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SCT tools process MRI data (NIfTI files) and can do fully automatic tasks such as:

  • Segmentation of the spinal cord and gray matter

  • Segmentation of pathologies (eg. multiple sclerosis lesions)

  • Detection of anatomical highlights (eg. ponto-medullary junction, spinal cord centerline, vertebral levels)

  • Registration to template, and deformation (eg. straightening)

  • Motion correction for diffusion and functional MRI time series

  • Computation of quantitative MRI metrics (eg. diffusion tensor imaging, magnetization transfer)

  • Texture analysis (eg. grey level co-occurrence matrix)

  • Extraction of metrics within anatomical regions (eg. white matter tracts)

SCT also has low-level tools:

  • Help out with manual labeling and segmentation with a Graphical User Interface (GUI)

  • GUI plugin for FSLeyes

  • Warping field creation and application

  • NIFTI volume manipulation tools for common operations

You may now proceed to Installation and Getting Started.