JEMRIS  2.8.2
open-source MRI simulations
First steps tutorial - simulation

For simulation control JEMRIS provides a 2nd GUI, JEMRIS_sim.

You will see the following empty Simulation GUI where a simple spherical phantom slice with adjustable values is presented accompanied by some default values. JEMRIS_sim is described in some detail here: ug_usage_simulation_gui.


Let us load our EPI sequence, MyEPI:

The simulation GUI indicates the chosen sequence in red letters at the top left: Seqeunce: MyEPI.xml. Should you have succeeded in building the multi processor simulator, pjemris, you may now choose to setup the simulation for execution with mpirun. Otherwise jump over the next intruction block.

It is now safe to immediately start the simulation. A progress bar will pop up and resemble the advancing simulation process.

The simulation should take less than 4 minutes to run a single EPI scan of the 2D sphere preselected on the left on a single 2.4 GHz Pentium 6 core. The parallel execution should deliver its results on a Quadcore Pentium 6 at 2.4 GHz in less than 45 seconds.

After completion you are prompted with the resulting signal. The following screen shot was taken after successful simulation of the above experimental setup:


You are also prompted with some information in the text field at the top right, titled simulation message dump. These are in order from top to bottom the applied physical model, the simulated sample, the transmit and recieve coils, the aggregated sequence, and some further information regarding computation time, number of simulated isoschromats etc.

For this tutorial, the simulator output revealed the following information:


Model : Bloch , solver = CVODE
Sample : 2D sphere , spins = 7825
TxArray : /usr/local/share/jemris/matlab/uniform.xml
RxArray : /usr/local/share/jemris/matlab/uniform.xml
Sequence : /data/mr_cluster/home/kvahed/JEMRIS2/app/src/MyEPI.xml

nmrpc03 -> Master Process: send MR sample (7825 spins) to 4 slave(s)

nmrpc03 -> slave 1: received 1957 spins for simulation ...
nmrpc03 -> slave 2: received 1956 spins for simulation ...
nmrpc03 -> slave 3: received 1956 spins for simulation ...
nmrpc03 -> slave 4: received 1956 spins for simulation ...

MPI Process Wtime = 39.6328 seconds

Should you want to have a look at the simulation result in image- and k-space, you will able to find corresponding options in the drop-down at the bottom right. Just select the desired view.

-- last change 24.05.2018 | Tony Stoecker | Imprint | Data Protection --