Magnetic Software Packages Old

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 Packages

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

STI Packages

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