Module separation 

Susceptibility source separation

This module provides algorithms for separating total magnetic susceptibility into paramagnetic (χ+, primarily iron) and diamagnetic (χ-, primarily myelin) components using local field maps and R2’ relaxation data.

Methods

• chi_sep_ilsqr: the original Shin 2021 projected-CG algorithm (SNU-LIST toolbox chi_sep_iLSQR), initialized from a conventional QSM
• chi_sep_medi: MEDI-based Gauss-Newton optimization with coupled field + R2’ constraints
• r2star_qsm: closed-form separation from a QSM + R2* (Dimov 2022, no R2’ needed)
• wavesep: wavelet-L1 proximal-gradient separation from a QSM + R2’ (Fang 2023)
• decompose: signal-domain 3-compartment per-voxel fit from a QSM + multi-echo magnitude (Chen 2021)
• hc_chisep: hollow-cylinder χ-separation with signal-derived fiber orientation from a QSM + R2’ + multi-echo magnitude (Wharton & Bowtell model)

Reference

Shin, H., et al. (2021). “χ-separation: Magnetic susceptibility source separation toward iron and myelin mapping in the brain.” NeuroImage, 240:118371.

Re-exports

pub use chi_sep_ilsqr::chi_sep_ilsqr;

pub use chi_sep_ilsqr::ChiSepIlsqrParams;

pub use chi_sep_medi::chi_sep_medi;

pub use chi_sep_medi::ChiSepParams;

pub use decompose::decompose;

pub use decompose::DecomposeParams;

pub use hc_chisep::hc_chisep;

pub use hc_chisep::HcChisepParams;

pub use r2star_qsm::r2star_qsm;

pub use r2star_qsm::r2star_qsm_from_magnitude;

pub use r2star_qsm::R2starQsmParams;

pub use wavesep::wavesep;

pub use wavesep::WaveSepParams;

pub use susep_net::susep_net;

pub use susep_net::SusepNetNorm;

pub use chisepnet::chisepnet;

pub use chisepnet::ChiSepNetNorm;

Modules

chi_sep_ilsqr

χ-separation via the original Shin 2021 projected-CG algorithm.

chi_sep_medi

Chi-separation using MEDI-based coupled optimization

chisepnet

χ-sepnet deep-learning χ-separation (onnx feature).

decompose

DECOMPOSE-QSM: signal-domain paramagnetic/diamagnetic source separation.

hc_chisep

HC-ChiSep: hollow-cylinder χ-separation with signal-derived fiber orientation.

r2star_qsm

R2*-QSM: susceptibility source separation from gradient-echo data alone.

susep_net

SUSEP-Net deep-learning χ-separation (onnx feature).

wavesep

WaveSep: wavelet-based susceptibility source separation.