JEMRIS  2.8.1
open-source MRI simulations
Introduction


Summary

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.


Features

JEMRIS supports the following features:


Framework

Main Executable Program

All core routines of Jemris are written in C++. Simplified, the mode of action of the main simulator program is as follows: a master process splits the sample into equal portions which are distributed to the compute node processes. Here, the MRI sequence returns values of all pulse axes (RF magnitudes and phases for all transmit coils plus 3 gradient axes) at desired time points to the physical model which numerically solves the Bloch equation individually for each spin. The coil array receives and sums the net signal at every desired time point, which is sent back to the master process where finally the bulk signal is summed and stored. Read this chapter , if you prefer directly running the main execucatbles from the command line.

Graphical User Interfaces

Our experience showed that acceptance of the software is increased if a GUI is provided, and data I/O is supported from Matlab such that users can easily test self-written Matlab code for either sample construction or signal processing. For these reasons, three Matlab GUIs were developed: one for interactively designing the MRI sequence, another for defining the coil configuration, and one for the set-up and execution of the main simulator, respectively. The latter provides some predefined samples, such as the MNI human brain phantom, as well as the possibility for the input of a user-defined sample.


Disclaimer

JEMRIS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. See the GNU General Public License for more details.

Feedback and bug reports are very wellcome. See www.jemris.org to contact the authors. It should be noted that the Matlab GUIs are preliminary. They are stable enough to serve as good starting tools. However, this part of the software might be changed in a later version. Bug reports and feature wishes concerning the GUIs are also very wellcome also any reaction might be shifted to the next major release of JEMRIS.



-- last change 17.06.2016 | Tony Stoecker | Imprint --