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Cite SpinePrep

If you use SpinePrep in your research, please cite the software and the underlying tools it relies on. SpinePrep is an integration pipeline — most of the scientific method it applies was developed by others, and those authors deserve credit alongside SpinePrep itself.

Software

Until a peer-reviewed paper is available, cite the software release:

BibTeX

@software{spineprep,
  title   = {SpinePrep: a containerised BIDS-App for reproducible
             spinal-cord fMRI preprocessing},
  author  = {Sharifi, Kiomars},
  year    = {2026},
  version = {26.0.0},
  doi     = {10.5281/zenodo.21294696},
  url     = {https://spineprep.com},
  note    = {https://github.com/SpinePrep/SpinePrep}
}

The repository ships a CITATION.cff, so GitHub's "Cite this repository" button will always give the current, correct form.

DOI

Each tagged release is archived on Zenodo and receives its own DOI.

Author ORCID: 0000-0002-7032-7995.

Tools you should also cite

SpinePrep calls the following tools. Cite the ones your run actually used — the auto-generated methods boilerplate in each run's report lists them explicitly, and the NOTICE file records their licenses.

Tool Used for Canonical reference
Spinal Cord Toolbox (SCT) cord segmentation, registration, PAM50 De Leener et al., NeuroImage 145 (2017) 24–43
PAM50 template template space De Leener et al., NeuroImage 165 (2018) 170–179
FSL (topup, PNM) distortion correction, physiological regressors Jenkinson et al., NeuroImage 62 (2012) 782–790
topup susceptibility distortion Andersson et al., NeuroImage 20 (2003) 870–888
RETROICOR / PNM cardiac & respiratory regressors Brooks et al., NeuroImage 39 (2008) 680–692
ANTs image registration Avants et al., NeuroImage 54 (2011) 2033–2044

Please also check each tool's own website for its preferred, up-to-date citation, as these can change.

Publications using SpinePrep

Work that uses SpinePrep will be listed here as it appears. If you publish with it, let us know via a GitHub issue and we will add it.

Acknowledgements

SpinePrep builds directly on the work of others:

  • Spinal Cord Toolbox (SCT) — the core cord processing algorithms.
  • fMRIPrep — the design philosophy (BIDS-native, containerised, QC-first) that SpinePrep follows for the spinal cord.
  • BIDS — the data-organisation standard.