def test_getdirs2(self):
ndirs=6
gutest, nb0s = difunc.get_dirs(ndirs)
gpred = np.array([[-0.283341, -0.893706, -0.347862],
[-0.434044, 0.799575, -0.415074],
[0.961905, 0.095774, 0.256058],
[-0.663896, 0.491506, 0.563616],
[-0.570757, -0.554998, 0.605156],
[-0.198848, -0.056534, -0.978399]])
self.assertEqual(nb0s, 1)
np.testing.assert_allclose(gpred, gutest)
def test_getdirs3(self):
ndirs=12
gutest, nb0s = difunc.get_dirs(ndirs)
gpred = np.array([[ 0.648514, 0.375307, 0.662249],
[-0.560493, 0.824711, 0.075496],
[-0.591977, -0.304283, 0.746307],
[-0.084472, -0.976168, 0.199902],
[-0.149626, -0.006494, -0.988721],
[-0.988211, -0.056904, -0.142130],
[0.864451, -0.274379, -0.421237],
[-0.173549, -0.858586, -0.482401],
[-0.039288, 0.644885, -0.763269],
[0.729809, 0.673235, -0.118882],
[0.698325, -0.455759, 0.551929],
[-0.325340, 0.489774, 0.808873]])
self.assertEqual(nb0s, 1)
np.testing.assert_allclose(gpred, gutest)
slice_thickness = 2.5e-3
n_slices = 1
# Partial Fourier
pF = 0.75
Nyeff = int (pF*Ny)
te=84e-3
tr=1
pe_enable = 1
nbvals=0
ndirs=1
#gradient scaling
gscl=np.sqrt(np.linspace(0., 1., nbvals+1))
gdir, nb0s = difunc.get_dirs(ndirs)
#to avoid exceeding gradient limits
gdfact = 1.0
tr_per_slice = tr / n_slices
system = 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)
b0 = 2.89
sat_ppm = -3.45
sat_freq = sat_ppm * 1e-6 * b0 * system.gamma
rf_fs, _, _ = make_gauss_pulse(flip_angle=110 * math.pi / 180, system=system, duration=8e-3, bandwidth=abs(sat_freq),
freq_offset=sat_freq)
gz_fs = make_trapezoid(channel='z', system=system, delay=calc_duration(rf_fs), area=1 / 1e-4)
def test_getdirs1(self):
ndirs=3
gutest, nb0s = difunc.get_dirs(ndirs)
gpred = np.array([[1, 0, 0],[0, 1, 0],[0, 0, 1]])
self.assertEqual(nb0s, 1)
np.testing.assert_allclose(gpred, gutest)
def test_getdirs4(self):
ndirs=60
gutest, nb0s = difunc.get_dirs(ndirs)
gpred = np.array([[-0.811556, 0.245996, -0.529964],
[-0.576784, -0.313126, 0.754502],
[-0.167946, -0.899364, -0.403655],
[0.755699, -0.512113, -0.408238],
[0.116846, 0.962654, -0.244221],
[0.495465, 0.208081, 0.843337],
[0.901459, 0.385831, -0.196230],
[-0.248754, 0.420519, -0.872516],
[-0.047525, 0.444671, 0.894432],
[- 0.508593, 0.857494, -0.077699],
[0.693558, 0.614042, 0.376737],
[0.990394, -0.134781, -0.030898],
[0.019140, -0.684235, 0.729010],
[0.385221, - 0.339346, - 0.858166],
[- 0.440289, - 0.853536, 0.278609],
[0.680515, - 0.559825, 0.472752],
[- 0.146029, 0.872237, 0.466774],
[0.317352, 0.195118, - 0.928018],
[- 0.796280, - 0.129004, - 0.591013],
[- 0.711299, 0.249255, 0.657211],
[- 0.838383, - 0.538321, - 0.085587],
[0.202544, - 0.966710, 0.156357],
[-0.296747, - 0.476761, - 0.827430],
[0.545225, 0.637023, - 0.544914],
[-0.887097, 0.451265, 0.097048],
[0.034752, - 0.124211, 0.991647],
[0.469222, - 0.766720, - 0.438145],
[-0.948457, - 0.088803, 0.304209],
[-0.354311, 0.664176, - 0.658281],
[-0.462117, - 0.833550, - 0.302724],
[0.949202, - 0.022353, 0.313871],
[0.791248, 0.065354, - 0.607994],
[-0.004026, 0.992213, 0.124488],
[- 0.357034, 0.107223, - 0.927917],
[0.414504, 0.685422, 0.598651],
