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Spinal Cord Toolbox documentation

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Overview

Introduction
SCT Concepts
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Testimonials
Studies using SCT

User section

Installation
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Getting Started
SCT Courses
Tutorials
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- Segmentation
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- Vertebral labeling
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- Shape analysis
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  - Compute CSA (and other shape metrics)
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  - Quantify spinal cord compression
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- Lesion analysis
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- Registration to template
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  - Registering labeled anatomical images to the PAM50 template
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  - Registering images to the PAM50 template based on spinal nerve rootlets
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  - Coregistering additional data (MT, DT) to the PAM50 template
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  - Registering lumbar images to the PAM50 template
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- Multimodal registration
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  - Computing MTR using co-registration between MT0 and MT1 data
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  - Contrast-agnostic registration with deep learning
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- Gray matter segmentation
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  - Segmenting the gray and white matter for T2* data
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  - Computing metrics using GM and WM segmentations
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  - Improving registration results using white and gray matter segmentations
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- Atlas-based analysis
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- Diffusion-weighted MRI
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- Functional MRI
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- Other features
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  - Spinal cord smoothing as a preprocessing operation
  - Visualizing misaligned cords with 2D sagittal flattening
- Analysis pipelines with SCT
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Command-Line Tools
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- Segmentation
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  - sct_create_mask
  - sct_deepseg
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  - sct_deepseg_gm
  - sct_deepseg_lesion
  - sct_deepseg_sc
  - sct_get_centerline
  - sct_propseg
- Segmentation analysis
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- Labeling
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- Registration
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- Diffusion MRI
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- Magnetization transfer
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  - sct_compute_mtr
  - sct_compute_mtsat
- Functional MRI
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  - sct_fmri_compute_tsnr
  - sct_fmri_moco
- Metric processing
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  - sct_analyze_texture
  - sct_extract_metric
- Image manipulation
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- Miscellaneous
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- System
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  - sct_check_dependencies
  - sct_version
- Help text (-h) for all tools
Analysis pipelines
FSLeyes Integration
Help
Citing SCT

Developer section

Contributing to SCT
Changelog
License

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sct_version¶

7.3

Help text (-h) for all tools

sct_check_dependencies

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