MRI sequence development and simulation environment
Tony Stöcker¹, Kaveh Vahedipour, Daniel Pflugfelder2
Stable release 2.8.1 (GNU GPL v2 or later)
JEMRIS is an extensible MRI simulation framework which provides an MRI sequence development and simulation environment for the MRI community. The development was driven by the desire to achieve generality of simulated 3D MRI experiments reflecting modern MRI systems hardware. The accompanying computational burden is overcome by means of parallel computing. Many aspects are covered which have not hitherto been simultaneously investigated in general MRI simulations such as parallel transmit and receive, important off-resonance effects, non-linear gradients, and arbitrary spatiotemporal parameter variations at different levels. The latter can be used to simulate various types of motion, for instance. The JEMRIS user interface is very simple to use but, nevertheless, it presents few limitations. MRI sequences with arbitrary waveforms and complex inter-dependent modules are modelled in a GUI-based environment requiring no further programming.
JEMRIS supports the following features:
- Utilising an optimised library for numerical solutions of differential equations (CVODE) provides accurate 3D MRI simulation results in cases where no analytical solution is available, e.g. to simulate complex nonlinear RF waveforms for selective excitation or adiabatic full passage pulses.
- JEMRIS can deal with arbitrary RF and gradient waveforms, arbitrary multi-channel Tx-Rx coil geometries and configurations, as well as many important physical concepts, such as nonlinear gradients, chemical shift, reversible spin dephasing (T2*), susceptibility-induced off-resonance, temporal varying processes of the object (e.g. movement or flow), concomitant gradient fields, etc.
- Symbolic mathematical calculations are supported by means of the GiNaC library. Thus, many extensions are readily available with no additional programming involved.
- The core simulation routines take advantage of massive parallel processing (using the MPI standard) and are available on different hardware architectures. JEMRIS simulations scale on single-core hardware, small HPC clusters and also on massively parallel supercomputers.
- A Matlab graphical user interface (GUI) is provided with which all simulation parameters are configured, including nearly arbitrary complex MRI sequences. The GUI stores these configurations in XML format which is parsed by the simulator using the Xerces library.
JEMRIS is open source and the community is encouraged to make contributions to the project under www.jemris.org. It has been successfully tested on Linux, Windows and Mac OS X.
1DZNE Bonn, Germany 2IBG-2, Research Center Juelich, Germany