Spinal Cord Toolbox

Developer(s)	Polytechnique Montreal (NeuroPoly research laboratory)
Initial release	28 September 2013
Stable release	7.0 / 24 April 2025; 5 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

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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