Commands

QSMxT is a single binary with a set of subcommands. Run qsmxt <command> --help for the complete, authoritative options of any command.

Pipeline & datasets

Command	Description
run	Run the full QSM pipeline on a BIDS dataset
init	Generate a pipeline configuration file (TOML)
validate	Validate BIDS dataset structure for QSM processing
dicom-convert	Convert a DICOM directory to BIDS with automatic classification
example	Download an example BIDS dataset to try the pipeline on
slurm	Generate SLURM job scripts for HPC execution: one job per run, then an aggregation job
aggregate	Run the dataset-level steps over runs processed with run --no-dataset-steps
tui	Launch the interactive TUI
update	Check for and install the latest release

Standalone NIfTI tools

These operate directly on NIfTI files (in/out), independent of the BIDS pipeline, and run the same code as the corresponding pipeline stage. See Standalone tools.

Command	Description
mask	Masking: thresholds, BET, HD-BET, RS2-Net, MindGrab, the --mask-preset recipes, morphology, and/or
combine	Multi-coil phase combination (MCPC-3D-S)
unwrap	Phase unwrapping (ROMEO, Laplacian)
fieldmap	Multi-echo B0 field mapping from phase, in ppm
bgremove	Background field removal (V-SHARP, PDF, LBV, …, mSMV, BFRnet)
invert	Dipole inversion: every classical and deep-learning method, plus COSMOS and STI
separate	Susceptibility source separation (paramagnetic / diamagnetic)
qsmart	QSMART vessel-aware reconstruction from the total field
swi	Susceptibility-weighted imaging with CLEAR-SWI (and minimum-intensity projection)
segment	SynthSeg whole-brain segmentation of a magnitude image
r2star	R2* mapping from multi-echo magnitude
t2star	T2* mapping from multi-echo magnitude
r2	R2 mapping from multi-echo spin-echo (MESE) magnitude
r2prime	R2′ = R2* − R2, over the region R2 covers
homogeneity	Inhomogeneity correction on magnitude data
resample	Resample an oblique volume to axial orientation
quality-map	Compute a ROMEO phase-quality map

Every command, subcommand and option, with accepted values and defaults, is listed in the generated CLI reference.

Global

qsmxt --help       # list all commands
qsmxt --version    # print version
qsmxt <cmd> --help # full help for a command

run options at a glance

Option	Purpose
--config <FILE>	Load settings from a TOML configuration
--include <GLOB>… / --exclude <GLOB>…	Select runs by pattern
--num-echoes <N>	Limit echoes processed
--qsm-algorithm <A>	Dipole inversion method
--unwrapping-algorithm <A>	Phase unwrapping method
--bf-algorithm <A>	Background field removal method
--mask-preset <P>	Masking recipe (robust-threshold, bet, hd-bet, bet-and-phase, rs2-net, mindgrab)
--mask <SECTION>	Custom mask section, repeatable (e.g. magnitude,bet:0.5,erode:2)
--mask-combine <or|and>	How multiple --mask sections combine (default or)
--mask-refine <OP>	Refinement applied to the combined mask, repeatable (e.g. fill-holes:0)
--masking-input <A>	Override the image the mask is derived from
--phase-offset-removal <bool>	Multi-echo phase-offset removal
--bipolar-correction	Bipolar readout correction (≥ 3 echoes)
--romeo-*	Fine-grained ROMEO unwrapping controls
--do-chisep / --chisep <M>	Susceptibility source separation
--do-segmentation / --do-analysis	SynthSeg parcellation and per-structure statistics
--qsm-reference <SPEC>	What χ’s zero is pinned to: mean, none, or a parcellation region
--export-dicom	Also write each final map as a DICOM series
--source-dicom <DIR>	Inherit patient/study identity from the original DICOMs when exporting
--dicom-outputs <TOKEN>…	Restrict the DICOM export to these maps (default: all produced)

See Algorithms for what each algorithm option’s values do, and the CLI reference for every option of every command.