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pypulseq

Pulseq in Python

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(#references). The pulse sequences can be exported as a .seq file to be run on Siemens/[GE](toppe)/[Bruker](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 2(#references).

It is strongly recommended to first read the [Pulseq specification](pulseq-spec) before proceeding. The specification document defines the concepts required for pulse sequence design using pypulseq.

1. 1. 1 minute demo
2. Clone this repository.
3. cd into this repository (or set as working directory in an IDE).
4. Run any of the example scripts on Python 3.6 or above.
5. Inspect plots!

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

Custom pulse sequences

Getting started with pulse sequence design using pypulseq is simple:

1. pip install pypulseq in your virtual environment (>=Python 3.6).
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
   
   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, 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') `

Community guidelines

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

1. 1. References
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.

2. 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 [contrib-covenant]: http://contributor-covenant.org [contrib-guidelines]: https://github.com/imr-framework/pypulseq/blob/master/CONTRIBUTING [pulseq-gpi-branch]: https://github.com/imr-framework/pypulseq/tree/pypulseq-gpi [pulseq-spec]: https://pulseq.github.io/specification.pdf [toppe]: https://toppemri.github.io