Crate qsm_core 

QSM-Core

A Rust library for Quantitative Susceptibility Mapping (QSM) of the brain.

QSM-Core provides a complete set of algorithms for reconstructing magnetic susceptibility maps from MRI phase data, including brain extraction, phase unwrapping, background field removal, dipole inversion, and susceptibility source separation.

Pipeline Overview

A typical QSM pipeline follows these steps:

1. Brain extraction (bet) — mask the brain region from magnitude images
2. Phase unwrapping (unwrap) — remove 2π wraps from MRI phase data
3. Background field removal (bgremove) — isolate the local field from background sources
4. Dipole inversion (inversion) — reconstruct susceptibility from the local field

Additional processing modules:

• SWI (swi) — Susceptibility Weighted Imaging (CLEAR-SWI)
• Chi-separation (separation) — decompose susceptibility into paramagnetic/diamagnetic components
• Multi-echo processing (utils) — R2*/T2* mapping, phase combination (MCPC-3D-S), bias correction

Feature Flags

• parallel — enables Rayon-based multi-threading for FFT and iterative solvers
• simd — enables SIMD acceleration via the wide crate

Algorithms

Stage	Methods
Brain extraction	BET
Phase unwrapping	ROMEO, Laplacian
Background removal	V-SHARP, SHARP, PDF, iSMV, LBV, SDF
Dipole inversion	TKD, TSVD, Tikhonov, TV-ADMM, NLTV, RTS, MEDI, TGV, iLSQR
SWI	CLEAR-SWI
Separation	Chi-separation (MEDI-based)
Multi-echo	MCPC-3D-S, R2*/T2* (ARLO), bias correction
Utilities	Frangi vesselness, surface curvature, Otsu thresholding, QSMART

Modules

bet

BET (Brain Extraction Tool) Implementation

bgremove

Background field removal methods

fft

FFT wrapper for 3D transforms using rustfft

inversion

Dipole inversion methods for QSM

kernels

Kernel functions for QSM processing

nifti_io

NIfTI file I/O for WASM

par

Conditional parallelism macros.

priority_queue

region_grow

separation

Susceptibility source separation

solvers

Iterative solvers for QSM

swi

Susceptibility Weighted Imaging (SWI)

unwrap

Phase unwrapping methods

utils

Utility functions for QSM processing

Macros

maybe_par_chunks_mut

Parallel or sequential chunks iterator.

maybe_par_iter

Parallel or sequential immutable iterator over a slice.

maybe_par_iter_mut

Parallel or sequential mutable iterator over a slice.