[-0.331743, - 0.552720, 0.764492],
[-0.749058, 0.641807, - 0.164305],
[0.238666, - 0.655691, - 0.716315],
[0.619125, 0.784982, 0.022082],
[0.123966, - 0.872070, 0.473419],
[-0.185240, 0.122014, 0.975089],
[-0.980282, - 0.189151, - 0.057166],
[0.637873, - 0.084335, 0.765510],
[-0.668960, 0.723273, 0.171375],
[-0.775822, - 0.381543, 0.502519],
[-0.636044, - 0.425049, - 0.644035],
[0.229220, 0.809364, - 0.540729],
[-0.538340, 0.531550, 0.653946],
[0.906105, - 0.354129, 0.231445],
[-0.166743, - 0.191681, - 0.967189],
[0.324636, - 0.927784, - 0.183922],
[0.551291, - 0.398459, 0.733014],
[0.537753, - 0.032690, - 0.842468],
[-0.306182, - 0.951456, - 0.031381],
[0.875976, 0.329209, 0.352545],
[0.902989, - 0.218632, - 0.369879],
[-0.456427, 0.801551, - 0.386251],
[0.089001, 0.716134, 0.692265],
[-0.714965, - 0.648438, 0.261444],
[0.076308, 0.420804, - 0.903936]])
self.assertEqual(nb0s, 3)
np.testing.assert_allclose(gpred, gutest)
def generate_SeqFile_SpiralDiffusion(gx, gy, tr, n_shots, mg, ms, fA, n_slices,
reps, st, tPlot, tReport, b_values,
n_dirs, fov, Nx):
#%% --- 1 - Create new Sequence Object + Parameters
seq = Sequence()
# =========
# Parameters
# =========
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
# =========
# Code parameters
# =========
fatsat_enable = 0 # Fat saturation
kplot = 0
# =========
# Acquisition Parameters
# =========
TR = tr # Spin-Echo parameters - TR in [s]
n_TR = math.ceil(
TR * i_raster_time) # Spin-Echo parameters - number of points TR
bvalue = b_values # b-value [s/mm2]
nbvals = np.shape(bvalue)[0] # b-value parameters
ndirs = n_dirs # b-value parameters
Ny = Nx
slice_thickness = st # Acquisition Parameters in [m]
Nshots = n_shots
# =========
# Gradient Scaling
# =========
gscl = np.zeros(nbvals + 1)
gscl[1:] = np.sqrt(bvalue / np.max(bvalue))
gdir, nb0s = difunc.get_dirs(ndirs)
# =========
# Create system
# =========
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
#%% --- 2 - Fat saturation
if fatsat_enable:
fatsat_str = "_fatsat"
b0 = 1.494
sat_ppm = -3.45
sat_freq = sat_ppm * 1e-6 * b0 * system.gamma
rf_fs, _, _ = make_gauss_pulse(flip_angle=110 * math.pi / 180,
system=system,
duration=8e-3,
bandwidth=abs(sat_freq),
freq_offset=sat_freq)
gz_fs = make_trapezoid(channel='z',
system=system,
delay=calc_duration(rf_fs),
area=1 / 1e-4)
else:
fatsat_str = ""
#%% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
flip90 = fA * pi / 180
rf, gz, _ = make_sinc_pulse(flip_angle=flip90,
system=system,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
# =========
# Refocusing pulse with spoiling gradients
# =========
rf180, gz180, _ = make_sinc_pulse(flip_angle=math.pi,
system=system,
duration=5e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
rf180.phase_offset = math.pi / 2
gz_spoil = make_trapezoid(channel='z',
system=system,
area=6 / slice_thickness,
duration=3e-3)
#%% --- 4 - Gradients
# =========
# Spiral trajectory
# =========
G = gx + 1J * gy
#%% --- 5 - ADCs / Readouts
delta_k = 1 / fov
adc_samples = math.floor(
len(G) / 4
) * 4 - 2 # Apparently, on Siemens the number of samples needs to be divisible by 4...
