JEMRIS 2.9.1
open-source MRI simulations
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First steps tutorial: simulation


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

  • Start up the Simulation GUI by following command in your MATLAB shell
    >> 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: MRI Simulation tool: JEMRIS_sim.

Let us load our EPI sequence, MyEPI:

  • Click on File | open Sequence.
  • In the presented dialog click on MyEPI.xml to highlight it.
  • Click on Open.

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.

  • Click in the menubar on Settings | Computation | localhost (parallel).

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 i7 core. The parallel execution should deliver its results in about 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:

Parallel jemris 2.8.2 (4a3461f8)

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 : /Users/stoeckert/DZNE/tmp/jemris-doc/MyEPI.xml

DZNEM339 -> Master Process: send MR sample (7825 spins) to 8 slave(s)

Simulating | ************************************************** | 100% done

Actual simulation took 49.08 seconds.

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

Now you may want to continue to the In depth tutorial - Part 1: analytic pulse shapes


-- last change 03.10.2023 | Tony Stoecker | Imprint | Data Protection --