A comprehensive software for the processing and analysis of multiparametric MRI data of the spinal cord.


Benjamin De Leener1, Sara M Dupont1, Simon Lévy1, Pierre-Olivier Quirion1,2, Charley Gros1, Vladimir Fonov3, Louis Collins3, Virginie Callot4, Julien Cohen-Adad1,2

Estimated cost



Stable release v3.0, license MIT

Spinal Cord Toolbox (SCT) is a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-of-the-art MRI templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series.

SCT is tailored towards standardization and automation of the processing pipeline, versatility, modularity, and it follows guidelines of software development and distribution. Preliminary applications of SCT cover a variety of studies, from cross-sectional area measures in large databases of patients, to the precise quantification of mpMRI metrics in specific spinal pathways and fMRI studies of pain and sensory inputs.

SCT features:

  • spinal cord template;
  • atlas of gray and white matter + spinal pathways;
  • fast, robust and automatic segmentation of spinal cord;
  • robust registration methods;
  • miscellaneous tools dedicated to spinal cord;



1NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada;
2Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada;
3Montreal Neurological Institute, McGill University, Montreal, QC, Canada;
4Aix-Marseille Université, CNRS, CRMBM UMR 7339, Marseille, France.