Introduction to spinal cord MRI analysis

Introduction to spinal cord MRI analysis

"This tutorial introduces basics of spinal cord MRI data analysis using the Spinal Cord Toolbox. The tutorial will cover the installation of the Spinal Cord Toolbox, the processing of spinal cord MRI data, and the visualization of the results."

Information

The estimated time to complete this training module is 3h.

The prerequisites to take this module are:

Contact Jan Valosek if you have questions on this module, or if you want to check that you completed successfully all the exercises.

Resources

The main resource for this module is the 2023 Spinal Cord Toolbox Course given by Prof. Julien Cohen-Adad and his team at NeuroPoly lab.

The workshop is available on YouTube:

For the purpose of this module, we will focus on the following chapters of the workshop:

  • 18:39 2. Installation
  • 31:37 3. Segmentation
  • 47:35 4. Vertebral labeling
  • 1:07:30 5. Shape-based analysis
  • 1:31:03 6. Registration to template (only up to 1:48:00)

The slides are available here.

Exercise

  • Watch the selected chapters of the Spinal Cord Toolbox Course.
  • Install the Spinal Cord Toolbox on your local machine.
  • Download the sample data as described in the 2. Installation chapter.
  • Do the segmentation of the spinal cord using two methods (e.g., sct_deepseg_sc, sct_propseg, sct_deepseg) and compare the results. TIP: to visualize the results, you can use viewer of your choice (e.g., fsleyes, itk-snap) or python (nibabel and matplotlib).
  • Perform the vertebral labeling.
  • Compute cross-sectional area (CSA) of the spinal cord at the C2-C3 levels.
  • Do the registration of the T2w image to the template.
  • Follow up with your local TA to validate you completed the exercises correctly.
  • 🎉 🎉 🎉 you completed this training module! 🎉 🎉 🎉

More resources

If you want to learn more about spinal cord MRI data analysis and Spinal Cord Toolbox, please check: