MRI data acquired between July 2002 and February 2023. The data consisted of T2-weighted MRI scans acquired using different scanner manufacturers with various image resolutions (isotropic and anisotropic) and orientations (axial and sagittal). Patients had different lesion etiologies (traumatic, ischemic, and hemorrhagic) and lesion locations across the cervical, thoracic, and lumbar spine. A deep learning model, SCIseg (which is open source and accessible through the Spinal Cord Toolbox, version 6.2 and above), was trained in a three-phase process involving active learning for the automatic segmentation of intramedullary SCI lesions and the spinal cord. The segmentations from the proposed model were visually and quantitatively compared with those from three other open-source methods (PropSeg, DeepSeg, and contrast-agnostic, all part of the Spinal Cord Toolbox). The Wilcoxon signed rank test was used to compare quantitative MRI biomarkers of SCI (lesion volume, lesion length, and maximal axial damage ratio) derived from the manual reference standard lesion masks and biomarkers obtained automatically with SCIseg segmentations. Results The study included 191 patients with SCI (mean age, 48.1 years ± 17.9 [SD]; 142 [74%] male patients). SCIseg achieved a mean Dice score of 0.92 ± 0.07 and 0.61 ± 0.27 for spinal cord and SCI lesion segmentation, respectively. There was no evidence of a difference between lesion length (
Indexed as
Deep LearningMagnetic Resonance ImagingSpinal Cord InjuriesAdultAgedFemaleHumansImage Interpretation, Computer-AssistedMaleMiddle AgedRetrospective StudiesConvolutional Neural Network (CNN)MR ImagingSegmentationSpinal CordSupervised LearningTrauma
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