Computing Resources

QSM Data Processing Tools

JHU/KKI QSM Toolbox v3.0

Description of the package

JHU/KKI QSM Toolbox v3.0 is MATLAB software with graphic user interface (GUI) for doing Quantitative Susceptibility Mapping (QSM) processing from MR magnitude and phase data acquired with gradient echo sequence (GRE). It includes different pipelines for doing multistep QSM, inlcuding phase unwrapping, background field removal and QSM diple inversion.

This toolbox uses some processing routine from FSL, e.g. bet, thus FSL must be installed.

To test this tool, after downloading the package, run QSM.m which will show the graphic interface. For detailed usage and description of the toolbox, read the Manual.

Two example datasets are also included in the package. These are acquired on human subjects at our Philips 3T scanner with whole bain coverage, 1 mm isotropic resolution and 6 echoes (TE1/deltaTE/TR=6/6/46 ms). It is in Philips par/rec file format.


If you process data using this package for any publication, please cite the following publications:

  1. van Bergen, J.M., Hua, J., Unschuld, P.G., Lim, I.A., Jones, C.K., Margolis, R.L., Ross, C.A., van Zijl, P.C., Li, X., 2016. Quantitative Susceptibility Mapping Suggests Altered Brain Iron in Premanifest Huntington Disease. AJNR Am J Neuroradiol 37, 789-796.

  2. Chen, L., Hua, J., Ross, C.A., Cai, S., van Zijl, P.C.M., Li, X., 2019. Altered brain iron content and deposition rate in Huntington's disease as indicated by quantitative susceptibility MRI. J Neurosci Res 97, 467-479.

  3. Li, X., Chen, L., Kutten, K., Ceritoglu, C., Li, Y., Kang, N.D., Hsu, J.T., Qiao, Y., Wei, H.J., Liu, C.L., Miller, M.I., Mori, S., Yousem, D.M., van Zijl, P.C.M., Faria, A.V., 2019. Multi-atlas tool for automated segmentation of brain gray matter nuclei and quantification of their magnetic susceptibility. NeuroImage 191, 337-349.

Thank you.

More detailed citation list for each method used in the pipeline can be found in the Manual.

iRSHARP Background Field Removal Tool

Description of the package

This package, the iRSHARP tool was developed for removing the background field variation, which is an important preprocessing step for multi-step quantitative susceptibility mapping (QSM).

To test this tool, run Example_run.m which will load the example MR phase dataset included in this package (both raw phase and unwrapped phase acquired at 7T with TE of 12 ms) and call the main function iRSHARP.m . This function then gives the local field change and background field.


If you process data using the package for any publication, please cite the following publications:

  1. Fang J, Bao L, Li X, van Zijl PCM, Chen Z. Background field removal for susceptibility mapping of human brain with large susceptibility variations. Magn Reson Med. 2019 Mar; 81(3):2025-2037.

  2. Fang J, Bao L, Li X, van Zijl PCM, Chen Z. Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain. J Magn Reson. 2017 Aug;281:130-140.

Thank you.


These packages are available publicly, in the hope that it will be useful, but without any warranty and without even the implied warranty of merchantability or fitness for a particular purpose. They are designed to help researchers in the field of Magnetic Resonance Imaging who may have interests in doing QSM. They are not intended for use in a clinical setting.


Download the packages.


Part of this work was supported by National Institutes of Health grant P41 EB015909.

©2019 Kennedy Krieger Institute. Baltimore, Maryland.
All rights reserved.