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
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. See Standalone tools.

Command	Description
mask	Masking operations (Otsu, value, percentile, BET, morphology)
unwrap	Phase unwrapping
bgremove	Background field removal
invert	Dipole inversion
swi	Susceptibility-weighted imaging
r2star	R2* mapping from multi-echo magnitude
t2star	T2* mapping from multi-echo magnitude
homogeneity	Inhomogeneity correction on magnitude data
resample	Resample an oblique volume to axial orientation
quality-map	Compute a ROMEO phase-quality map

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)
--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

See Algorithms for the valid values of each algorithm option.