MRI Sequence definitions

The MRzeroCore Sequence is a Python list of Repetitions, each of which is starting with an instantaneous Pulse. To construct sequences, you can

• load from .seq files: Pulseq Integration
• construct with pulseq-zero: Pulseq-zero
• defined in the MR-zero directly:

import MRzeroCore as mr0
import numpy as np

seq = mr0.Sequence()

# Iterate over the repetitions
for i in range(64):
    rep = seq.new_rep(2 + 64 + 2)
    
    # Set the pulse
    rep.pulse.usage = mr0.PulseUsage.EXCIT
    rep.pulse.angle = 5 * np.pi/180
    rep.pulse.phase = i**2 * 117*np.pi/180

    # Set encoding
    rep.gradm[:, :] = ...

    # Set timing
    rep.event_time[:] = ...

    # Set ADC
    rep.adc_usage[2:-2] = 1
    rep.adc_phase[2:-2] = np.pi - rep.pulse.phase

Sequence

Defines an MRI sequence. Derived from a Python list.

Sequence(repetitions, normlized_grads=True)

• Sequence.cpu(): move sequence data to CPU
• Sequence.cuda(device=None): move sequence data to selected or default CUDA device
• Sequence.device (property): the device of the repetition data
• Sequence.clone(): make a copy of the repetition with cloned
• Sequence.new_rep(event_count): appends a Repetition.zero(event_count) to the sequence
• Sequence.get_kspace(): Returns the kspace trajectory of the measured signal as a single tensor (ADC events only, concatenated repetitions)
• Sequence.get_full_kspace(): Returns the full kspace trajectory as a list of per-repetition tensors (containing all events)
• Sequence.plot_kspace_trajectory(): Plot the result of get_full_kspace()
• Sequence.get_contrast_mask(contrast): Returns a bool mask for the selected contrast which can be applied to the simulated signal or kspace
• Sequence.get_contrasts(): Returns a list of all used contrast IDs (apply for all repetitions)
• Sequence.shift_contrasts(offset): Shift all contrast IDs by offset (apply for all repetitions)
• get_duration(): Return the total duration of the sequence in seconds

Sequences can be imported from Pulseq .seq files or Siemens .dsv files:

Sequence.import_file(file_name, exact_trajectories, print_stats, default_shim, ref_voltage, resolution)

chain

Helper function to combine multiple sequences into a multi-contrast sequence.

chain(*sequences, oneshot=False)

Returns a new sequence object. If oneshot is set to:

• True, sequences are simply concatenated.
• False, the adc_usages are shifted so that every sub-sequence has their own set of IDs.

Repetition

Part of a Sequence, containing an RF pulse and a list of event_count events.

Repetition(pulse: Pulse, event_time, gradm, adc_phase, adc_usage)

• Repetition.event_count (property): number of events in this repetition
• Repetition.cpu(): move repetition data to CPU
• Repetition.cuda(device=None): move repetition data to selected or default CUDA device
• Repetition.device (property): the device of the repetition data
• Repetition.zero(event_count): create a zero’d repetition with the given number of events
• Repetition.clone(): make a copy of the repetition with cloned
• Repetition.get_contrasts(): return a list of all used adc_usage values (except zero)
• Repetition.shift_contrasts(offset): add offset to all adc_usage values (except zero)

Pulse

Contains the definition of an instantaneous RF Pulse.

Pulse(usage: PulseUsage, angle, phase, shim_array, selective)

• Pulse.cpu(): move pulse data to CPU
• Pulse.cuda(device=None): move pulse data to selected or default CUDA device
• Pulse.device (property): the device of the pulse data
• Pulse.zero(): alternative constructor which zero-initializes everything
• Pulse.clone(): make a copy of the pulse with cloned

PulseUsage

Used for computing the k-space trajectory or to select the pulse type in legacy exporters.