QSMxT
A fast, BIDS-native Quantitative Susceptibility Mapping (QSM) pipeline and
interactive TUI, built in Rust. QSMxT takes you from raw scanner DICOMs to
quantitative susceptibility maps with a single self-contained binary — no
environment to manage, no toolbox sprawl.
The website has everything: installation, guides, the command reference, and
algorithm details. This README is just a quick pointer.
Highlights
- End-to-end pipeline — masking, phase unwrapping, echo combination,
background field removal, dipole inversion, and referencing.
- Interactive TUI — convert, configure, and run from the terminal; it also
shows the equivalent CLI command as you go.
- DICOM → BIDS — built-in conversion with automatic series classification.
- 50+ algorithms — five masking presets, 10 background-field removers, 21
classical and 11 deep-learning dipole inversions, 8 χ-separation methods, and
multi-orientation COSMOS / STI.
- More than χ — CLEAR-SWI, SMWI, T2* / R2* and R2 / R2′ maps, plus
SynthSeg segmentation with per-structure statistics.
- Methods text — every run writes a methods paragraph with the citations
for exactly what ran.
- Built for scale — disk caching, memory-aware parallelism, and SLURM support.
All reconstruction algorithms are provided by
QSM.rs.
Install
# Linux / macOS
curl -fsSL https://raw.githubusercontent.com/QSMxT/QSMxT/main/install.sh | sh
# Windows (PowerShell)
irm https://raw.githubusercontent.com/QSMxT/QSMxT/main/install.ps1 | iex
No install needed to experiment — try it in your browser.
See the installation guide
for manual downloads, building from source, and details.
Quick start
# Easiest: do everything interactively (convert, configure, run)
qsmxt tui
# Or on the command line:
qsmxt dicom-convert /path/to/dicoms study/bids # DICOM → BIDS
qsmxt run study/bids # run the pipeline
No data to hand? Fetch a real in-vivo subject and reconstruct it:
qsmxt example study/bids # download an example dataset
qsmxt run study/bids # run the pipeline
Full guides and the complete command reference are on the
documentation site (or run qsmxt --help).
Coming from QSMxT 8.x (Python)?
v9 is a ground-up rewrite in Rust. Template and group-space building and the web
UI are not part of v9 — the Python line remains available on the
python-legacy branch and the
v8.3.4 release.
See what changed.
Citation
Stewart AW, Robinson SD, O'Brien K, et al. "QSMxT: Robust masking and artifact
reduction for quantitative susceptibility mapping." Magnetic Resonance in
Medicine 87.3 (2022): 1289–1300. https://doi.org/10.1002/mrm.29048
License
GPL-3.0-only.
