Magnetic Software Packages

This page depicts a collection of software packages for the processing of data for Magnetic Tissue Properties Mapping, including QSM, SWI, and STI. Also, check out the following presentation about tools used in EMTP: EMTP Study Group meeting 2021 Tools Roundup.

Please help us to stay updated by sending your suggestions to magneticadmin@emtphub.org.

QSM Packages

A) Toolboxes

SEPIA (by Kwok-Shing Chan, RU) Includes a comprehensive set of phase unwrapping, background field removal, and dipole inversion methods
Neurodesk (by Steffen Bollman et al.) Includes ROMEO, TGV, QSMxT, CLEAR
MEDI (Cornell Group)
STI Suite (by Chunlei Liu, UC Berkeley)
JHUKKI QSM Toolbox (by Bergen + Li, JHU + KKI)
FANSI (by Carlos Milovic, UC + UCL)
QSM software (by Hongfu Sun, Ualberta)
QSMxT pipeline (by Bollman + Stewart + Shaw, UQ)
pyQSM (by Alan Kuurstra, UWO)
DeepMRI (by Y. Gao + Z. Xiong + H. Sun, CSU + UQ + UON) Includes iQSM/iQSM+, DCRNet, xQSM, BFRnet

B) Phase Unwapping

ROMEO (by Korbinian Eckstein, MUW)
SEGUE (by Anita Karsa, UCL)
BEST PATH (by Alan Kuurstra, UWO)

C) Dipole Inversion

INR-QSM (AMRI-Lab)
AMP-PE (by Shuai Huang, Emory CN2L)
ALOHA (BISPL Lab)
NDI (by Daniel Polak, Siemens Healthineers)
QSM software collection (by Berkin Bilgic, MGH) Includes BM4D; TGV; COSMOS; L1; L1 & L2; CF-L2
QSMbox (by Julio Acosta-Cabronero, UCL)
QSMnet & QSMnet⁺ (SNU-LIST Lab)
TKD & Tikhonov (by A. Karsa & K. Shmueli, UCL)
LPCNN (by Lai + Li + Sulam, JHU)
DeepQSM (by S. Bollman, UQ)
QSMGAN (by J. Chen et al., UC Berkeley)

D) Susceptibility (Chi) Separation

Decompose QSM (by J. Chen & Ch. Liu, UC Berkeley; available upon request from Chunlei Liu)
APART-QSM (by Z. Li & H. Wei, SJTU)
Chi-separation (by H. Shin & M. Kim, SNU-LIST Lab)

E) Single-Step Methods

TGV (Neuroimaging Group – MUG)
Water-fat TFI (by Christof Boehm, TUM)
QSM Software Collection (by Berkin Bilgic, MGH) Includes TGV and L2
TV (by Alan Kuurstra, UWO)
AutoQSM (AMRI-Lab)
MoDL-QSM (AMRI-Lab)

F) Utilities & Metrics

QSM-CI online challenge (by Ashley Stewart, UQ)
Bi-parametric Segmentation Toolbox (by Fahad Salman, UB)
QSM tilt correction (by Oliver Kiersnowski, UCL)
QSM ESP metric (by Maximilian Diefenbach, TUM)
XSIM metric (by Carlos Milovic, PUCV)

SWI/ STI Packages

Susceptibility Weighted Imaging

CLEAR-SWI (by Korbinian Eckstein, MUW, included also in SEPIA and Neurodesk toolboxes)
SMwI (by SNU-LIST Lab)

Susceptiblity Tensor Imaging

STI Suite (by Chunlei Liu’s Lab, UC Berkeley)
DeepSTI (by Zhenghan Fang, JHU)

If you have any suggestions, do not hesitate to contact us.