Software
Open-source tools for spinal cord MRI preprocessing, analysis, and quantification.
| Name | Purpose | Reference |
|---|---|---|
| Processing | ||
| Spinal Cord Toolbox | Segmentation of the spinal cord, gray matter, lesions; detection of anatomical highlights; registration to templates; motion correction for diffusion and functional MRI time series; computation of quantitative MRI metrics, etc. | De Leener et al. Neuroimage 2017 |
| TotalSpineSeg | Tool for automatic instance segmentation of all vertebrae, intervertebral discs (IVDs), spinal cord, and spinal canal in MRI images | Warszawer et al., 2025 |
| SpineReport | Automated extraction of spinal morphometrics and generation of structured radiological reports from MRI data. | Molinier et al., 2026 |
| T2*w SC MRI with navigator | Navigator-based correction pipelines for demodulating time dependent field variations on spinal cord imaging. | Beghini et al., Magn Reson Med. 2025 |
| Neptune - SC fMRI | User-interface-based MATLAB toolbox for processing spinal cord functional magnetic resonance imaging (fMRI) data. | Rangaprakash & Barry, 2026 |
| SpinePrep - SC fMRI | Containerised BIDS-App for spinal cord fMRI preprocessing | Sharifi et al., 2026 |
| Pastis - SC MR Spectroscopy | Python package for the processing and quantification of single-voxel MR Spectroscopy data. Originally developed to reconstruct, process and quantify spinal cord MRS data at 7 T | Roussel et al., Magn Reson Med. 2022 |
| 7T-DSC-MRI-Toolbox - SC Perfusion / DSC | Python-based toolbox for the processing of cardiac-gated spinal cord Dynamic Susceptibility Contrast (DSC) perfusion MRI at 7T | Lévy et al., Magn Reson Med. 2021 |
| MWI - not SC specific | Julia tools for decomposing multi-exponential signals which arise from multi spin-echo MRI scans into exponential components | (Doucette et al., Z Med Phys. 2020) |
| Templates | ||
| SC Template | Framework for creating unbiased MRI templates of the spinal cord | |
| PAM50 | T1w/T2w/T2*w template with 15WM/3GM bilateral parcels. Aligned with MNI ICBM152 template (Collins et al., 1999) | De Leener et al., Neuroimage 2018 |
| AMU7T | T2*w/qT1 template with 15 WM + 8 GM bilateral and 4 inter-hemispheric parcels. | Le Troter et al., 2023 |
| PAMhisto | WM template from high resolution electron microscopy | Duval et al., Neuroimage 2019 |
| Ex-vivo template | 9.4T T2 template from 13 ex-vivo specimens | Gros et al., 2020 |
| Synthetic SC MRI | ||
| SynSpine | DL model to generate SC synthetic data with varying atrophy levels | Ganzetti et al., Front. Neuroinform. 2025 |
| LesionSCynth | SC MS lesion synthesis method to improve DL segmentation model training | Walsh et al., Imaging Neuroscience 2025 |
If your software is not listed, please fork this repository and submit a pull request.