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Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Shell · 43 lines · 982 B · MIT

  1. #!/bin/sh
  3. set -eu
  5. method="$1"
  6. script_name="$2"
  8. cp -r /app/* /work
  9. cp -r /snakebids /src
  10. script="'${script_name}' tests/data tests/result participant -c1 --skip-bids-validation"
  11. case "$method" in
  12. "setuptools" )
  13. python -m venv .venv
  14. .venv/bin/python -m pip install --no-color .
  15. PATH=".venv/bin:$PATH" eval "$script"
  16. ;;
  17. "poetry" )
  18. poetry install --no-ansi
  19. eval "poetry run $script"
  20. ;;
  21. "uv" )
  22. uv pip install --system .
  23. eval "uv run $script"
  24. ;;
  25. "hatch" )
  26. hatch env create
  27. eval "hatch env run -- $script"
  28. ;;
  29. "pdm" )
  30. pdm install
  31. eval "pdm run $script"
  32. ;;
  33. "docs" )
  34. python -m venv .venv
  35. .venv/bin/python -m pip install .
  36. .venv/bin/python -m pip install -r docs/requirements.txt
  37. .venv/bin/sphinx-build docs build/docs -W
  38. ;;
  39. * )
  40. >&2 echo "Invalid method"
  41. exit 1
  42. ;;
  43. esac

test-template.sh at commit 1d97fee, under MIT · at the source

Overview

Authors: Damien J Mannion1, Maria del Mar Quiroga1, Jacob M Paul2, Marta I Garrido2,3
ORCID iDs: Damien J Mannion, Maria del Mar Quiroga, Jacob M Paul, Marta I Garrido
  1. Melbourne Data Analytics Platform (MDAP), The University of Melbourne, Parkville, Australia
  2. Melbourne School of Psychological Sciences, The University of Melbourne, Parkville, Australia
  3. Graeme Clark Institute for Biomedical Engineering, The University of Melbourne, Parkville, Australia
Institutions: The University of Melbourne (Australia)
Journal: Brain structure & function, volume 231, issue 8, article 131
Dates: received 13 May 2026; accepted 20 August 2026; published online 4 September 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1007/s00429-026-03189-3 · PMID 42696207 · PMCID PMC13545037 · OpenAlex W7128988335
Open access: hybrid, a free copy (OpenAlex)
Preprint: doi:10.31234/osf.io/fmdvn_v1
Status: code verified
Categories: human (organism), methods / tools (subfield)
Methods: Connectivity, fMRI & imaging
Keywords: Workflow, Data processing, Data analysis, Infrastructure, Computing
MeSH: Image Processing, Computer-Assisted*, Neuroimaging*, Software*, Workflow*, Humans (* major topic)
Topic: Scientific Computing and Data Management (Information Systems and Management, Decision Sciences), according to OpenAlex
Funding: University of Melbourne
Citations: not cited yet (Europe PMC); 25 references in the paper

Abstract

The processing of neuroimaging data typically involves a complicated set of operations, which often require different software packages and have intensive computational and storage demands. Although there are many options available for the neuroimaging researcher to establish their preferred set of processing operations, there is relatively little guidance on how to orchestrate such operations within a coherent data processing workflow. Here, by describing the construction of a simplified neuroimaging processing workflow, we demonstrate how the established general-purpose workflow manager ‘Snakemake’ can be used to facilitate neuroimaging data processing. Snakemake allows researchers to use a Python-based markup language to describe how input files are transformed into output files. Snakemake then uses these rules to schedule and execute the computational jobs that are required to generate the output files, without unnecessary recreation of existing output files. This allows the complete processing workflow to be executed with a single command and creates workflows that are interpretable, efficient, and reproducible.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above.

unimelbmdap/neuroimaging_containers

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 99380e076a3d62ce7025f8770f2cf9d7880f114e, 12 February 2026
Size: 23 files, 0 scripts
Software Heritage: not checked
Found in: the text, “Footnotes”
Holds: README, environment (definitions/afni.def, definitions/ants.def, definitions/bids_validator.def, definitions/bidsphysio.def, definitions/dcm2niix.def, definitions/deepret.def, definitions/fsl.def, definitions/fsl5.def, definitions/laynii.def, definitions/matlab.def, definitions/mb.def, definitions/neuropythy.def)
Not found: license file, CITATION.cff, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
1 file
At the source: github.com/unimelbmdap/neuroimaging_containers

khanlab/snakebids

License: MIT
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 1d97feeb39fde9e47b4a403c8f277bd0e8781eef, 13 March 2026
Languages: Python (93), Shell (1)
Size: 277 files, 94 scripts
Software Heritage: archived
Found in: the text, “Footnotes”
Holds: README, license file, environment (pyproject.toml, uv.lock, containers/test-template/Dockerfile), tests, continuous integration, documentation
Not found: CITATION.cff
Tools: PyBIDS (7 files), BIDS Validator (1 file), Snakemake (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
96 files
At the source: github.com/khanlab/snakebids

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 94 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability

The example workflow is available at https://github.com/unimelbmdap/snakemake_paper_demo_workflow. The raw data that is used in the workflow can be obtained via the workflow available at https://github.com/unimelbmdap/snakemake_paper_demo_workflow_data.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 3, 28 September 2026

  • Publisher: n/a → Springer Science+Business Media

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 5 keywords, 5 MeSH terms, 1 funder, 21 references.

Cite

This paper

Mannion, D. J., Quiroga, M. d. M., Paul, J. M., & Garrido, M. I. (2026). Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager. Brain structure & function, 231(8), 131. https://doi.org/10.1007/s00429-026-03189-3

BibTeX

@article{mannion2026orchestrating,
author = {Mannion, Damien J and Quiroga, Maria del Mar and Paul, Jacob M and Garrido, Marta I},
title = {{Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager}},
journal = {Brain structure \& function},
year = {2026},
month = sep,
volume = {231},
number = {8},
pages = {131},
publisher = {Springer Science+Business Media},
issn = {1863-2653},
doi = {10.1007/s00429-026-03189-3},
url = {https://doi.org/10.1007/s00429-026-03189-3},
pmid = {42696207},
pmcid = {PMC13545037}
}

RIS

TY - JOUR
AU - Mannion, Damien J
AU - Quiroga, Maria del Mar
AU - Paul, Jacob M
AU - Garrido, Marta I
TI - Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager
T2 - Brain structure & function
J2 - Brain Struct Funct
PY - 2026
DA - 2026/09/04
VL - 231
IS - 8
SP - 131
SN - 1863-2653
PB - Springer Science+Business Media
DO - 10.1007/s00429-026-03189-3
UR - https://doi.org/10.1007/s00429-026-03189-3
LA - en
ER -

CSL-JSON

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"id": "10.1007/s00429-026-03189-3",
"type": "article-journal",
"title": "Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager",
"container-title": "Brain structure & function",
"author": [
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"family": "Mannion",
"given": "Damien J"
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"container-title-short": "Brain Struct Funct",
"volume": "231",
"issue": "8",
"page": "131",
"DOI": "10.1007/s00429-026-03189-3",
"PMID": "42696207",
"PMCID": "PMC13545037",
"ISSN": "1863-2653",
"publisher": "Springer Science+Business Media",
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"language": "en",
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"date-parts": [
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]
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}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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