Creating a Simple Pacing Simulation on EP Workbench

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Creating a Simple Pacing Simulation on EP Workbench

This is a guide on how to run a simple pacing simulation on EP Workbench.

(1) Load your OpenEP case.

This can also be an OpenCARP or VTK file

• Select File > Load from the Systems manager and choose the file openep_dataset_1.mat or your preffered model.

NOTE: Try from our example datasets: openep-py/openep/_datasets/OpenEP-MATLAB at dev · ecci-cvs/openep-py · GitHub. Press on the openep_dataset_1.mat then press on the download icon on the right.

• Once loaded you should see a mesh in the left-hand window; the 3D viewer.

(2) Add a pacing site

To run a pacing simulation, we need to define a location on the mesh surface to pace from.

• On the 3D Viewer menu select Tool > Landmark Picker, this will display a list of landmarks on the left pane.

• Scroll to the bottom of the left pane, and press on + Add landmark.
• On the dropdown options, select Pacing site and give your site a name, e.g. P1 (see below)
• Then right-click on the atrial surface to select a point to pace from (you will see a black mark). If you made a mistake, you can just press right-click again to select the correct location.

• Press confirm to finalise the location and name of your pacing site. You will see a blue cylinder on the pacing site that has been confirmed.

(3) Ensure you have configured your Run Machine

NOTE: Only do this step if you haven’t already configured your Run Machine as Docker.

A run machine defines where you want to run the simulation. On EP Workbench you can run it in three ways: Directly on your machine (Native), using a container (Docker) or on a remote machine (for HPCs).

In this example we will connect with OpenCARP docker.

• First ensure you have installed Docker and OpenCARP on your machine (please see Brief Instructions for Setup for more information).
• Go to Preferences (in the bottom right window) and select Machine.
• Fill in the information as follows:
  • Working directory: A path to an empty directory to store cached data.
  • Resource manager: Docker
  • Docker Exe Path: /usr/local/bin/docker (* see note below)
  • Docker image: http://docker.opencarp.org/opencarp/opencarp:latest
• PRESS Apply button!!

(*) NOTE: Windows users can set this to simply docker (case sensitive), Mac users can find this by typing “which docker” into your terminal, usually /usr/local/bin/docker.

(4) Create a Simulation Task

• Now we will create a simulation task or tab, on the top right corner press Simulation tab and then press New Simulation. This will create a teal colored simulation tab.
• Press on tab itself (for example, where it says Simulation), this will open up the Simulation Properties pane.
• Fill this according your simulation experiment, for a simple experiment make the follwong changes:
  • Name: MySimulation
  • System: 0
  • Run Machine: Local
  • Press on the button + pacing site, then press on [+] Pacing site to expand the settings.
  • In the Pacing Site settings: Ensure the Location is “P1”, and for this example we will use Number of beats: 3
  • Press Save at the bottom of the form.

Notice that the teal tab now shows “MySimulation” instead of “Simulation”. (See below).

(5) Run your simulation

• Start Docker Desktop in the background.
• Press the play button on the right (only press it once, there may be a delay).

• When running it should look like this:

• Once successfully run, it should look like this:

(6) Retrieve your simulation

• Press the Retrieve button once the simulation has completed.
• Select a folder to save the simulation to, it will automatically load the simulation into EP Workbench.
• Press the Play button to see the simulation run!