We are sharing a software package for post-processing multi-spin-echo datasets into proton density and T2 maps. The package is written in MATLAB and C++ and used through execution of MATLAB scripts and a graphical user interface.
Genuine quantification of T2 relaxation in vivo is highly challenging due to the very long scan times associated with full spin-echo acquisitions and, in the case of multi-spin-echo protocols, due to an inherent bias of the T2 values resulting from contamination of the echo train by stimulated and indirect echoes, non rectangular slice profiles, and inhomogeneous B1+ field profiles.
The package is based on a T2 mapping technique called the echo modulation curve algorithm, which relies on accurate Bloch simulations to model the exact signal evolution in multi-spin-echo pulse-sequences. The algorithm employs the exact RF pulse shapes and other experimental parameters. Simulations are repeated for B1+ inhomogeneity values ranging from 50 to 130 percent and T2 values ranging from 1 to 1,000 ms. These simulations produce a database of echo modulation curves, each associated with a unique [B1+,T2] value pair. The desired T2 parametric map is generated by matching experimentally acquired multi-spin-echo data to the echo modulation curve database via l2-norm minimization of the difference between experimental and pre-calculated echo modulation curves. Proton density maps are then calculated by back-projecting the first echo image to time t=0 using the calculated T2 map.
Rapid and accurate T2 mapping from multi-spin-echo data using Bloch-simulation-based reconstruction.
Magn Reson Med. 2015 Feb;73(2):809-17. doi: 10.1002/mrm.25156
Accelerated in Vivo Mapping of T2 Relaxation from Radially Undersampled Datasets Using Compressed Sensing and Model-Based Reconstruction.
Proc Intl Soc Magn Reson Med. 22 (2014). p 4274.
Accelerated and motion-robust in vivo T2 mapping from radially undersampled data using bloch-simulation-based iterative reconstruction.
Magn Reson Med. 2016 Mar;75(3):1346-54. doi: 10.1002/mrm.25558
Method and device for accurate quantification of T2 relaxation times based on fast multi spin-echo NMR sequences.
US patent 10,281,544 B2. May 7, 2019.
Please cite these publications if you are using EMC-based T2 mapping in your research.
Get the Code
The software available on this page is provided free of charge and comes without any warranty. CAI²R and NYU Grossman School of Medicine do not take any liability for problems or damage of any kind resulting from the use of the files provided. Operation of the software is solely at the user’s own risk. The software developments provided are not medical products and must not be used for making diagnostic decisions.
The software is provided for non-commercial, academic use only. Usage or distribution of the software for commercial purpose is prohibited. All rights belong to the authors (Noam Ben-Eliezer, Tobias Block) and NYU Grossman School of Medicine. If you use the software for academic work, please give credit to the author in publications and cite the related publications. For information regarding commercial use of the package or the underlying algorithm, get in touch with Noam Ben-Eliezer.
Installation and Use
The package is implemented in MATLAB using standard script code, embedded with dedicated C++ API. Using the package requires:
- standard MATLAB installation
- software development kit (SDK) – for executing the C++ code from within MATLAB
The downloaded zip file contains three different sub-packages:
- pkg_I. EMC database generator:
MATLAB and C++ script code for generating new echo modulation curve (EMC) databses based on input parameter values.
- pkg_II. T2 map reconstruction GUI:
MATLAB-based graphical user interface (GUI) for post-processing experimental multi-spin-echo set of DICOMs to produce T2 parametric maps (requires a previously generated EMC database). DICOMs can be arbitrarily reconstructed, hence any sampling trajectories or reconstruction techniques are allowed.
Once the installation requirements have been met, the package code should be copied to any folder on the post-processing computer and operated from MATLAB by typing in the GUI name in the command line
- pkg_III. Iterative model-based reconstruction code:
C++ code package for post processing radially sampled multi SE data. In its basis this package will generate T2 & PD maps through the use of an iterative non-linear conjugate-gradient algorithm implementing a three-parameter [B1+,T2,PD] optimization. True estimation of the T2 parametric maps is enabled in this case by integrating the EMC database into the signal model used by the algorithm. For further details, see the related publication from the 2014 annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), for further details.
T2 map reconstruction (pkg_II) requires an EMC database to which experimental data are matched. A database can be generated using pkg_I. Alternatively, if no database is found please send an email the author with the experimental DICOM parameters (or the set of DICOMs that needs to be matched), and a database will be generated for your data. DICOM parameters appear in the bottom part of the GUI.
For more information, see the EMC DB GUI User Manual.
|4.0||Added ability to generate synthetic T2 weighted imaged at arbitrary echo-times (TEs). |
Fixed bug in mono-exponential fit of very low-SNR data.
|3.0||Added multi-slice support.|
Fixed miscellaneous bugs.
|2.0||Improved T2 mapping GUI.|
Added EMC database code generator.
Added iterative model-based reconstruction package.
Questions about this resource may be directed to Noam Ben-Eliezer, PhD.