/pypulseq

Pulseq in Python

Primary LanguagePythonGNU Affero General Public License v3.0AGPL-3.0

PyPulseq

PyPulseq: A Python Package for MRI Pulse Sequence Design

Compatible with Pulseq 1.4.0

🚨🚨🚨 NOTE: This is the dev branch which hosts the bleeding edge version. For the most recent, stable release, switch to the master branch by clicking here. 🚨🚨🚨

Table of contents 🧾

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

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 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, cite the following publications:

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 section to learn how!

1. 👥 Contributors (alphabetical)

  • @bilal-tasdelen
  • @calderds
  • @mavel101
  • @nnmurthy
  • @sairamgeethanath
  • @schuenke
  • @skarrea
  • @tonggehua

Please email me/submit PR/open an issue if any contributors are missing.

2. 📚 Citations (reverse chronological)

  1. Hennig, J., Barghoorn, A., Zhang, S. and Zaitsev, M., 2022. Single shot spiral TSE with annulated segmentation. Magnetic Resonance in Medicine.
  2. Niso, G., Botvinik-Nezer, R., Appelhoff, S., De La Vega, A., Esteban, O., Etzel, J.A., Finc, K., Ganz, M., Gau, R., Halchenko, Y.O. and Herholz, P., 2022. Open and reproducible neuroimaging: from study inception to publication.
  3. Tong, G., Gaspar, A.S., Qian, E., Ravi, K.S., Vaughan, J.T., Nunes, R.G. and Geethanath, S., 2022. Open-source magnetic resonance imaging acquisition: Data and documentation for two validated pulse sequences. Data in Brief, 42, p.108105.
  4. Tong, G., Gaspar, A.S., Qian, E., Ravi, K.S., Vaughan Jr, J.T., Nunes, R.G. and Geethanath, S., 2022. A framework for validating open-source pulse sequences. Magnetic resonance imaging, 87, pp.7-18.
  5. Karakuzu, A., Appelhoff, S., Auer, T., Boudreau, M., Feingold, F., Khan, A.R., Lazari, A., Markiewicz, C., Mulder, M.J., Phillips, C. and Salo, T., 2021. qMRI-BIDS: an extension to the brain imaging data structure for quantitative magnetic resonance imaging data. medRxiv.
  6. Karakuzu, A., Biswas, L., Cohen‐Adad, J. and Stikov, N., 2021. Vendor‐neutral sequences and fully transparent workflows improve inter‐vendor reproducibility of quantitative MRI. Magnetic Resonance in Medicine.
  7. Geethanath, S., Single echo reconstruction for rapid and silent MRI. (ISMRM) (2021).
  8. Qian, E. and Geethanath, S., Open source Magnetic rEsonance fingerprinting pAckage (OMEGA). (ISMRM) (2021).
  9. Ravi, K.S., O'Reilly, T., Vaughan Jr, J.T., Webb, A. and Geethanath, S., Seq2prospa: translating PyPulseq for low-field imaging. (ISMRM) (2021).
  10. Ravi, K.S., Vaughan Jr, J.T. and Geethanath, S., PyPulseq in a web browser: a zero footprint tool for collaborative and vendor-neutral pulse sequence development. (ISMRM) (2021).
  11. Ravi, K.S. and Geethanath, S., 2020. Autonomous magnetic resonance imaging. Magnetic Resonance Imaging, 73, pp.177-185.
  12. 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).
  13. Loktyushin, Alexander, et al. "MRzero--Fully automated invention of MRI sequences using supervised learning." arXiv preprint arXiv:2002.04265 (2020).
  14. 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).
  15. Clarke, William T., et al. "Multi-site harmonization of 7 tesla MRI neuroimaging protocols." NeuroImage 206 (2020): 116335.
  16. Geethanath, Sairam, and John Thomas Vaughan Jr. "Accessible magnetic resonance imaging: a review." Journal of Magnetic Resonance Imaging 49.7 (2019): e65-e77.
  17. Tong, Gehua, et al. "Virtual Scanner: MRI on a Browser." Journal of Open Source Software 4.43 (2019): 1637.
  18. 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).
  19. Pizetta, Daniel Cosmo. PyMR: a framework for programming magnetic resonance systems. Diss. Universidade de São Paulo (2018).

3. 🔨 Installation

>=Python 3.6, virtual environment recommended:

pip install pypulseq

4. ⚡ Lightning-start - PyPulseq in your browser!

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

Or, explore an example notebook:

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

5. 🏃‍♂ Quickstart - example scripts

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

  1. Install PyPulseq
  2. Download and run any of the example scripts.

6. 🤿 Deep dive - custom pulse sequences

Getting started with pulse sequence design using PyPulseq is simple:

  1. Install PyPulseq
  2. 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)
  3. 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)
  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: 
    seq.add_block(rf90)
seq.add_block(gx, adc)
  5. Visualize plots: 
    seq.plot()
  6. Generate a .seq file to be executed on a real MR scanner: 
    seq.write('demo.seq')

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

7. 👥 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.

8. 📖 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.