Introduction

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

• Automatic identification (segmentation) of the spinal cord
• Automatic vertebral labeling
• Segmentation of spinal cord white matter and gray matter
• Registration to template, and deformation (eg. straightening)
• Detection of anatomical highlights (eg. PMJ, spinal cord centerline)
• Correction (motion compensation, eddy currents correction)
• Measurements (for quantitative MRI)
• Help out with manual labeling and segmentation with a GUI

It also has low-level tools:

• Warping field creation and application
• NIFTI volume manipulation tools for common operations

You may now proceed to Installation and Getting Started.