Spinal Cord Toolbox

Developer(s)	Polytechnique Montreal (NeuroPoly research laboratory)
Initial release	28 September 2013
Stable release	7.0 / 24 April 2025;4 months ago
Repository	github.com/spinalcordtoolbox/spinalcordtoolbox
Written in	Python
Operating system	Linux, Mac OS X, Windows
Size	140 MB
Available in	English
Type	Digital imaging
License	LGPLv3

Last updated September 06, 2025

Spinal Cord Toolbox (SCT) ^[4] is a suite of analysis tools optimized for spinal cord images acquired with magnetic resonance imaging. Main features include segmentation, registration and calculation of anatomical metrics.

Features

Propseg Automatic spinal cord segmentation.^[5]
The PAM50 template is an anatomical template of the spinal cord that covers the full spinal cord and brainstem and is available for T1-, T2- and T2*-weighted MRI contrasts. The PAM50 template includes probabilistic segmentation of white matter, gray matter, CSF as well as probabilistic atlases of gray matter subregions and white matter pathways.^[6]^[7] The template also include segmentation of spinal levels for automatic assessment of metrics at specific locations.^[8]
A White Matter atlas including 29 partial volume masks of which matter tracts.^[9]

References

↑ "Spinal Cord Toolbox". SourceForge.net . 2013-09-28. Archived from the original on 2015-10-30. Retrieved 2025-07-03.
↑ "Release 7.0 - spinalcordtoolbox/spinalcordtoolbox". GitHub . 2025-04-24. Retrieved 2025-07-03.
↑ "spinalcordtoolbox/LICENSE at master". GitHub . 2020-09-21. Retrieved 2025-07-03.
↑ De Leener B, Lévy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, et al. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage. 2017;145: 24–43. doi:10.1016/j.neuroimage.2016.10.009
↑ De Leener B, Cohen-Adad J, Kadoury S. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. Medical Imaging, IEEE Transactions on (in press). DOI: 10.1109/TMI.2015.2437192
↑ Fonov V, Le Troter A, Taso M, De Leener B, Leveque G, Benhamou M, Sdika M, Benali H, Pradat PF, Collins DL, Callot V, Cohen-Adad J. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014. DOI: 10.1016/j.neuroimage.2014.08.057
↑ De Leener B, Fonov V, Collins DL, Callot V, Stikov N, Cohen-Adad J. PAM50: Multimodal template of the brainstem and spinal cord compatible with the ICBM152 space. Proceedings of the 25th Annual Meeting of ISMRM, Honolulu, USA. 2017.
↑ Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Mikulis D, Fehlings MG. Resolving the anatomic variability of the human cervical spinal cord: a solution to facilitate advanced neural imaging. Proceedings of the 22nd Annual Meeting of ISMRM, Milan, Italy 2014:1719.
↑ Lévy S, Benhamou M, Naaman C, Rainville P, Callot V, Cohen-Adad J. White matter atlas of the human spinal cord with estimation of partial volume effect. Neuroimage. 2015;119: 262–271. doi:10.1016/j.neuroimage.2015.06.040

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[1] "Spinal Cord Toolbox". SourceForge.net . 2013-09-28. Archived from the original on 2015-10-30. Retrieved 2025-07-03.

[2] "Release 7.0 - spinalcordtoolbox/spinalcordtoolbox". GitHub . 2025-04-24. Retrieved 2025-07-03.

[3] "spinalcordtoolbox/LICENSE at master". GitHub . 2020-09-21. Retrieved 2025-07-03.

[4] De Leener B, Lévy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, et al. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage. 2017;145: 24–43. doi:10.1016/j.neuroimage.2016.10.009

[5] De Leener B, Cohen-Adad J, Kadoury S. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. Medical Imaging, IEEE Transactions on (in press). DOI: 10.1109/TMI.2015.2437192

[6] Fonov V, Le Troter A, Taso M, De Leener B, Leveque G, Benhamou M, Sdika M, Benali H, Pradat PF, Collins DL, Callot V, Cohen-Adad J. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014. DOI: 10.1016/j.neuroimage.2014.08.057

[7] De Leener B, Fonov V, Collins DL, Callot V, Stikov N, Cohen-Adad J. PAM50: Multimodal template of the brainstem and spinal cord compatible with the ICBM152 space. Proceedings of the 25th Annual Meeting of ISMRM, Honolulu, USA. 2017.

[8] Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Mikulis D, Fehlings MG. Resolving the anatomic variability of the human cervical spinal cord: a solution to facilitate advanced neural imaging. Proceedings of the 22nd Annual Meeting of ISMRM, Milan, Italy 2014:1719.

[9] Lévy S, Benhamou M, Naaman C, Rainville P, Callot V, Cohen-Adad J. White matter atlas of the human spinal cord with estimation of partial volume effect. Neuroimage. 2015;119: 262–271. doi:10.1016/j.neuroimage.2015.06.040

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