Spinal Cord Toolbox (SCT) - New release v5.1.0

Hello everyone, I’m involved with the Montréal Polytechnique neuroimaging research laboratory.

I wanted to let you know that our team has released version 5.1.0 of SCT, our comprehensive open-source neuroimaging software application to process & analyze spinal cord MRI data.

Functionality changes for this release include:

  • An improved GUI for manual cord centerline labeling.
  • Added support for multiclass and multichannel models in sct_deepseg.
  • Added support for custom models in sct_deepseg.
  • Re-added the sct_concat_transfo command.
  • New default values for sct_register_multimodal to improve reproducibility.
  • Removed -denoise argument for sct_label_vertebrae.

This also includes three new features from 5.0.1:

  • sct_run_batch now handles the case of unexecutable scripts.
  • sct_label_utils now emits a message to let you know about the resulting generated files.
  • When scripts are called from the commandline, they will now display which command (and parameters) called them.


  • We have now created a Twitter account for Spinal Cord Toolbox (with the handle “spinaltoolbox”), as well as various accounts for our lab’s other major open-source software projects (which you can all find on our lab’s Twitter profile).
  • At least 18 bugs have been fixed since SCT 5.0! You can find out more in the link found inside the release tag linked above (at the top of this post),

If you’d like to try out SCT, check out the installation instructions. If you have any technical questions or feature requests, please post in the SCT forum!

Happy processing,
The Spinal Cord Toolbox Team