Spinal Cord Toolbox

Spinal Cord Toolbox (SCT) [1] 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.

Developer(s)NeuroPoly
Stable release
3.0.3 / 26 April 2017 (2017-04-26)
Repositorygithub.com/neuropoly/spinalcordtoolbox
Written inPython
Operating systemLinux, Mac OS X
Size140 MB
Available inEnglish
TypeDigital imaging
LicenseMIT Licence

Features
  • Propseg Automatic spinal cord segmentation.[2]
  • 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.[3][4] The template also include segmentation of spinal levels for automatic assessment of metrics at specific locations.[5]
  • A White Matter atlas including 29 partial volume masks of which matter tracts.[6]

References
  1. 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
  2. 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
  3. 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
  4. 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.
  5. 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.
  6. 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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