t_exwd = t_ex + system.rf_ringdown_time + system.rf_dead_time
t_ref = 2e-3
t_refwd = t_ref + system.rf_ringdown_time + system.rf_dead_time
t_sp = 0.5 * (TE - readout_time - t_refwd)
t_spex = 0.5 * (TE - t_exwd - t_refwd)
fsp_r = 1
fsp_s = 0.5
rf_ex_phase = np.pi / 2
rf_ref_phase = 0
# ======
# CREATE EVENTS
# ======
flip_ex = 90 * np.pi / 180
rf_ex, gz, _ = pp.make_sinc_pulse(flip_angle=flip_ex, system=system, duration=t_ex, slice_thickness=slice_thickness,
apodization=0.5, time_bw_product=4, phase_offset=rf_ex_phase, return_gz=True)
gs_ex = pp.make_trapezoid(channel='z', system=system, amplitude=gz.amplitude, flat_time=t_exwd, rise_time=dG)
flip_ref = rf_flip[0] * np.pi / 180
rf_ref, gz, _ = pp.make_sinc_pulse(flip_angle=flip_ref, system=system, duration=t_ref, slice_thickness=slice_thickness,
apodization=0.5, time_bw_product=4, phase_offset=rf_ref_phase, use='refocusing',
return_gz=True)
gs_ref = pp.make_trapezoid(channel='z', system=system, amplitude=gs_ex.amplitude, flat_time=t_refwd, rise_time=dG)
ags_ex = gs_ex.area / 2
gs_spr = pp.make_trapezoid(channel='z', system=system, area=ags_ex * (1 + fsp_s), duration=t_sp, rise_time=dG)
gs_spex = pp.make_trapezoid(channel='z', system=system, area=ags_ex * fsp_s, duration=t_spex, rise_time=dG)
delta_k = 1 / fov
k_width = Nx * delta_k
# ======
seq = pp.Sequence() # Create a new sequence object
# Define FOV and resolution
fov = 256e-3
Nx = 64
Ny = 64
# Set system limits
system = pp.Opts(max_grad=32, grad_unit='mT/m', max_slew=130, slew_unit='T/m/s', rf_ringdown_time=30e-6,
rf_dead_time=100e-6, adc_dead_time=20e-6)
# ======
# CREATE EVENTS
# ======
# Create 90 degree slice selection pulse and gradient
rf, gz, _ = pp.make_sinc_pulse(flip_angle=np.pi / 2, system=system, duration=3e-3, slice_thickness=3e-3,
apodization=0.5, time_bw_product=4, return_gz=True)
# Define other gradients and ADC events
delta_k = 1 / fov
k_width = Nx * delta_k
readout_time = 3.2e-4
gx = pp.make_trapezoid(channel='x', system=system, flat_area=k_width, flat_time=readout_time)
adc = pp.make_adc(num_samples=Nx, system=system, duration=gx.flat_time, delay=gx.rise_time)
# Pre-phasing gradients
pre_time = 8e-4
gz_reph = pp.make_trapezoid(channel='z', system=system, area=-gz.area / 2, duration=pre_time)
# Do not need minus for in-plane prephasers because of the spin-echo (position reflection in k-space)
gx_pre = pp.make_trapezoid(channel='x', system=system, area=gx.area / 2 - delta_k / 2, duration=pre_time)
gy_pre = pp.make_trapezoid(channel='y', system=system, area=Ny / 2 * delta_k, duration=pre_time)
system = pp.Opts(max_grad=28,
grad_unit='mT/m',
max_slew=100,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
# ======
# CREATE EVENTS
# ======
# Create alpha-degree slice selection pulse and gradient
rf, gz, gz_reph = pp.make_sinc_pulse(flip_angle=alpha * np.pi / 180,
duration=1e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=2,
center_pos=1,
system=system,
return_gz=True)
# Align RO asymmetry to ADC samples
Nxo = np.round(ro_os * Nx)
ro_asymmetry = np.round(ro_asymmetry * Nxo / 2) / Nxo * 2
# Define other gradients and ADC events
delta_k = 1 / fov / (1 + ro_asymmetry)
ro_area = Nx * delta_k
gx = pp.make_trapezoid(channel='x',
flat_area=ro_area,
flat_time=ro_duration,
system=system)
sp.disp_pulse(pulse, 0, tb, duration, system)
# Convert and integrate with pypulseq
rf, gz, gzr, _ = sp.sig_2_seq(pulse=pulse,
flip_angle=alpha * math.pi / 180,
system=system,
duration=duration,
slice_thickness=slice_thickness,
return_gz=True,
time_bw_product=tb,
rf_freq=0)
else:
rf, gz, gzr = pp.make_sinc_pulse(flip_angle=alpha * math.pi / 180,
duration=duration,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=tb,
system=system,
return_gz=True)
# Define other gradients and ADC events
delta_k = 1 / fov
gx = pp.make_trapezoid(channel='x',
flat_area=Nx * delta_k,
flat_time=3.2e-3,
system=system)
adc = pp.make_adc(num_samples=Nx,
duration=gx.flat_time,
delay=gx.rise_time,
system=system)
gx_pre = pp.make_trapezoid(channel='x',
rf_dead_time=100e-6)
# ======
# CREATE EVENTS
# ======
# Create fat-sat pulse
B0 = 2.89
sat_ppm = -3.45
sat_freq = sat_ppm * 1e-6 * B0 * system.gamma
rf_fs = pp.make_gauss_pulse(flip_angle=110 * np.pi / 180, system=system, duration=8e-3, bandwidth=abs(sat_freq),
freq_offset=sat_freq)
gz_fs = pp.make_trapezoid(channel='z', system=system, delay=pp.calc_duration(rf_fs), area=1 / 1e-4)
# Create 90 degree slice selection pulse and gradient
rf, gz, gz_reph = pp.make_sinc_pulse(flip_angle=np.pi / 2, system=system, duration=t_RF_ex,
slice_thickness=slice_thickness, apodization=0.5, time_bw_product=4,
return_gz=True)
# Create 90 degree slice refocusing pulse and gradients
rf180, gz180, _ = pp.make_sinc_pulse(flip_angle=np.pi, system=system, duration=t_RF_ref,
slice_thickness=slice_thickness, apodization=0.5, time_bw_product=4,
phase_offset=np.pi / 2, use='refocusing', return_gz=True)
_, gzr1_t, gzr1_a = pp.make_extended_trapezoid_area(channel='z', Gs=0, Ge=gz180.amplitude, A=spoil_factor * gz.area,
system=system)
_, gzr2_t, gzr2_a = pp.make_extended_trapezoid_area(channel='z', Gs=gz180.amplitude, Ge=0,
A=-gz_reph.area + spoil_factor * gz.area, system=system)
if gz180.delay > (gzr1_t[3] - gz180.rise_time):
gz180.delay -= gzr1_t[3] - gz180.rise_time
else:
rf180.delay += (gzr1_t[3] - gz180.rise_time) - gz180.delay
gz180n = pp.make_extended_trapezoid(channel='z', system=system,