PyPulseq: A Python Package for MRI Pulse Sequence Design

PyPulseq (v1.4.2) is compatible with all Pulseq interpreter sequences with version >= 1.4.0

Table of contents 🧾

1. 📃 General Information
2. 🔨 Installation
3. ⚡ Lightning-start - PyPulseq in your browser!
4. 🏃‍♂ Quickstart - example scripts
5. 🤿 Deep dive - custom pulse sequences
6. 👥 Contributing and Community guidelines
7. 📖 References

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1. General Information

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]. The pulse sequences can be exported as a .seq file to be run on Siemens, GE, Bruker and now also Philips 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].

👉 Currently, PyPulseq is compatible with Pulseq >= 1.4.0. 👈

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.

If you use PyPulseq in your work, please cite the publications listed under References.

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2. 🔨 Installation

PyPulseq is available on the python Package Index PyPi and can be installed using the command

pip install pypulseq

To use the sigpy functionality of make_sigpy_pulse.py run pip install pypulseq[sigpy] to install the required dependencies and enable this functionality.

The latest features and minor bug fixes might not be included in the latest release version. If you want to use the bleeding edge version of PyPulseq, you can install it directly from the development branch of this repository using the command

pip install git+https://github.com/imr-framework/pypulseq@dev

👉 PyPulseq is not yet available on conda, but this is planned for the future 👈

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3. ⚡ Lightning-start - PyPulseq in your browser

1. Create a new notebook on Google Colab
2. Install PyPulseq using pip install pypulseq
3. Get going!

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4. 🏃‍♂ Example scripts

The PyPulseq repository contains several example sequences in the seq_examples folder. Every example script or example notebook creates a pulse sequence, plots the pulse timing diagram and finally saves the sequence as a .seq file to disk.

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5. 🤿 Deep dive - custom pulse sequences

Getting started with pulse sequence design using PyPulseq is simple:

1. First, define system limits in Opts and then create a Sequence object with it:

   import pypulseq as pp
   
   system = pp.Opts(max_grad=32, grad_unit='mT/m', max_slew=130, slew_unit='mT/m/ms')
   seq = pp.Sequence(system=system)

2. Then, design gradient, RF or ADC pulse sequence events:

   Nx, Ny = 256, 256 # matrix size
   fov = 220e-3 # field of view
   delta_k = fov / Nx
   
   # RF sinc pulse with a 90 degree flip angle
   rf90 = pp.make_sinc_pulse(flip_angle=90, duration=2e-3, system=system, slice_thickness=5e-3, apodization=0.5,
      time_bw_product=4)
   
   # Frequency encode, trapezoidal event
   gx = pp.make_trapezoid(channel='x', flat_area=Nx * delta_k, flat_time=6.4e-3, system=system)
   
   # ADC readout
   adc = pp.make_adc(num_samples=Nx, duration=gx.flat_time, delay=gx.rise_time, system=system)

3. Add these pulse sequence events to the Sequence object. 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:

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

4. Visualize plots:

   seq.plot()

5. Generate a .seq file to be executed on a real MR scanner:

   seq.write('demo.seq')

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6. 👥 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.

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7. 📖 References

1. 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.