README.org

Trabecular Bone QSM

Description

Example source code to perform Quantitative Susceptibility Mapping (QSM) to measure trabecular bone density from the article

Diefenbach, M. N., Meineke, J., Ruschke, S., Baum, T., Gersing, A., & Karampinos, D. C., On the sensitivity of quantitative susceptibility mapping for measuring trabecular bone density, Magnetic Resonance in Medicine, (), (2018). http://dx.doi.org/10.1002/mrm.27531

@article{diefenbach18_sensit_quant_suscep_mappin_measur,
  author =       {Maximilian N. Diefenbach and Jakob Meineke and
                  Stefan Ruschke and Thomas Baum and Alexandra Gersing
                  and Dimitrios C. Karampinos},
  title =        {On the Sensitivity of Quantitative Susceptibility
                  Mapping for Measuring Trabecular Bone Density},
  journal =      {Magnetic Resonance in Medicine},
  year =         2018,
  doi =          {10.1002/mrm.27531},
  url =          {https://doi.org/10.1002/mrm.27531},
}

Repository Overview

• scripts/: batch processing functionality
  • demo.m: runs QSM method from the paper on example dataset
  • WFI_subject.m: function to run field mapping step on a single subject dataset
  • BFR_subject.m: function to run background field removal step on a single subject dataset
  • QSM_subject.m: function to run dipole inversion step on a single subject dataset
  • …
• code/: core algorithms
  • 3rd: third party libraries
  • …
• data/: includes data of one examplary subject
  • 20180406_502_CT.nrrd: CT image
  • 20180406_144018_0302_bFFEhires.nii.gz: high res bSSFP image
  • 20180406_144018_0302_ImDataParams.mat: TIMGRE data
• figures/: LaTeX/TikZ code to reproduce figures from the paper

Example Result

Output from the script demo.m:

License