Flow MRI simulation in complex 3D geometries: Application to the cerebral venous network

A new open-source software project is presented, JEMRIS, the Jülich Extensible MRI Simulator, 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 three-dimensional MRI experiments reflecting modern MRI systems hardware. The accompanying computational burden is overcome by means of parallel computing. Many aspects are covered that have not hitherto been simultaneously investigated in general MRI simulations such as parallel transmit and receive, important off-resonance effects, nonlinear 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 interdependent modules are modeled in a graphical user interface-based environment requiring no further programming. This manuscript describes the concepts, methods, and performance of the software. Examples of novel simulation results in active fields of MRI research are given. (c) 2010 Wiley-Liss, Inc.

This paper gives an overview of SIMRI, a new 3D MRI simulator based on the Bloch equation. This simulator proposes an efficient management of the T2* effect, and in a unique simulator integrates most of the simulation features that are offered in different simulators. It takes into account the main static field value and enables realistic simulations of the chemical shift artifact, including off-resonance phenomena. It also simulates the artifacts linked to the static field inhomogeneity like those induced by susceptibility variation within an object. It is implemented in the C language and the MRI sequence programming is done using high level C functions with a simple programming interface. To manage large simulations, the magnetization kernel is implemented in a parallelized way that enables simulation on PC grid architecture. Furthermore, this simulator includes a 1D interactive interface for pedagogic purpose illustrating the magnetization vector motion as well as the MRI contrasts.

Functional magnetic resonance imaging (FMRI) is a noninvasive method of imaging brain function in vivo. However, images produced in FMRI experiments are imperfect and contain several artifacts that contaminate the data. These artifacts include rigid-body motion effects, B0-field inhomogeneities, chemical shift, and eddy currents. To investigate these artifacts, with the eventual aim of minimizing or removing them completely, a computational model of the FMR image acquisition process was built that can simulate all of the above-mentioned artifacts. This paper gives an overview of the development of the FMRI simulator. The simulator uses the Bloch equations together with a geometric definition of the object (brain) and a varying T2* model for the BOLD activations. Furthermore, it simulates rigid-body motion of the object by solving Bloch equations for given motion parameters that are defined for an object moving continuously in time, including during the read-out period, which is a novel approach in the area of MRI computer simulations. With this approach it is possible, in a controlled and precise way, to simulate the full effects of various rigid-body motion artifacts in FMRI data (e.g. spin-history effects, B0-motion interaction, and within-scan motion blurring) and therefore formulate and test algorithms for their reduction. Copyright 2006 Wiley-Liss, Inc.