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Spinal Cord Toolbox documentation
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Overview

  • Introduction
  • SCT Concepts
    • PAM50 Template
    • Inspecting the results of your analysis (Quality Control, FSLeyes)
    • Voxels Space Orientation and Coordinate Conventions
    • Temporary Directories
    • Warping fields
  • Testimonials
  • Studies using SCT

User section

  • Installation
    • Installation for MacOS
    • Installation for Linux
    • Installation for Windows
    • Installating FSLeyes
  • Getting Started
  • Tutorials and Courses
    • 1. Spinal cord segmentation for anatomical images
      • 1.1. Before starting this tutorial
      • 1.2. Contrasts
      • 1.3. Algorithm #1: sct_propseg
      • 1.4. Hands-on Example: T2
      • 1.5. Hands-on Example: T1
      • 1.6. Fixing a failed sct_propseg segmentation
      • 1.7. Algorithm #2: sct_deepseg_sc
      • 1.8. Hands-on Example: T1
      • 1.9. Choosing between segmentation algorithms
    • 2. Vertebral labeling for anatomical images
      • 2.1. Before starting this tutorial
      • 2.2. Labeling conventions
      • 2.3. Labeling algorithm: sct_label_vertebrae
      • 2.4. Applying the labeling algorithm
      • 2.5. Alternative #1: Manually labeling the C2-C3 disc
      • 2.6. Alternative #2: Manual labeling all labels
      • 2.7. How many vertebral labels should I use for registration?
      • 2.8. Extracting specific labels for registration
    • 3. Registering anatomical images to the PAM50 template
      • 3.1. Before starting this tutorial
      • 3.2. Registration algorithm: sct_register_to_template
      • 3.3. Applying the registration algorithm
      • 3.4. Customizing the registration command
      • 3.5. Transforming the template using warping fields
    • 4. Computing shape metrics for PAM50-registered data
      • 4.1. Before starting this tutorial
      • 4.2. CSA (Averaged across vertebral levels)
      • 4.3. CSA (Per level)
      • 4.4. CSA (Per axial slice)
      • 4.5. Other shape metrics
      • 4.6. Verifying the correctness of the metrics
    • 5. Coregistering additional data (MT, DT) to the PAM50 template
      • 5.1. Before starting this tutorial
      • 5.2. Spinal cord segmentation for MT1 data
      • 5.3. Creating a mask around the segmentation
      • 5.4. Registration Option 1: Reusing previous warping fields
      • 5.5. Registration Option 2: Direct registration to the template
      • 5.6. Transforming the template using warping fields
    • 6. Computing MTR for PAM50-registered MT data
      • 6.1. Before starting this tutorial
      • 6.2. Coregistering MT0 with MT1
      • 6.3. Computing MTR using coregistered MT data
  • Command-Line Tools
  • FSLeyes Integration
  • Help
  • Citing SCT

Developer section

  • Contributing to SCT
  • Changelog
  • License

SCT ConceptsΒΆ

This section documents some SCT concepts and other useful things to know.

  • PAM50 Template
  • Inspecting the results of your analysis (Quality Control, FSLeyes)
  • Voxels Space Orientation and Coordinate Conventions
  • Temporary Directories
  • Warping fields
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PAM50 Template
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Introduction
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