qsm-ci 0.2.0

Submit, test, and score QSM reconstruction algorithms for the QSM-CI challenge.

QSM-CI

An open challenge and leaderboard for Quantitative Susceptibility Mapping (QSM) reconstruction.

Submit a QSM algorithm — in any language, as a container — and QSM-CI runs it on standardized data, scores it against held-out ground truth, and publishes the result to an interactive leaderboard. Every published algorithm gets a citable Zenodo DOI and can be run by anyone with one command.

→ https://qsmxt.github.io/QSM-CI

• Leaderboard — per-stage tables and the background-removal × dipole-inversion combination matrix, with an interactive volume viewer.
• Run an algorithm — locally or from a workflow engine (nipype, Pydra, CWL, Snakemake, Nextflow).
• Submit yours — open a pull request adding a folder under algorithms/.

Run an algorithm

pip install qsm-ci
qsm-ci list                                   # the published algorithms you can run
qsm-ci run sharp --totalfield tf.nii.gz --mask mask.nii.gz

Algorithms are fetched from Zenodo and run in their pinned container, so results are reproducible. See the running guide for details.

Submit an algorithm

A submission is a folder under algorithms/<slug>/ — your run.sh, a stage: declaration, and a container environment — reading and writing canonical artifacts (all fields and χ in ppm). Your code is mounted, not baked. QSM is scored stage-aware (field-mapping → background removal → dipole inversion, plus combined spans), both isolated and composed with other stages.

Start from the Submit guide; the full rules are in CONTRACT.md and the machine-readable stages.yml. MATLAB is welcome via the license-free MATLAB Runtime.

Repository layout

Path	What it is
algorithms/<slug>/	One submission each
qsm_ci/	The qsm-ci CLI (published to PyPI)
eval/	qsm-eval — the Python scorer (metrics ported from QSM.rs)
scripts/pipeline.py	Isolated + composed evaluation runner
web/, results/index.json	The leaderboard site and the scores that feed it
CONTRACT.md, stages.yml	The submission contract and stage registry