Hide navigation sidebar

Hide table of contents sidebar

Toggle site navigation sidebar

Spinal Cord Toolbox documentation

Toggle table of contents sidebar

Overview

Introduction
SCT Concepts
Toggle navigation of SCT Concepts
Testimonials
Studies using SCT

User section

Installation
Toggle navigation of Installation
Getting Started
SCT Courses
Tutorials
Toggle navigation of Tutorials
- Segmentation
  Toggle navigation of Segmentation
- Vertebral labeling
  Toggle navigation of Vertebral labeling
- Shape analysis
  Toggle navigation of Shape analysis
  - Compute CSA (and other shape metrics)
    Toggle navigation of Compute CSA (and other shape metrics)
  - Quantify spinal cord compression
    Toggle navigation of Quantify spinal cord compression
- Registration to template
  Toggle navigation of Registration to template
  - Registering labeled anatomical images to the PAM50 template
    Toggle navigation of Registering labeled anatomical images to the PAM50 template
  - Coregistering additional data (MT, DT) to the PAM50 template
    Toggle navigation of Coregistering additional data (MT, DT) to the PAM50 template
  - Registering lumbar images to the PAM50 template
    Toggle navigation of Registering lumbar images to the PAM50 template
- Multimodal registration
  Toggle navigation of Multimodal registration
  - Computing MTR using co-registration between MT0 and MT1 data
    Toggle navigation of Computing MTR using co-registration between MT0 and MT1 data
  - Contrast-agnostic registration with deep learning
    Toggle navigation of Contrast-agnostic registration with deep learning
- Gray matter segmentation
  Toggle navigation of Gray matter segmentation
  - Segmenting the gray and white matter for T2* data
    Toggle navigation of Segmenting the gray and white matter for T2* data
  - Computing metrics using GM and WM segmentations
    Toggle navigation of Computing metrics using GM and WM segmentations
  - Improving registration results using white and gray matter segmentations
    Toggle navigation of Improving registration results using white and gray matter segmentations
- Atlas-based analysis
  Toggle navigation of Atlas-based analysis
- Diffusion-weighted MRI
  Toggle navigation of Diffusion-weighted MRI
- Functional MRI
  Toggle navigation of Functional MRI
- Other features
  Toggle navigation of Other features
  - Spinal cord smoothing as a preprocessing operation
  - Visualizing misaligned cords with 2D sagittal flattening
- Analysis pipelines with SCT
  Toggle navigation of Analysis pipelines with SCT
Command-Line Tools
Analysis pipelines
FSLeyes Integration
Help
Citing SCT

Developer section

Contributing to SCT
Changelog
License

v: latest

Versions: latest; stable; 6.2; 6.1; 6.0; 5.8; 5.7; 5.6; 5.5; 5.4; 5.3.0; 5.2.0; 5.1.0; 5.0.1; 5.0.0; jn-2857-tutorials-with-theme; jn-2857-template-registration-tutorial

Downloads

On Read the Docs: Project Home; Builds

Toggle table of contents sidebar

Contributing to SCT¶

Thank you for your interest in contributing to Spinal Cord Toolbox! 🎉

Please refer to SCT’s GitHub Developer Wiki for contributing guidelines.

Copyright © 2020, SCT Contributors

Made with Sphinx and @pradyunsg's Furo