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QSM Tools

List of open-source quantitative susceptibility mapping (QSM) MRI software packages and data.

Please open an issue or pull request if you believe any corrections or additions to the list should be made.

Tools

  • MEDI Toolbox

    Details
    • Language: MATLAB
    • License: Academic-only, signup required
    • Methods:
      • Morphology Enabled Dipole Inversion (MEDI)
      • Truncated singular value decomposition (TSVD)
      • Truncated k-space division (TKD)
      • Iterative SWIM (iSWIM)
      • TV with Split-Bregmann (TVSB)

  • Berkin Bilgic's QSM software collection

    Details
    • Language: MATLAB
    • License: Unknown
    • Methods:
      • Single-Step QSM with Total Generalized Variation regularization
      • Fast Total Generalized Variation regularized QSM
      • Reconstruction for Multi-orientation QSM and Susceptibility Tensor Imaging
      • Single-Step QSM with l2-Regularization
      • Fast l1-Regularized QSM with Magnitude Weighting and SHARP background filtering
      • Closed-form l2-Regularized QSM
      • l1- and l2-Regularized QSM and PDF background filtering

  • TGV QSM Algorithm

    Details
    • Language: Python
    • License: Unknown
    • Methods:
      • Total generalized variation

  • QSM Pipeline

    Details
    • Language: Docker and Singularity image bundles.
      • Core QSM tools written in Python
    • License: Unkown
    • Methods:
      • Total generalized variation

  • STI Suite(alternate link)

    Details
    • Language: MATLAB
    • License: Non-commercial academic use only, email signup required
    • Methods:
      • Quantitative Susceptibility Mapping without spatial constraints

  • QSM SSTV

    Details
    • Language: MATLAB
    • License: Unknown
    • Methods:
      • Single step total variation

  • pyQSM

    Details
    • Language: Python
    • License: Unknown
    • Methods:
      • Dipole inversion

Data

  • QSM reconstruction challenge 2016

    Details
    • Field strength: 3.0 Tesla
    • Resolution: 1.06 mm
    • Subject: Healthy volunteer
    • Other:
      • A reference susceptibility map computed using the susceptibility tensor imaging algorithm on data acquired at 12 head orientations.

  • STI Suite

    Details
    • Human Brain Single Echo 2D
      • Field strength: 3.0 Tesla
      • Resolution: 1.8 x 1.8 x 3.0 mm3
      • Subject: Human
    • Human Brain Single Echo 3D
      • Field strength: 3.0 Tesla
      • Resolution: 1.25 x 1.25 x 2.0 mm3
      • Subject: Human
    • Human Brain Multi Echo 3D
      • Field strength: 3.0 Tesla
      • Resolution: 1.25 x 1.25 x 2.0 mm3
      • Subject: Human
    • Mouse Brain 3D
      • Field strength: 9.4 Tesla
      • Resolution: 1.0 x 1.0 x 2.0 um3
      • Subject: Human

  • MEDI Toolbox

    Details
    • Field strength: Unkown
    • Resolution: 0.9375 x 0.9375 x 2.0 mm3
    • Subject: Human and simulation
    • Other:
      • Siemens and GE datasets

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