Open source pulse sequence programming

Flexibility in designing pulse sequences has a direct impact on the development of diverse acquisition techniques and strategies (Handbook of MR pulse sequences). This flexibility is typically leveraged to achieve improved tissue contrast, faster acquisition times and enhanced Signal-to-Noise Ratio (SNR). However, this requires knowledge of specific programming environments that are MR vendor dependent (Pulseq, TOPPE. Pulseq-GPI). These environments are also specific to vendor hardware (generations) and software (revisions) intended for implementation. This requires considerable effort and impedes the pace of prototyping. To this end, multiple tools have been developed to enable rapid prototyping and/or deployment of these sequences.   


Open source pulse sequence programming has been in practice since the time of the first MR scanners in laboratories (). However, new pulse programming frameworks have been shared publicly since 2004 (ODIN). Recent developments related to the separation of pulse sequence programming from vendor-specific hardware has allowed for vendor-agnostic tools (Pulseq, TOPPE, Pulseq-GPI).


An open source pulse sequence programming framework is distinguished in its ability to separate programming from hardware (Pulseq, TOPPE). This involves the development of wrappers and/or file formats that are interpretable by one or more hardware setups.  


Important features of these frameworks include: 

  • simulation tools (Bloch equations, Extended Phase Graphs),
  • libraries for designing and visualizing radiofrequency and gradient waveforms,
  • ordering these waveforms to form pulse sequences,
  • a high-level description of the sequences to easily modulate acquisition parameters

A key distinguishing feature is the ability to deploy on different hardware platforms. Some frameworks also provide support for the reconstruction of acquired data, compatibility with standard raw data formats such as ISMRMD, and rudimentary image analysis methods. These software packages are typically programmed in Python, MATLAB and C++. Examples of such frameworks include ODIN, JEMRIS, SpinBench, MRILab, SequenceTree, GPIlab, Pulseq, TOPPE, Pulseq-GPI, etc. Benefits of these frameworks include rapid prototyping of pulse sequence, non-Cartesian image acquisition and reconstruction,  harmonization of sequences across vendor platforms, pragmatic teaching tools among others.   


Spiral imaging of the ADNI phantom using pyPulseq (Pulseq-GPI)
Spiral imaging of the ADNI phantom using pyPulseq (Pulseq-GPI)



Comparisons of the frameworks

The table indicates a suggestive list of features and the ability of a framework to address some or all of the features above.









Current applications and adoption

Open source pulse sequence programming frameworks have been primarily used for demonstration of novel sequences, teaching tools, rapid prototyping of non-Cartesian sequences and  comparing sequences on multiple platforms.


Free scanning of open source pulse sequences - Scanner as an online service

Some MR centers actively developing open source pulse programming allow uploading of MR sequence files for playing out on their scanners. For example, pulse sequence developers could upload their pyPulseq generated sequence to https://docs.google.com/forms/d/e/1FAIpQLSf3MIC6bcOpV20-yYrqmO_OhK4wNgsKZu3oBqRYe4CLbzIT8A/viewform and test out their development.

See also

List of tools at https://www.opensourceimaging.org/projects/

MR Hub at https://www.ismrm.org/MR-Hub/https://ismrm.github.io/mrhub/



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Further reading

Coming soon!



External links         

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Page last modified on Wednesday May 15, 2019 01:49:56 GMT-0000 by ImSG.