Tutorials

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.

Written tutorials

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

1. Segmentation

2. Registration to template

   • Vertebral labeling for anatomical images

   • Registering labeled anatomical images to the PAM50 template

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

   • Registering lumbar images to the PAM50 template

3. Shape analysis

   • Compute CSA (and other shape metrics)

   • Quantify spinal cord compression

4. Multimodal registration

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

   • Contrast-agnostic registration with deep learning

5. 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

6. Atlas-based analysis

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

8. Other features

   • Functional MRI (Motion correction, Spinal level labeling)

   • Spinal cord smoothing

   • Visualizing misaligned cords

9. Analysis pipelines with SCT

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.