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Pulseq Integration

MRzero Core provides seamless integration with the Pulseq standard, making it easy to simulate any Pulseq sequence file in just one line of code.

Get Started Immediately

Simplest possible - one line simulation:

import MRzeroCore as mr0

# That's it - simulate any .seq file with automatic phantom download!
signal, ktraj_adc = mr0.util.simulate(seq)  # Downloads standard phantom if not found

seq.plot(plot_now=False)
mr0.util.insert_signal_plot(seq=seq, signal =signal.numpy())  # show sequence plots with simulated signals inserted in ADC plot.
plt.show()

Full control with prepass-mainpass:

import MRzeroCore as mr0
obj_p = mr0.VoxelGridPhantom.brainweb('subject05.npz') #load a phantom object from file
obj_p = obj_p.interpolate(64, 64, 32).slices([15])
obj_p = obj_p.build()

seq0 = mr0.Sequence.import_file('your_sequence.se')  # Read in the Pulseq seq file

graph = mr0.compute_graph(seq0, obj_p, 2000, 1e-4)  # pre-pass
signal = mr0.execute_graph(graph, seq0, obj_p, print_progress=False) # main-pass

seq.plot(plot_now=False)
mr0.util.insert_signal_plot(seq=seq, signal =signal.numpy())
plt.show()

Try now: mr0_upload_seq.ipynb

Simplified Workflows

Utily functions

MRzero now includes streamlined utility functions for common simulation tasks:

  1. One line - automatic everything 
    # Quickest 2D brain phantom simulation 
signal, ktraj_adc = mr0.util.simulate(seq)  # Downloads standard phantom automatically
  2. Two lines - custom phantom parameters 
    # Quick 2D brain phantom sim with modifications
obj = mr0.util.load_phantom([128,128], B0_polynomial=(0,0,-150,1,1,0))  # Custom B0 map
signal, ktraj_adc = mr0.util.simulate(seq, obj)
  3. Three lines - full control 
    # Custom phantom from URL/file with arbitrary modifications and high accuracy
obj = mr0.util.load_phantom([128,128], B0_polynomial=(0,0,-150,1,1,0), url='numerical_brain_cropped.mat')  
obj.B1 = obj.B1**3     # Very inhomogeneous B1+ field
signal, ktraj_adc = mr0.util.simulate(seq, obj, accuracy=1e-5)

Direct PyPulseq Integration

import pypulseq as pp

# Create sequence with PyPulseq
seq = pp.Sequence()
# ... build sequence ...

# Simulate directly - no need to write/read .seq file!
signal, ktraj_adc = mr0.util.simulate(seq)  # seq can be PyPulseq object

For MATLAB Pulseq Users

See MATLAB integration

Examples - Ready-to-run in Google Colab

NotebookComplexity
Simulate own uploaded seq filesBeginnermr0_upload_seq.ipynb
FLASH 2D sequenceBeginnermr0_FLASH_2D_seq.ipynb
GRE EPI 2D sequenceIntermediatemr0_EPI_2D_seq.ipynb
DWI SE EPI 2D sequenceAdvancedmr0_DWI_SE_EPI.ipynb
TSE 2D sequenceAdvancedmr0_TSE_2D_multi_shot_seq.ipynb

Browse All 20+ Examples →

Further Features

Visualization


# Plot PyPulseq sequence plot with MR-zero signals
seq.plot(plot_now=False)
mr0.util.insert_signal_plot(seq=seq, signal =signal.numpy())
plt.show()

# Plot the detected k-space used by MR-zero
seq.plot_kspace_trajectory()

#Plot the phase distribution graph
graph = mr0.compute_graph(seq0, obj_p, 2000, 1e-4)  # pre-pass
graph.plot()

Simulation

# Simple simulation
signal = mr0.util.simulate(seq)

# With custom phantom
phantom = mr0.util.load_phantom(size=(64, 64))
signal, kspace = mr0.util.simulate(seq, phantom)

Getting Help

Quick help: