27th ISMRM Annual Meeting • 11-16 May 2019 • Montréal, QC, Canada

Weekend Educational Session
Open-Source Software Tools for MR Pulse Design, Simulation & Reconstruction

Back to Program-at-a-Glance

Open-Source Software Tools for MR Pulse Design, Simulation & Reconstruction
Weekend Course

ORGANIZERS: Michael Lustig, Tony Stoecker, Lawrence Wald

Sunday, 12 May 2019
Room 710B  08:00 - 16:00 Moderators:  Daniel Gallichan, Valentina Taviani

Skill Level: Basic to Advanced

Session Number: WE-21AB

In order to enable participants to actively follow the software demos in the afternoon, we will utilize Amazon AWS to launch remote machines that have the software installed, and connect to them. This requires an AWS account to be set up —PRIOR— to the course.

To get the most out of the course, we suggest that you follow the following instructions as soon as possible so you are familiar with the process.
    • Instructions for Mac OSX, and Windows 10 (pdf)
    • Windows 7/8:   Install Putty (https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html)

Special instructions for packages:
    • Pulseq: Please install X2GO (https://wiki.x2go.org/doku.php)
    • GPILab: please install a VNC client (RealVNC for Windows https://www.realvnc.com) Detailed instructions at: http://gpilab.com/2019/05/ismrm-demo-primer/

Please note that running a remote AWS machine is not free, and amazon will charge your account for usage. The cost would not be more than a few USD (<5$) for the duration of the demo. Make sure to turn off all the instances at the end of the demo.


In this weekend educational course, we overview available open-source software tools developed to facilitate MR research. The software packages will be described during the morning lectures, and hands-on training with the packages will occur in the afternoon.

Target Audience
Attendees interested in learning about the breadth of sequence, simulation, and recon tools available for MR practitioners.

Educational Objectives
As a result of attending this course, participants should be able to:


  Bloch Simulation & Pulse Sequences Tools
Maxim Zaitsev
  Designing Reusable Software Components for Computational MRI
Video Permission Withheld
Martin Uecker
Computational techniques play an important part in the development of new methods for Magnetic Resonance Imaging (MRI). Based on our experience developing software for computational MRI, this talk will explain how to develop reusable software components that preserve our scientific knowledge in a reproducible, useful, and sustainable way.

  Usinig cloud computing for exploration and scale
Eric Jonas
The rise of “cloud computing” offerings has enabled many recent advances in data science, simulation, and data analytics. Current cloud providers offer a previously-unimaginable combination of scale, storage, and compute capabilities but it can be difficult for a newcomer to navigate the ecosystem. This tutorial session is targeted at developers and users who have not used cloud computing infrastructure before, or have only recently started experimenting. I will outline the offerings from the various providers, compare and contrast their capabilities, and show how they can enable rapid experimentation and analysis at very low cost. I will highlight several open-source projects, developed by my research group and others, to make this onboarding process easier. I will point out some common pitfalls from migrating existing workloads to the cloud, and suggest means of avoiding them.

Open-Source Reconstruction Systems
Adrienne Campbell-Washburn
This talk will summarize the features of open source MR image reconstruction software projects and provide illustrative examples of software usage. 

  Break & Meet the Teachers
  MRiLab: Realistic MRI Simulations Based on Parallel Computing & Generalized Tissue Model
Fang Liu
  JEMRIS: A General-Purpose MRI Simulator
Daniel Pflugfelder
  The KSFoundation Abstraction Layer for EPIC
Stefan Skare
  gammaSTAR: Platform-Independent MR Sequence Development
Cristoffer Cordes
  Live Cross-Vendor Sequence Programming with Pulseq
Maxim Zaitsev
  RF & Gradient Optimization Tools
John Pauly
  Gradient Optimization Toolbox {GrOpt}
Matthew J. Middione
  Yarra Framework: Open-Source Toolkit for Clinical-Translational MRI Research
Roy Wiggins
  Automated Reconstruction Handling
Eric Borisch
  MRIReco.jl: An Extensible Open-Source Image Reconstruction Framework Written in Julia
Tobias Knopp
  BART Reconstruction Toolbox / Iterative Reconstruction Toolbox in Python
Jonathan Tamir
Hui Xue
Nicholas Zwart
  Lunch & Meet the Teachers
  Hands - On Demonstrations
Interactive parallel demonstration of the software packages (three repetitions)
13:30 Run 1
14:20 Run 2
15:10 Run 3
  Adjournment & Meet the Teachers
Back to Program-at-a-Glance   |   Back to Top
The International Society for Magnetic Resonance in Medicine is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.