adc = make_adc(num_samples=adc_samples,
system=system,
duration=adc_samples / i_raster_time)
# =========
# Pre-phasing gradients
# =========
pre_time = 1e-3
n_pre_time = math.ceil(pre_time * i_raster_time)
gz_reph = make_trapezoid(channel='z',
system=system,
area=-gz.area / 2,
duration=pre_time)
#%% --- 6 - Obtain TE and diffusion-weighting gradient waveform
# For S&T monopolar waveforms
# From an initial TE, check we satisfy all constraints -> otherwise increase TE.
# Once all constraints are okay -> check b-value, if it is lower than the target one -> increase TE
# Looks time-inefficient but it is fast enough to make it user-friendly.
# TODO: Re-scale the waveform to the exact b-value because increasing the TE might produce slightly higher ones.
# Calculate some times constant throughout the process
# We need to compute the exact time sequence. For the normal SE-MONO-EPI sequence micro second differences
# are not important, however, if we wanna import external gradients the allocated time for them needs to
# be the same, and thus exact timing is mandatory. With this in mind, we establish the following rounding rules:
# Duration of RFs + spoiling, and EPI time to the center of the k-space is always math.ceil().
# The time(gy) refers to the number of blips, thus we substract 0.5 since the number of lines is always even.
# The time(gx) refers to the time needed to read each line of the k-space. Thus, if Ny is even, it would take half of the lines plus another half.
n_duration_center = 0 # The spiral starts right in 0 -- or ADC_dead_time??
rf_center_with_delay = rf.delay + calc_rf_center(rf)[0]
n_rf90r = math.ceil((calc_duration(gz) - rf_center_with_delay + pre_time) /
seq.grad_raster_time)
n_rf180r = math.ceil((calc_duration(rf180) + 2 * calc_duration(gz_spoil)) /
2 / seq.grad_raster_time)
n_rf180l = math.floor(
(calc_duration(rf180) + 2 * calc_duration(gz_spoil)) / 2 /
seq.grad_raster_time)
# =========
# Find minimum TE considering the readout times.
# =========
n_TE = math.ceil(20e-3 / seq.grad_raster_time)
n_delay_te1 = -1
while n_delay_te1 <= 0:
n_TE = n_TE + 2
n_tINV = math.floor(n_TE / 2)
n_delay_te1 = n_tINV - n_rf90r - n_rf180l
# =========
# Find minimum TE for the target b-value
# =========
bvalue_tmp = 0
while bvalue_tmp < np.max(bvalue):
n_TE = n_TE + 2
n_tINV = math.floor(n_TE / 2)
n_delay_te1 = n_tINV - n_rf90r - n_rf180l
delay_te1 = n_delay_te1 / i_raster_time
n_delay_te2 = n_tINV - n_rf180r - n_duration_center
delay_te2 = n_delay_te2 / i_raster_time
# Waveform Ramp time
n_gdiff_rt = math.ceil(system.max_grad / system.max_slew /
seq.grad_raster_time)
# Select the shortest available time
n_gdiff_delta = min(n_delay_te1, n_delay_te2)
n_gdiff_Delta = n_delay_te1 + 2 * math.ceil(
calc_duration(gz_spoil) / seq.grad_raster_time) + math.ceil(
calc_duration(gz180) / seq.grad_raster_time)
gdiff = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad,
duration=n_gdiff_delta / i_raster_time)
