pypulseq/5e8a729e9fb2master
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README.md
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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/ Bruker hardware by leveraging their respective Pulseq interpreters. This tool is targeted at MR pulse sequence designers, MRI researchers 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 before proceeding. The specification document defines the concepts required for pulse sequence design using pypulseq. Checkout the [pypulseq-gpi](https://github.com/imr-framework/pypulseq/tree/pypulseq-gpi) branch to design pulse sequences on a GUI.
- 1 minute demo
- Clone this repository.
- Run any of the example scripts in your favourite IDE on Python 3.6 or above.
- 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:
- pip install pypulseq on Python 3.6 or above.
- 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) ` - 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- 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)
- 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) `
- 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) `
- Visualize plots: `python seq.plot() `
- Generate a .seq file to be executed on a real MR scanner: `python seq.write('demo.seq') ` ---
- References
- 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.
- Layton, Kelvin J., et al. "Pulseq: a rapid and hardware‐independent pulse sequence prototyping framework." Magnetic
resonance in medicine 77.4 (2017): 1544-1552.