matlab and python code to compute 1D metrics to assess QSM reconstructions
Diefenbach, M. N., Böhm, C., Meineke, J., Liu, C., & Karampinos, D. C., One-Dimensional k-Space Metrics on Cone Surfaces for Quantitative Susceptibility Mapping, Proceedings 27. Annual Meeting International Society for Magnetic Resonance in Medicine (pp. 0322) (2019). Montreal, Canada: https://cds.ismrm.org/protected/19MPresentations/abstracts/0322.html.
Example MATLAB code to perform the estimation and demodulation of field map contributions in magnetic resonance water–fat imaging from the article
Diefenbach, M. N., Ruschke, S., Eggers, H., Meineke, J., Rummeny, E. J., & Karampinos, D. C., Improving chemical shift encoding-based water-fat separation based on a detailed consideration of magnetic field contributions, Magnetic Resonance in Medicine, 80(3), 990–1004 (2018). http://dx.doi.org/10.1002/mrm.27097
Example source code (MATLAB) 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, accepted for publication in Magnetic Resonance in Medicine
also contains the implementation of the VARPRO solver for chemical species separation (CSS) described in
Diefenbach, M. N., Ruschke, S., & Karampinos, D. C., A generalized formulation for parameter estimation in mr signals of multiple chemical species, Proceedings 25. Annual Meeting International Society for Magnetic Resonance in Medicine (pp. 5181) (2017). Honolulu, Hawaii. http://archive.ismrm.org/2017/5181.html
vatsatseg is a python implementation of the matlab segmentation tool “SAT_VAT_segmentation” to segment Visceral and Subcutaneous Adipose Tissue (VAT, SAT) in water-fat MRI images used in
Shen, J., Baum, T., Cordes, C., Ott, B., Skurk, T., Kooijman, H., Rummeny, E. J., …, Automatic segmentation of abdominal organs and adipose tissue compartments in water-fat mri: application to weight-loss in obesity, European Journal of Radiology, 85(9), 1613–1621 (2016). http://dx.doi.org/10.1016/j.ejrad.2016.06.006
LaTeX package to create pulse sequence diagrams in magnetic resonance imaging