Spinal Cord Toolbox

The 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.

Main Features

• Propseg Automatic spinal cord segmentation.^[2]
• The MNI-Poly-AMU template is an anatomical template of the spinal cord with T2 weighting including segmentation of white matter, gray matter, CSF.^[3] The template also include segmentation of spinal levels for automatic assessment of metrics at specific locations.^[4]
• A White Matter atlas including 29 partial volume masks of which matter tracts.^[5]

References

1. ↑ De Leener B, Levy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, Callot V, Cohen-Adad J. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage 2016. 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. ↑ 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.
5. ↑ Benhamou M, Fonov V, Taso M, Le Troter A, Sdika M, Collins DL, Callot V, Cohen-Adad J. Atlas of white-matter tracts in the human spinal cord. Proceedings of the 22nd Annual Meeting of ISMRM, Milan, Italy 2014:0013.

External links

• Github page