TotalSpineSeg: Robust Spine Segmentation and Labeling Across Multiple MRI Contrasts
Motivation: Precise segmentation and labeling of vertebrae is essential to properly assess spine and spinal cord diseases such as spinal cord injury, degenerative diseases and scoliosis. Goal(s): Develop an automatic tool to segment and identify vertebrae on a wide range of MRI protocols, including different MRI sequences, contrasts, fields-of-view and resolutions. Approach: A three-step process including two nnUNetV21 models and an iterative labeling algorithm was used to segment and identify vertebrae using anatomical landmarks. Results: The model generalizes well across MRI sequences, with a segmentation Dice score of 0.84 and an average labeling accuracy of 0.99. Impact: TotalSpineSeg could enhance clinical workflows by providing automatic vertebrae segmentation, improving the diagnosis of various spinal pathologies and supporting informed clinical decision-making. It is available on GitHub (https://github.com/neuropoly/totalspineseg) and in Spinal Cord Toolbox v.6.514.
Authors
- Julien Cohen‐Adad (ORCID: https://orcid.org/0000-0003-3662-9532)
- Yehuda Warszawer (ORCID: https://orcid.org/0000-0001-7919-807X)
- Jan Valošek (ORCID: https://orcid.org/0000-0002-7398-4990)
- Nathan Molinier (ORCID: https://orcid.org/0000-0002-8312-8952)
- Virginie Callot (ORCID: https://orcid.org/0000-0003-0850-1742)
- Emanuel Shirbint
- Charidimos Tsagkas
- Tobias Granberg (ORCID: https://orcid.org/0000-0001-6700-1022)
- Feroze B. Mohamed (ORCID: https://orcid.org/0000-0002-0764-0612)
- Russell Ouellette (ORCID: https://orcid.org/0000-0001-9217-1445)
- Anat Achiron (ORCID: https://orcid.org/0000-0002-2020-3126)
- Kristin P. O’Grady (ORCID: https://orcid.org/0000-0002-4550-2026)
- Josef Bednařík (ORCID: https://orcid.org/0000-0001-7420-2383)
- Pierre‐Louis Benveniste (ORCID: https://orcid.org/0009-0003-3122-1957)
Publication Details
- Journal
- Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition
- Published
- 2025-09-16
- DOI
- https://doi.org/10.58530/2025/0624
- Primary Topic
- Medical Imaging and Analysis
- Type
- article
- Field-Weighted Citation Impact
- 0.00