Quantitative Susceptibility Mapping (QSM), a novel MRI contrast mechanism, offers a map of local tissue magnetic susceptibility. Whereas traditional hypointensity contrast — that in SWI or T2*-weighted images — detects only tissue susceptibility, reflects only regional, not local, tissue-susceptibility effects, and, depending on image parameters, is contaminated by various blooming artifacts, QSM utilizes both magnitude and phase data, performs a dipole deconvolution, and quantitatively investigates local-tissue susceptibility property. QSM is useful for identifying and quantifying specific biomarkers, including iron, calcium, gadolinium, and superparamagnetic iron oxide (SPIO) nanoparticles.
An outline of the MEDI QSM reconstruction. Typical QSM scan time is 7 minutes at 3T.
The MEDI Toolbox, a collection of MATLAB routines for reconstructing the Quantitative Susceptibility Map (QSM), uses the Morphology Enabled Dipole Inversion (MEDI) method. This toolbox also includes background field removal methods, including Projection onto Dipole Fields (PDF) and Laplacian Boundary Value (LBV).
Register here to download the Toolbox and sample data. A download link is provided on the confirmation page.
The code has been tested on 64-bit Windows, 7 MATLAB R2009a, Mac OSX 10.8 MATLAB R2013a, and Ubuntu 10.04 MATLAB R2009a.
Matlab code and test data from our review paper, "Quantitative Susceptibility Mapping (QSM): Decoding MRI Data for a Tissue Magnetic Biomarker," are available here.
We welcome all potential collaborators in our ongoing research and are interested in myriad applications for quantitative susceptibility mapping (QSM) in both human and animal imaging. If you are interested in collaborating with us, these are a few suggestions on your subject's imaging parameters and data format that will greatly facilitate data processing.
The following parameters have generated satisfactory images when tested on GE scanners. This extends to Philips and Siemens scanners, too. (Essential parameters are underlined).
Use a 3D multi-echo gradient echo sequence with flow compensation. The real & imaginary images or magnitude & phase images need to be saved in DICOM format. Parallel imaging can be turned on to reduce scan time, as long as the required images can be properly reconstructed.
Other parameters are as follows:
The following parameters have been tested on Bruker scanners to quantify SPIO on the order of 30ng. The detection limit is roughly proportional to 1/(SNR*TElast*B0). Please feel free to adjust the parameters accordingly. (Essential parameters are underlined).
Use a 3D multi-echo gradient echo sequence with flow compensation. True orthogonal planes are recommended. For Bruker scans, raw data (fid) and imaging parameters (acqp) are welcome. Otherwise, the real & imaginary images or magnitude & phase images need to be saved in DICOM format.
Other parameters are as follows:
General QSM information can be found on the QSM Wikipedia Page and at QSMMRI.com.
For further information, please contact Dr. Yi Wang (yiwang@med.cornell.edu). We are constantly optimizing these parameters. Please let us know if these protocols don't meet your needs, and we'll be glad to assess the situation and improve the acquisition.
