Quantitative Susceptibility Mapping (QSM) comprises a group of largely experimental methods by which the absolute concentrations of iron, calcium and other substances may be measured in tissues based on changes in local susceptibility.
QMENTA's QSM pipeline computes quantitative susceptibility maps using both phase and magnitude images and is based on tools developed by qMRLab. The pipeline uses the Split-Bregman method without magnitude weighting. For more information on the methods used, see here.
Example results
Required inputs
- Wrapped phase image
- 3D GRE acquisition (wrapped phase image)
- Must have tag 'phase'
- Magnitude image
- 3D GRE acquisition (magnitude part of image)
- Must have tag 'magnitude'
This analysis only accepts single Echo Time input data. All volumes should be acquired with the same TE.
Outputs
- FitResults.mat: Results matrix, containing all ouputs as workspace varaibles.
- chiL2: Susceptibility map created using L2 regularization without
magnitude weighting - chiSB: Susceptibility map created using Split-Bregman method without
magnitude weighting. - maskOut.nii.gz: Binary mask (maskSharp, gradientMask or same as the input).
- unwrappedPhase.nii.gz: Unwrapped phase image using Laplacian-based method.
Typical execution time
- < 2 minutes
References
- Bilgic et al. (2014), Fast quantitative susceptibility mapping with
L1-regularization and automatic parameter selection. Magn. Reson. Med.,
72: 1444-1459. doi:10.1002/mrm.25029 - Karakuzu A., Boudreau M., Duval T.,Boshkovski T., Leppert I.R., Cabana J.F.,
Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab:
Quantitative MRI analysis, under one umbrella doi: 10.21105/joss.02343