# delta only corresponds to the rectangle.
n_gdiff_delta = n_gdiff_delta - 2 * n_gdiff_rt
bv = difunc.calc_bval(system.max_grad, n_gdiff_delta / i_raster_time,
n_gdiff_Delta / i_raster_time,
n_gdiff_rt / i_raster_time)
bvalue_tmp = bv * 1e-6
# =========
# Show final TE and b-values:
# =========
print("TE:", round(n_TE / i_raster_time * 1e3, 2), "ms")
for bv in range(1, nbvals + 1):
print(
round(
difunc.calc_bval(system.max_grad * gscl[bv], n_gdiff_delta /
i_raster_time, n_gdiff_Delta / i_raster_time,
n_gdiff_rt / i_raster_time) * 1e-6, 2),
"s/mm2")
TE = n_TE / i_raster_time
TR = n_TR / i_raster_time
#%% --- 7 - Crusher gradients
gx_crush = make_trapezoid(channel='x',
area=2 * Nx * delta_k,
system=system)
gz_crush = make_trapezoid(channel='z',
area=4 / slice_thickness,
system=system)
# TR delay - Takes everything into account
# Distance between the center of the RF90s must be TR
# The n_pre_time here is the time used to drive the Gx, and Gy spiral gradients to zero.
n_spiral_time = adc_samples
n_tr_per_slice = math.ceil(TR / n_slices * i_raster_time)
if fatsat_enable:
n_tr_delay = n_tr_per_slice - (n_TE - n_duration_center + n_spiral_time) \
- math.ceil(rf_center_with_delay * i_raster_time) \
- n_pre_time \
- math.ceil(calc_duration(gx_crush, gz_crush) * i_raster_time) \
- math.ceil(calc_duration(rf_fs, gz_fs) * i_raster_time)
else:
n_tr_delay = n_tr_per_slice - (n_TE - n_duration_center + n_spiral_time) \
- math.ceil(rf_center_with_delay * i_raster_time) \
- n_pre_time \
- math.ceil(calc_duration(gx_crush, gz_crush) * i_raster_time)
tr_delay = n_tr_delay / i_raster_time
#%% --- 8 - Checks
# =========
# Check TR delay time
# =========
assert n_tr_delay > 0, "Such parameter configuration needs longer TR."
# =========
# Delay time,
# =========
# Time between the gradient and the RF180. This time might be zero some times, although it is not normal.
if n_delay_te1 > n_delay_te2:
n_gap_te1 = n_delay_te1 - n_delay_te2
gap_te1 = n_gap_te1 / i_raster_time
gap_te2 = 0
else:
n_gap_te2 = n_delay_te2 - n_delay_te1
gap_te2 = n_gap_te2 / i_raster_time
gap_te1 = 0
#%% --- 9 - b-zero acquisition
for r in range(reps):
for d in range(nb0s):
for nshot in range(Nshots):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Delay for RF180
seq.add_block(make_delay(delay_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Delay for spiral
seq.add_block(make_delay(delay_te2))
# Read k-space
# Imaging Gradient waveforms
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(
G[:, nshot].real),
system=system)
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(
G[:, nshot].imag),
system=system)
seq.add_block(gx, gy, adc)
# Make the spiral finish in zero - I use pre_time because I know for sure it's long enough.
# Furthermore, this is after readout and TR is supposed to be long.
amp_x = [G[:, nshot].real[-1], 0]
amp_y = [G[:, nshot].imag[-1], 0]
gx_to_zero = make_extended_trapezoid(channel='x',
amplitudes=amp_x,
times=[0, pre_time],
system=system)
gy_to_zero = make_extended_trapezoid(channel='y',
amplitudes=amp_y,
times=[0, pre_time],
system=system)
seq.add_block(gx_to_zero, gy_to_zero)
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
#%% --- 9 - DWI acquisition
for r in range(reps):
for bv in range(1, nbvals + 1):
for d in range(ndirs):
for nshot in range(Nshots):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Diffusion-weighting gradient
gdiffx = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad *
gscl[bv] * gdir[d, 0],
duration=calc_duration(gdiff))
gdiffy = make_trapezoid(channel='y',
system=system,
amplitude=system.max_grad *
gscl[bv] * gdir[d, 1],
duration=calc_duration(gdiff))
gdiffz = make_trapezoid(channel='z',
system=system,
amplitude=system.max_grad *
gscl[bv] * gdir[d, 2],
duration=calc_duration(gdiff))
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for RF180
seq.add_block(make_delay(gap_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Diffusion-weighting gradient
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for spiral
seq.add_block(make_delay(gap_te2))
# Read k-space
# Imaging Gradient waveforms
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(
G[:, nshot].real),
system=system)
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(
G[:, nshot].imag),
system=system)
seq.add_block(gx, gy, adc)
