FSLeyes Integration

FSLeyes is part of the larger FSL package, which is a library containing tools for FMRI, MRI, and DTI brain imaging data. FSLeyes is the image viewer for this package, and can be installed as either part of the FSL package, or as a standalone app.

Previously, SCT provided instructions on how to install FSLeyes into the SCT environment. However, we now request that you install FSLeyes separately and manage the installation on your own. You can find installation instructions for FSLeyes at this link.

SCT + FSLeyes

SCT has a plugin script that can be used with the FSLeyes interface (GUI).

To enable the SCT plugin:

  1. Open FSLeyes application.

  2. File -> Run script

  3. Select the script spinalcordtoolbox/contrib/fsl_integration/sct_plugin.py

You should see something like this appear in the FSLeyes interface:

SCT-FSLeyes Interface


The YouTube video below demonstrates the FSLeyes plugin in action: