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QSMxT
QSMxT v9 is a ground-up rewrite in Rust. Coming from the Python version (8.x)? See what changed →
qsmxt — run 
$ qsmxt run study/bids
  discovered 24 runs · 12 subjects
  ✓ masking          threshold
  ✓ phase unwrapping  romeo
  ✓ B0 mapping        multi-echo
  ✓ background field   v-sharp
  ✓ dipole inversion  rts
  ✓ referencing       mean
  → derivatives/qsmxt.rs/  ·  24 χ-maps in 3m12s

QSMxT

Quantitative Susceptibility Mapping, in Rust — a fast, BIDS-native pipeline and interactive TUI.
Get startedTry in your browserTry in NeurodeskView on GitHub

QSMxT takes you from raw scanner DICOMs to quantitative susceptibility maps with a single self-contained binary. It auto-discovers phase/magnitude pairs in BIDS datasets, runs the full reconstruction pipeline with sensible defaults, and writes tidy BIDS derivatives — no environment to manage, no toolbox sprawl.

Install it with a single command:

Terminal window
curl -fsSL https://raw.githubusercontent.com/QSMxT/QSMxT/main/install.sh | sh

See the installation guide for other options, or skip installing entirely and try it in your browser.

Why QSMxT

Section titled “Why QSMxT”

End-to-end pipeline

Masking, phase unwrapping, echo combination, background field removal, dipole inversion, and referencing — orchestrated for you.

10 inversion algorithms

RTS, TV, TKD, TSVD, TGV, Tikhonov, NLTV, MEDI, iLSQR, and QSMART, all provided by QSM.rs.

Interactive TUI

Convert, configure, and run from a polished terminal interface — the recommended way to drive QSMxT, no config file required.

BIDS-native

Auto-discovers phase/magnitude, reads JSON sidecars, and writes compliant derivatives to derivatives/qsmxt.rs/.

DICOM → BIDS

Built-in dicom-convert classifies series automatically — multi-echo, multi-coil, and combined/uncombined reconstructions included.

Built for scale

Disk caching skips completed steps on re-runs, memory-aware parallelism fills your cores, and SLURM scripts fan out across a cluster.

Coming from QSMxT 8.x?

Section titled “Coming from QSMxT 8.x?”

Try it in your browser

Section titled “Try it in your browser”

No install, no data to upload anywhere — qsmbly runs the very same reconstruction algorithms entirely in your browser. It’s the fastest way to experiment with QSM and get a feel for the methods before processing a full dataset with QSMxT.

Open qsmbly →Run the QSM algorithms in your browser at qsmbly.neurodesk.org

Get going

Section titled “Get going”
InstallationOne-line install for Linux, macOS, and Windows.
Quick startFrom raw data to QSM maps in minutes.
Running interactivelyConvert, configure, and run from the TUI — the recommended path.
AlgorithmsThe masking, unwrapping, background-field, and inversion methods.

How do I cite QSMxT?

Section titled “How do I cite QSMxT?”

If QSMxT is useful in your research, please cite:

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. doi.org/10.1002/mrm.29048

Every run also writes a references.txt listing citations for the specific methods your data and settings exercised.