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PyPulseq: A Python Package for MRI Pulse Sequence Design

Pulse sequence design is a significant component of MRI research. However, multi-vendor studies require researchers to be acquainted with each hardware platform's programming environment.

PyPulseq enables vendor-neutral pulse sequence design in Python 1,2(#references). The pulse sequences can be exported as a .seq file to be run on Siemens/[GE]/[Bruker] hardware by leveraging their respective Pulseq interpreters. This tool is targeted at MRI pulse sequence designers, researchers, students and other interested users. It is a translation of the Pulseq framework originally written in Matlab 3(#references). Currently, PyPulseq is compatible with Pulseq 1.2.0.

It is strongly recommended to first read the [Pulseq specification] before proceeding. The specification document defines the concepts required for pulse sequence design using PyPulseq. API docs can be found [here][api-docs].

If you use PyPulseq in your work, cite as:

Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design." Journal
of Open Source Software 4.42 (2019): 1725.

Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping
pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018):
9-15.

📢 Pulse sequence development in your browser!

Design pulse sequences using pypulseq in your browser! Check out the [Lightning-start ⚡][lightning-start] section to learn how!

📚 [Relevant literature][scholar-citations] (reverse chronological)

1. Ravi, K.S. and Geethanath, S., 2020. Autonomous magnetic resonance imaging. Magnetic Resonance Imaging, 73, pp.177-185.
2. Nunes, Rita G., et al. "Implementation of a Diffusion-Weighted Echo Planar Imaging sequence using the Open Source

Hardware-Independent PyPulseq Tool." ISMRM & SMRT Virtual Conference & Exhibition, International Society for Magnetic Resonance in Medicine (ISMRM) (2020).

3. Loktyushin, A., Herz, K., Dang, N., Glang, F., Deshmane, A., Weinmüller, S., Doerfler, A., Schölkopf, B., Scheffler, K. and Zaiss, M., 2021. MRzero‐Automated discovery of MRI sequences using supervised learning. Magnetic Resonance in Medicine, 86(2), pp.709-724.
4. Jimeno, Marina Manso, et al. "Cross-vendor implementation of a Stack-of-spirals PRESTO BOLD fMRI sequence using

TOPPE and Pulseq." ISMRM & SMRT Virtual Conference & Exhibition, International Society for Magnetic Resonance in Medicine (ISMRM) (2020).

5. Clarke, William T., et al. "Multi-site harmonization of 7 tesla MRI neuroimaging protocols." NeuroImage 206 (2020): 116335.
6. Geethanath, Sairam, and John Thomas Vaughan Jr. "Accessible magnetic resonance imaging: a review." Journal of

Magnetic Resonance Imaging 49.7 (2019): e65-e77.

7. Tong, Gehua, et al. "Virtual Scanner: MRI on a Browser." Journal of Open Source Software 4.43 (2019): 1637.
8. Archipovas, Saulius, et al. "A prototype of a fully integrated environment for a collaborative work in MR sequence

development for a reproducible research." ISMRM 27th Annual Meeting & Exhibition, International Society for Magnetic Resonance in Medicine (ISMRM) (2019).

9. Pizetta, Daniel Cosmo. PyMR: a framework for programming magnetic resonance systems. Diss. Universidade de São

Paulo (2018).

Installation

\>=Python 3.6, virtual environment recommended:

pip install pypulseq

1. 1. Lightning-start ⚡ - PyPulseq in your browser!
2. Create a new notebook on [Google Colab][google-colab]
3. [Install][installation] PyPulseq
4. Get going!

Or, explore an example notebook:

1. Copy URL of an example notebook from [here][notebook-examples]
2. On [Google Colab][google-colab], insert the copied link to get started

Quickstart 🏃‍♂ - example scripts

Every example script creates a pulse sequence, plots the pulse timing diagram and writes a .seq file to disk.

1. [Install][installation] PyPulseq
2. Download and run any of the [example][script-examples] scripts.

Deep dive 🤿 - custom pulse sequences

Getting started with pulse sequence design using PyPulseq is simple:

1. [Install][installation] PyPulseq
2. First, define system limits in Opts and then create a Sequence object with it: `python from pypulseq.opts import Opts from pypulseq.sequence.sequence import Sequence
   
   system = Opts(max_grad=32, grad_unit='mT/m', max_slew=130, slew_unit='mT/m/s') seq = Sequence(system=system) `
3. Then, design gradient, RF or ADC pulse sequence events: `python from pypulseq.make_sinc_pulse import make_sinc_pulse from pypulseq.make_trap_pulse import make_trapezoid from pypulseq.make_adc import make_adc
   
   Nx, Ny = 256, 256 # matrix size fov = 220e-3 # field of view delta_k = fov / Nx
   1. RF sinc pulse with a 90 degree flip angle rf90, _, _ = make_sinc_pulse(flip_angle=90, duration=2e-3, system=system, slice_thickness=5e-3, apodization=0.5, time_bw_product=4)
   2. Frequency encode, trapezoidal event gx = make_trapezoid(channel='x', flat_area=Nx * delta_k, flat_time=6.4e-3, system=system)
   3. ADC readout adc = make_adc(num_samples=Nx, duration=gx.flat_time, delay=gx.rise_time, system=system) `
4. Add these pulse sequence events to the Sequence object from step 2. One or more events can be executed

simultaneously, simply pass them all to the add_block() method. For example, the gx and adc pulse sequence events need to be executed simultaneously:

python
    seq.add_block(rf90)
    seq.add_block(gx, adc)

5. Visualize plots: `python seq.plot() `
6. Generate a .seq file to be executed on a real MR scanner: `python seq.write('demo.seq') `

Get in touch regarding running the .seq files on your Siemens/[GE]/[Bruker] scanner.

Contributing and Community guidelines

PyPulseq adheres to a code of conduct adapted from the [Contributor Covenant] code of conduct. Contributing guidelines can be found [here][contrib-guidelines].

1. 1. References
2. Ravi, Keerthi, Sairam Geethanath, and John Vaughan. "PyPulseq: A Python Package for MRI Pulse Sequence Design."

Journal of Open Source Software 4.42 (2019): 1725.

2. Ravi, Keerthi Sravan, et al. "Pulseq-Graphical Programming Interface: Open source visual environment for prototyping

pulse sequences and integrated magnetic resonance imaging algorithm development." Magnetic resonance imaging 52 (2018): 9-15.

3. Layton, Kelvin J., et al. "Pulseq: a rapid and hardware‐independent pulse sequence prototyping framework." Magnetic

resonance in medicine 77.4 (2017): 1544-1552.

[api-docs]: https://pypulseq.readthedocs.io/en/latest [Bruker]: https://github.com/pulseq/bruker_interpreter [Contributor Covenant]: http://contributor-covenant.org [contrib-guidelines]: https://github.com/imr-framework/pypulseq/blob/master/CONTRIBUTING.md [GE]: https://toppemri.github.io [google-colab]: https://colab.research.google.com/ [installation]: #installation [lightning-start]: #lightning-start----pypulseq-in-your-browser [notebook-examples]: https://github.com/imr-framework/pypulseq/tree/dev/pypulseq/seq_examples/notebooks [Pulseq specification]: https://pulseq.github.io/specification.pdf [scholar-citations]: https://scholar.google.com/scholar?oi=bibs&hl=en&cites=16703093871665262997 [script-examples]: https://github.com/imr-framework/pypulseq/tree/master/pypulseq/seq_examples/scripts