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@spinalcordtoolbox Spinal Cord Toolbox

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    44 repositories

    • spinalcordtoolbox

      Public
      Comprehensive and open-source library of analysis tools for MRI of the spinal cord.
      pythonmrineuroimagespinalcord
      Python
      •
      GNU Lesser General Public License v3.0
      •109•244•356•5•Updated Oct 23, 2025Oct 23, 2025

    • nnUNet-neuropoly

      Public
      Python
      •
      Apache License 2.0
      •2.2k•0•0•2•Updated Oct 22, 2025Oct 22, 2025

    • manual-correction

      Public
      Scripts for the manual correction of spinal cord labels
      Python
      •
      MIT License
      •0•4•28•3•Updated Oct 15, 2025Oct 15, 2025

    • PAM50-normalized-metrics

      Public
      Spinal cord morphometry in the PAM50 template space
      Python
      •0•3•9•1•Updated Oct 14, 2025Oct 14, 2025

    • PAM50

      Public
      MATLAB
      •1•4•19•4•Updated Oct 10, 2025Oct 10, 2025

    • sct_tutorial_data

      Public
      Data and scripts for SCT's tutorials and courses
      Shell
      •1•2•0•1•Updated Sep 25, 2025Sep 25, 2025

    • doc-figures

      Public
      Repository that contains most figures for spinalcordtoolbox documentation.
      0•0•0•0•Updated Sep 15, 2025Sep 15, 2025

    • report-ui

      Public
      Generate the portable HTML interface for quality control reports for Spinal Cord Toolbox
      TypeScript
      •0•1•8•0•Updated Jul 22, 2025Jul 22, 2025

    • disc-labeling-benchmark

      Public
      Development of a disc labeling benchmark on MRI images
      Python
      •
      GNU Lesser General Public License v2.1
      •0•1•3•2•Updated Jul 4, 2025Jul 4, 2025

    • sct_testing_data

      Public
      Very light data for testing the spinalcordtoolbox
      MIT License
      •2•2•2•1•Updated May 6, 2025May 6, 2025

    • template_AMU7T

      Public
      Data repository containing the AMU7T atlas and template
      Jupyter Notebook
      •
      MIT License
      •1•1•6•0•Updated May 5, 2025May 5, 2025

    • disc-labeling-playground

      Public
      Jupyter Notebook
      •
      GNU Lesser General Public License v2.1
      •0•1•2•1•Updated Apr 17, 2025Apr 17, 2025

    • spinalcordtoolbox-binaries

      Public
      Repo for packaging and hosting the C++ dependencies used by spinalcordtoolbox
      1•0•0•1•Updated Jan 9, 2025Jan 9, 2025

    • build_ANTs

      Public
      Repo for building and hosting the C++ ANTs binary files used by SCT
      0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • pediatric-template

      Public
      Repository for generating pediatric template
      2•2•2•0•Updated Nov 12, 2024Nov 12, 2024

    • disc-labeling-hourglass

      Public
      Labeling of intervertebral discs using the Hourglass deep learning architecture.
      Python
      •
      GNU Lesser General Public License v2.1
      •0•1•15•0•Updated Oct 18, 2024Oct 18, 2024

    • disc-labeling-list

      Public
      Awesome list of vertebral labeling methods
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • template-dog

      Public
      Repository to create spinal cord template of dogs. Data from VirginiaTech.
      Python
      •0•0•10•0•Updated Jul 9, 2024Jul 9, 2024

    • project_detect_compression

      Public
      Python
      •1•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • disc-labeling-nnunet

      Public
      Python
      •
      GNU Lesser General Public License v2.1
      •0•0•1•0•Updated Jan 3, 2024Jan 3, 2024

    • detect-compression

      Public
      Jupyter Notebook
      •
      GNU Lesser General Public License v2.1
      •0•1•3•0•Updated Aug 2, 2023Aug 2, 2023

    • deepseg_lesion_models

      Public
      0•0•0•1•Updated Jul 7, 2023Jul 7, 2023

    • deepseg_gm_models

      Public
      0•0•0•1•Updated Mar 11, 2023Mar 11, 2023

    • exvivo-template

      Public
      High resolution ex-vivo MRI template of the cervical spinal cord.
      0•1•2•0•Updated Dec 7, 2022Dec 7, 2022

    • build_biomedia_stitching

      Public
      This is a repository to facilitate the integration of BioMedIA's stitching module for spinal cord toolbox.
      1•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • spinalcordtoolbox-dev

      Public archive
      A backup of the `dev/` folder from the Spinal Cord Toolbox repository.
      C++
      •
      GNU Lesser General Public License v3.0
      •2•0•0•0•Updated Oct 11, 2022Oct 11, 2022

    • jupyter-book

      Public
      Jupyter Book demo
      Jupyter Notebook
      •
      MIT License
      •2•0•3•0•Updated Sep 28, 2022Sep 28, 2022

    • data-template

      Public template
      Template repo for making datasets we can include as pythonic dependencies of SCT.
      1•0•0•1•Updated Jun 6, 2022Jun 6, 2022

    • spinalcordtoolbox-binaries-old

      Public archive
      1•0•0•0•Updated May 6, 2022May 6, 2022

    • deepseg_keras_onnx_conversion

      Public archive
      Convert SCT's deepseg_{sc, gm, lesion} Keras HDF5 models into .ONNX representations
      Jupyter Notebook
      •0•0•0•0•Updated Mar 21, 2022Mar 21, 2022