Standalone tools
Beyond the end-to-end pipeline, QSMxT exposes each building block as a standalone command that reads and writes NIfTI files. These are handy for experimentation, teaching, scripting, or slotting a single step into another workflow.
Every command takes NIfTI input and produces NIfTI output. Run
qsmxt <command> --help (and qsmxt <command> <subcommand> --help) for exact
arguments.
Masking — qsmxt mask
Section titled “Masking — qsmxt mask”Generate or refine binary masks.
| Subcommand | Operation |
|---|---|
otsu |
Otsu automatic thresholding |
value |
Fixed-value thresholding |
percentile |
Percentile thresholding |
bet |
Brain extraction (BET) |
robust |
Robust threshold (Otsu + dilate + fill-holes + erode) |
erode / dilate |
Morphological erosion / dilation |
close |
Morphological closing |
fill-holes |
Fill holes in a binary mask |
smooth |
Gaussian smooth (re-thresholded at 0.5) |
Phase unwrapping — qsmxt unwrap
Section titled “Phase unwrapping — qsmxt unwrap”Unwrap a wrapped phase image (romeo or laplacian).
Background field removal — qsmxt bgremove
Section titled “Background field removal — qsmxt bgremove”Remove background fields from an unwrapped field map (vsharp, pdf, lbv,
ismv, sharp, resharp, harperella, iharperella).
Dipole inversion — qsmxt invert
Section titled “Dipole inversion — qsmxt invert”Invert a local field map into a susceptibility map. One subcommand per method:
| Subcommand | Method |
|---|---|
rts |
Regularized Total Strength |
tv |
Total Variation (ADMM) |
tkd |
Truncated K-space Division |
tsvd |
Truncated SVD |
tgv |
Total Generalized Variation |
tikhonov |
Tikhonov regularization |
nltv |
Nonlocal Total Variation |
medi |
Morphology-Enabled Dipole Inversion |
ilsqr |
Iterative Least-Squares QR |
# e.g. inspect the parameters of a methodqsmxt invert tgv --helpSupplementary maps
Section titled “Supplementary maps”| Command | Output |
|---|---|
swi |
Susceptibility-weighted image (and minimum-intensity projection) |
r2star |
R2* map from multi-echo magnitude |
t2star |
T2* map from multi-echo magnitude |
quality-map |
ROMEO phase-quality map |
Image utilities
Section titled “Image utilities”| Command | Purpose |
|---|---|
homogeneity |
Correct intensity inhomogeneity on magnitude data |
resample |
Resample an oblique volume to axial orientation |