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
news	Show the announcements from the QSMxT team, newest first

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, PRELUDE, MEDI region growing)
fieldmap	Multi-echo B0 field mapping from phase, in ppm
bgremove	Background field removal (V-SHARP, PDF, LBV, …, 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 (makehomogeneous or N4)
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)
--two-pass-mask <SECTION> / --two-pass-mask-combine <or|and>	The two-pass reliable mask’s sections, and how they combine (default: as --mask-combine)
--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.