For the past 25 years, the field of neuroimaging has witnessed the development of several software packages for processing multi-parametric magnetic resonance imaging (mpMRI) to study the brain. These software packages are now routinely used by researchers and clinicians, and have contributed to important breakthroughs for the understanding of brain anatomy and function.

However, for a long time, no software package had existed to process mpMRI data of the spinal cord. Despite the numerous clinical needs for such advanced mpMRI protocols (multiple sclerosis, spinal cord injury, cervical spondylotic myelopathy, etc.), researchers have been developing specific tools that, while necessary, do not provide an integrative framework that is compatible with most usages and that is capable of reaching the community at large. This has hindered cross-validation and the possibility to perform multi-center studies.


Spinal Cord Toolbox (SCT) brings together the spinal cord neuroimaging community by establishing standard templates and analysis procedures.

SCT is a comprehensive, free and open-source software dedicated to the processing and analysis 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. A list of these applications can be found in the Studies using SCT page, as well as in our 2024 Review “Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox”..