Tutorials

To get started using SCT, you may wish to read our 2024 Review “Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox”.

For a more hands-on approach, you can take a look at the tutorials below, or run the tutorials all at once using the Batch Processing script.

Written tutorials

We provide the following hands-on tutorials for SCT’s command-line tools.

1. Spinal cord segmentation

2. Vertebral labeling

3. Shape analysis

   • Compute CSA (and other shape metrics)

   • Quantify spinal cord compression

4. Lesion analysis

5. Registration to template

   • Registering labeled anatomical images to the PAM50 template

   • Registering images to the PAM50 template based on spinal nerve rootlets

   • Coregistering additional data (MT, DT) to the PAM50 template

   • Registering lumbar images to the PAM50 template

6. Multimodal registration

   • Computing MTR using co-registration between MT0 and MT1 data

   • Contrast-agnostic registration with deep learning

7. Gray matter segmentation

   • Segmenting the gray and white matter for T2* data

   • Computing metrics using GM and WM segmentations

   • Improving registration results using white and gray matter segmentations

8. Atlas-based analysis

9. Diffusion-weighted MRI (Motion correction, DTI computation)

10. Functional MRI (Motion correction, Spinal level labeling)

11. Other features

    • Spinal cord smoothing

    • Visualizing misaligned cords

12. Processing batches of subjects using pipeline scripts

Note

The following tutorials make use of Quality Control (QC) reports for inspecting processed image data. Optionally, we also recommend trying out FSLeyes to visualize the data from these tutorials, too.

Batch processing script

If you would prefer to run all of the individual commands from the tutorials at once as a complete bash script, we provide this as well.

The batch_single_subject.sh script performs a typical analysis of multi-parametric MRI data, including cross-sectional area measurements, magnetization transfer, diffusion tensor imaging metrics computation and extraction within specific tracts, and functional MRI pre-processing. This script will download an example dataset containing T1w, T2w, T2*w, MT, DTI and fMRI data.

To launch the script run:

$SCT_DIR/batch_single_subject.sh

While the script is running, we encourage you to understand the meaning of each command line that is listed in the script. Comments are here to help justify some choices of parameters. If you have any question, please do not hesitate to ask for Help.

Video tutorials

SCT have a YouTube channel which contains additional tutorials.

SCT Course

If you would prefer to learn how to use SCT in a guided workshop setting, we provide an in-person SCT course each year. You can learn more about past and future courses in the course section.

SCT Pipeline

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