ISMRM Demo Primer

Posted by Nicholas Zwart on Sun 05 May 2019

GPI is going to be presented at the ISMRM 2019 Open-Source Software Tools for MR Pulse Design, Simulation & Reconstruction Weekend Course. The format of this session will be to allow developers to pitch their designs and then provide a break-out tutorial session to give participants a chance to interact with the software directly. To that end, this post is about installing the latest demo examples via virtual machine or via a free-tier Amazon-EC2 instance.

This guide is split into two sections:

  • Using Amazon-EC2 via AMI
  • Using a Virtual Machine Locally

If you are not familiar with either of these technologies, it would behoove you to take some time before the meeting to get one of these setups working.

Using Amazon-EC2 via AMI

Lets start by introducing some terms:

  • EC2: Elastic Compute Cloud (the '2' is meant to save space by doubling the abbreviated 'C')
    • The "elastic compute" generally referes to a computer in the cloud that you can use by secure shelling (ssh) into and starting services like an jupyter notebook or web-server, etc...
  • AMI: Amazon Machine Image (if you say "Amazon-AMI", you could then shorten it by saying A2MI)
    • The "machine image" is a freeze dried, pre-installed system that can be run on an EC2 instance. -Giving you the ability to choose the EC2 hardware that you'd like to run the "machine image" on.

The idea is that the GPI demo can be pre-installed on an AMI and the interested ISMRM participant can simply start their own private EC2 instance to test-drive the software. This mechanism for software demos is a new initiative setup by the organizing committee (see the Call for Community Software page for details).

There is still some setup, you'll have to get an Amazon Web Services (AWS) account, find the GPI-AMI, start an instance, setup an ssh tunnel to interact with the cloud system. Since GPI is a graphical desktop application, we've chosen to use VNC as a remote desktop client.

I'm going to include instructions for MacOS, Ubuntu Linux and Windows. -Take the Windows steps with a grain of salt, I'm listing some instructional links but this isn't the method I'm personally familiar with.

1. Install an SSH Client

To connect to the EC2 instance (of an AMI) you'll need a secure shell client application. This is already part of MacOS and Linux, so you're set. If you're using Windows then you'll need a client like Putty.

2. Install VNC

Each OS has various VNC capabilities. MacOS has it by default, it can be accessed by pressing the key sequence Command-k with the in focus.

Ubuntu Linux

I prefer tightVNC since it has nice compression features and has been available nearly for ever.

   $ sudo apt-get update
   $ sudo apt-get install xtightvncviewer


Find and install a VNC client. It appears that RealVNC has a free trial version.

3. Sign up for a Free Amazon Web Service Account

Point your browser to and sign up. You'll have to enter a credit card, but if you only select 'free tier' services (which are labelled at every step), then you won't incur any charges... probably.

4. Run the GPI-AMI on EC2

There are few menus to navigate through to get to the AMI instance that we've setup for the demo:

  • Click the Region button in the upper right hand corner of the page.
    • Mine says "Ohio", but you can choose either "Ohio" or "Oregon", this will allow you to find the AMI
  • Click the link "Launch a virtual machine"
    • this brings you to a page that has various pre-configure images
  • Click the "Community AMIs" tab on the left hand side of the page.
    • use the search bar to find either of the following AMIs:
      • Name: GPILAB, AMI-Name: GPILAB-DEMO, AMI ID: ami-02203acf16dd4a983 Region: (US East, Ohio)
      • Name: GPILAB, AMI-Name: GPILAB-DEMO, AMI ID: ami-0080216529b04243b Region: (US West, Oregon)
  • Click the checkbox next to the list AMI and then click the "Launch" button above the list
    • Choose the "General purpose" (t2.micro) machine config
    • Press "Review and Launch"
    • Then Press "Launch"

At this point you'll see a dialog box that is asking you to generate a "key-pair". This is for secure shelling into your instance, and its the only way to do so. So choose "create a new key pair" and download the PEM file to your home directory (remember what you named it, and where you put it). Hit the final "Launch" button and then hit the "View Instance" button.

5. Connect to Your EC2 Instance

Almost connected! Within the "EC2 Instance" view right click on your newly running instance to get a popup-dialog, from there hit connect for another popup that shows the following information:

To access your instance:

1. Open an SSH client. (find out how to connect using PuTTY)
2. Locate your private key file (GPILAB_Demo.pem). The wizard automatically detects the key you used to launch the instance.
3. Your key must not be publicly viewable for SSH to work. Use this command if needed:

    chmod 400 GPILAB_DEMO.pem

4. Connect to your instance using its Public DNS:


    ssh -i "GPILAB_DEMO.pem"

Please note that in most cases the username above will be correct, however please ensure that you read your AMI usage instructions to ensure that the AMI owner has not changed the default AMI username.

You'll need to take that information to parameterize your ssh client (with your instances domain and the user 'ubuntu').

MacOS and Linux

In a terminal enter the following command (after you replace the relevant parts with your instance information):

    $ ssh -i "GPILAB_DEMO.pem" -L 5900:localhost:5900

The -L 5900:localhost:5900 is used to forward the VNC port over the ssh connection.


Take note of the PEM file location, the port forwarding command, the username and domain; these will be entered into Putty to perform the ssh link and VNC tunnel.

Follow this guide to ensuring that Putty and VNC are setup correctly.

6. Start the VNC Client

With the ssh connection established (and the VNC port forwarded to localhost). You can fire up your VNC client and enter the following information:


Focus the and hit Command-k. In the dialog box labelled 'server address' type:


Then press connect.


In a terminal enter:

    $ xtightvncviewer localhost:5900


Follow this guide to ensuring that Putty and VNC are setup correctly.

The VNC Password is gpilab

Assuming the ISMRM conference wifi has enough bandwidth to tunnel a VNC connection, you should be good to go ;).

Start GPI

There is a script on the desktop called startGPI, just double click to get started.

If you'd like more information on the process of setting up an AMI, the ISMRM organizers have a nice guide (with pictures) used in a past DL tutorial.

Using A Virtual Machine Locally

If your not convinced you'll be able to connect to an Amazon EC3 instance or perhaps you're more used to using a virtual machine locally, we've got an open virtual appliance that's ready to go. You'll need to download and install either VirtualBox or VMware:

Then you'll have to download our pre-installed GPI virtual machine from the release page or directly:

Open your chosen virtual machine client and import the downloaded OVA file. After a few dialog boxes you should be able to start your VM directly.

Start GPI

There is a script on the desktop called startGPI, just double click to get started.