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SCT is a comprehensive, free and open-source software dedicated to the processing and analysis of spinal cord MRI data.

Introduction

SCT overview

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, no software package exists 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 hinders cross-validation and the possibility to perform multi-center studies.

Spinal Cord Toolbox (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. We anticipate that SCT will bring together the spinal cord neuroimaging community by establishing standard templates and analysis procedures.

Installation

Install from package (release)

The simplest way to install SCT is to do it via a stable release. First, download the latest release. Major changes to each release are listed here.

Dependencies:

Once you have downloaded SCT, unpack it (note: Safari will automatically unzip it). Then, open a new Terminal, go into the created folder and launch the installer:

./install_sct

Install from Github (development)

Download source code from Github (N.B. you need to have git installed):

git clone --branch=master https://github.com/neuropoly/spinalcordtoolbox.git sct

Then install SCT:

cd sct
./install_sct

At anytime, you can update your local SCT installation to the latest version on Github:

git pull

Installation with Windows Subsystem for Linux (Windows 10).

Windows subsystem for Linux (WSL) is available on Windows 10 and it makes it possible to run native Linux programs, such as SCT.

Tutorial to install SCT on WSL

Installation with Docker

If none of the above solution work, SCT can be installed via Docker.

Tutorial to install SCT via Docker

Getting started

The best way to learn about the main functionalities of SCT is to run a typical processing pipeline, in the form of a batch script. We provide an example dataset (includes T1w, T2w, T2*w, DTI and fMRI) with a collection of commands to process those files and output quantitative parameters.

If you would like to get more examples about what SCT can do, please visit this address. Each repository is a pipeline dedicated to a specific research project.

Courses

We organize free SCT courses, each year after the ISMRM conference. If you'd like to be added to the mailing list, please send an email to spinalcordtoolbox@gmail.com. The past courses handouts are listed below:

Video tutorials

Please visit our video tutorials here.

References

Spinal Cord Toolbox

Template and Atlas

Segmentation

Registration

Applications

Citing spinalcordtoolbox

When citing SCT please use this BibTeX entry:

@article{DeLeener201724,
title = "SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord \{MRI\} data ",
journal = "NeuroImage ",
volume = "145, Part A",
number = "",
pages = "24 - 43",
year = "2017",
note = "",
issn = "1053-8119",
doi = "https://doi.org/10.1016/j.neuroimage.2016.10.009",
url = "http://www.sciencedirect.com/science/article/pii/S1053811916305560",
author = "Benjamin De Leener and Simon Lévy and Sara M. Dupont and Vladimir S. Fonov and Nikola Stikov and D. Louis Collins and Virginie Callot and Julien Cohen-Adad",
keywords = "Spinal cord",
keywords = "MRI",
keywords = "Software",
keywords = "Template",
keywords = "Atlas",
keywords = "Open-source ",
}

Contributors

This project exists thanks to all the people who contribute. If you would like to contribute as well, please follow the contribution guidelines.

License

The MIT License (MIT)

Copyright (c) 2014 École Polytechnique, Université de Montréal

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.