<p align="center"> <img src="logo.png"/> </p>

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!

1. 1. [Relevant literature][scholar-citations] (reverse chronological)
2. Ravi, Keerthi Sravan, and Sairam Geethanath. "Autonomous Magnetic Resonance Imaging." medRxiv (2020).
3. 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, Alexander, et al. "MRzero--Fully automated invention of MRI sequences using supervised learning." arXiv

preprint arXiv:2002.04265 (2020).

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