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
gr_acq = pp.make_trapezoid(channel='x', system=system, flat_area=k_width, flat_time=readout_time, rise_time=dG)
# 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)
# Phase blip in shortest possible time
dur = math.ceil(2 * math.sqrt(delta_k / system.max_slew) / 10e-6) * 10e-6
gy = pp.make_trapezoid(channel='y', system=system, area=delta_k, duration=dur)
# Refocusing pulse with spoiling gradients
rf180 = pp.make_block_pulse(flip_angle=np.pi, system=system, duration=500e-6, use='refocusing')
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)
adc = pp.make_adc(num_samples=Nxo,
duration=gx.flat_time,
delay=gx.rise_time,
system=system)
adc.delay = adc.delay - 0.5 * adc.dwell # compensate for the 0.5 samples shift
gx_pre = pp.make_trapezoid(channel='x',
area=-(gx.area - ro_area) / 2 - ro_area / 2 *
(1 - ro_asymmetry),
system=system)
# Gradient spoiling
gx_spoil = pp.make_trapezoid(channel='x',
area=0.2 * Nx * delta_k,
system=system)
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',
area=-gx.area / 2,
duration=1e-3,
system=system)
gz_reph = pp.make_trapezoid(channel='z',
area=-gz.area / 2,
duration=1e-3,
system=system)
phase_areas = (np.arange(Ny) - Ny / 2) * delta_k
spoil_factor = 1.5 # Spoiling gradient around the pi-pulse (rf180)
# 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)
# ======
# 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):
