Tutorials and Courses

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.

Tutorial pages

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

   • Computing shape metrics for PAM50-registered data

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

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

3. 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

4. Atlas-based analysis

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

6. Other features

   • Functional MRI (Motion correction, Spinal level labeling)

   • Spinal cord smoothing

   • Visualizing misaligned cords

7. Analysis pipelines with SCT

SCT Course

We also organize a free in-person SCT course each year after the ISMRM conference. The course provides a guided walkthrough of SCT, with developers and researchers on-hand to provide support and to answer any questions you may have. If you’d like to be added to the mailing list for course announcements, please visit this link.

The past courses handouts are listed below:

• SCT course (v4.2.1), London, 2020-01-21 | Video recording

• SCT course (v4.0.0), Beijing, 2019-08-02 | Slides with Chinese translation

• SCT course (v4.0.0_beta.4), London, 2019-01-22

• SCT course (v3.2.2), Paris, 2018-06-12

• SCT course (v3.0.3), Honolulu, 2017-04-28

• SCT course (v3.0_beta14), Geneva, 2016-06-28

• SCT course (v3.0_beta9), Singapore, 2016-05-13

• SCT course (v3.0_beta1), Montreal, 2016-04-19

• SCT Hands-on Workshop (v2.0.4), Toronto, 2015-06-15

Video tutorials

SCT also has a YouTube channel which contains additional tutorials.