Running interactively

The interactive terminal interface (TUI) is the recommended way to use QSMxT. It takes you through the whole workflow — converting DICOMs, configuring the pipeline, and running it — without writing a single command flag or config file.

qsmxt tui

What you can do

• Convert DICOMs to BIDS — point at a DICOM directory, review the automatic series classification, relabel anything that needs it, and convert. (See DICOM → BIDS for what the classifier handles.)
• Point at a dataset and let QSMxT discover the phase/magnitude runs.
• Choose algorithms for masking, unwrapping, background-field removal, and dipole inversion from menus — no need to memorise flag names or valid values.
• Adjust parameters for each stage, with sensible defaults pre-filled.
• Copy the equivalent command — as you configure, the TUI shows the matching qsmxt run command and updates it live, and saves your settings to a config file. It’s the easiest way to build a run command without memorising flags.
• Run the pipeline and watch progress without leaving the terminal.
• Submit to a cluster — generate and launch SLURM jobs for large cohorts directly from the TUI; scaling out doesn’t require the command line.

The TUI writes the same configuration the CLI consumes, so anything you set up interactively can be saved and reproduced noninteractively with qsmxt run --config — or by copying the generated command.

Prefer the browser?

You can try the same reconstruction algorithms with no installation at all in qsmbly — a browser build of the QSM engine. It’s a great way to experiment before processing a full dataset with QSMxT.

Note

The TUI is ideal for exploring a new dataset and dialling in parameters. Once you’re happy, capture the configuration to a TOML file and reuse it noninteractively for scripted batch processing.