Algorithms

Every stage of the pipeline is configurable. The numerical methods are provided by QSM.rs; QSMxT orchestrates them over your BIDS data. Below are the valid values for each algorithm option.

Masking

Set with --masking-algorithm, and choose what it operates on with --masking-input.

Value	Method
`threshold`	Intensity thresholding (default)
`bet`	Brain Extraction Tool

Masking input (--masking-input): magnitude-first, magnitude, magnitude-last, phase-quality.

Phase unwrapping

Set with --unwrapping-algorithm.

Value	Method
`romeo`	Rapid Opensource Minimum-spanning-tree Echo Optimisation (default)
`laplacian`	Laplacian-based unwrapping

Background field removal

Set with --bf-algorithm.

Value	Method
`vsharp`	Variable-kernel SHARP (default)
`pdf`	Projection onto Dipole Fields
`lbv`	Laplacian Boundary Value
`ismv`	Iterative Spherical Mean Value
`sharp`	Sophisticated Harmonic Artifact Reduction
`resharp`	Regularization-enabled SHARP
`harperella`	HARPERELLA
`iharperella`	Iterative HARPERELLA

Dipole inversion

Set with --qsm-algorithm. Ten methods are available, spanning fast direct methods through to regularised iterative reconstructions.

Value	Method
`rts`	Regularized Total Strength (default)
`tv`	Total Variation (ADMM)
`tkd`	Truncated K-space Division
`tsvd`	Truncated Singular Value Decomposition
`tgv`	Total Generalized Variation
`tikhonov`	Tikhonov regularization
`nltv`	Nonlocal Total Variation
`medi`	Morphology-Enabled Dipole Inversion
`ilsqr`	Iterative Least-Squares QR
`qsmart`	QSMART two-stage reconstruction

Per-algorithm parameters

Each algorithm exposes its own parameters (regularisation weights, kernel sizes, iteration counts, …). The easiest way to discover them — and to build a run command — is the TUI: it exposes every option with sensible defaults and shows the equivalent qsmxt run command live as you change them. You can also set them in a configuration file, or run the matching standalone tool (e.g. qsmxt invert tgv --help) to experiment directly.