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]. 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 [2].

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.

Pulseq compatibility

Currently, PyPulseq is compatible with Pulseq 1.2.0.

Dependencies

1. numpy>=1.16.3
2. matplotlib>=3.0.3

1 minute demo

1. Clone this repository.
2. Set as working directory in your IDE.
3. Install dependencies.
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:

   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:

   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
   
   # 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)
   
   # Frequency encode, trapezoidal event
   gx = make_trapezoid(channel='x', flat_area=Nx * delta_k, flat_time=6.4e-3, system=system)
   
   # 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:

   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')

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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References

1. 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.