# Make the spiral finish in zero - I use pre_time because I know for sure it's long enough.
# Furthermore, this is after readout and TR is supposed to be long.
amp_x = [G[:, nshot].real[-1], 0]
amp_y = [G[:, nshot].imag[-1], 0]
gx_to_zero = make_extended_trapezoid(
channel='x',
amplitudes=amp_x,
times=[0, pre_time],
system=system)
gy_to_zero = make_extended_trapezoid(
channel='y',
amplitudes=amp_y,
times=[0, pre_time],
system=system)
seq.add_block(gx_to_zero, gy_to_zero)
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq, TE, TR, fatsat_str
def generate_SeqFile_EPIDiffusion(FOV, nx, ny, ns, mg, ms, reps, st, tr, fA,
b_values, n_dirs, partialFourier, tPlot,
tReport):
#%% --- 1 - Create new Sequence Object + Parameters
seq = Sequence()
# =========
# Parameters
# =========
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
# =========
# Code parameters
# =========
fatsat_enable = 0 # Fat saturation
kplot = 0
# =========
# Acquisition Parameters
# =========
fov = FOV
Nx = nx
Ny = ny
n_slices = ns
TR = tr # Spin-Echo parameters - TR in [s]
n_TR = math.ceil(
TR * i_raster_time) # Spin-Echo parameters - number of points TR
bvalue = b_values # b-value [s/mm2]
nbvals = np.shape(bvalue)[0] # b-value parameters
ndirs = n_dirs # b-value parameters
slice_thickness = st # Acquisition Parameters in [m]
# =========
# Partial Fourier
# =========
pF = partialFourier
Nyeff = int(pF * Ny) # Number of Ny samples acquired
if pF is not 1:
pF_str = "_" + str(pF) + "pF"
else:
pF_str = ""
# =========
# Gradient Scaling
# =========
gscl = np.zeros(nbvals + 1)
gscl[1:] = np.sqrt(bvalue / np.max(bvalue))
gdir, nb0s = difunc.get_dirs(ndirs)
# =========
# Create system
# =========
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
#%% --- 2 - Fat saturation
if fatsat_enable:
fatsat_str = "_fatsat"
b0 = 1.494
sat_ppm = -3.45
sat_freq = sat_ppm * 1e-6 * b0 * system.gamma
rf_fs, _, _ = make_gauss_pulse(flip_angle=110 * math.pi / 180,
system=system,
duration=8e-3,
bandwidth=abs(sat_freq),
freq_offset=sat_freq)
gz_fs = make_trapezoid(channel='z',
system=system,
delay=calc_duration(rf_fs),
area=1 / 1e-4)
else:
fatsat_str = ""
#%% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
flip90 = fA * pi / 180
rf, gz, _ = make_sinc_pulse(flip_angle=flip90,
system=system,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
# =========
# Refocusing pulse with spoiling gradients
# =========
rf180, gz180, _ = make_sinc_pulse(flip_angle=math.pi,
system=system,
duration=5e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
rf180.phase_offset = math.pi / 2
gz_spoil = make_trapezoid(channel='z',
system=system,
area=6 / slice_thickness,
duration=3e-3)
#%% --- 4 - Define other gradients and ADC events
delta_k = 1 / fov
k_width = Nx * delta_k
dwell_time = seq.grad_raster_time # Full receiver bandwith
readout_time = Nx * dwell_time # T_acq (acquisition time)
flat_time = math.ceil(
readout_time / seq.grad_raster_time) * seq.grad_raster_time
gx = make_trapezoid(channel='x',
system=system,
amplitude=k_width / readout_time,
flat_time=flat_time)
adc = make_adc(num_samples=Nx,
duration=readout_time,
delay=gx.rise_time + flat_time / 2 -
(readout_time - dwell_time) / 2)
# =========
# Pre-phasing gradients
# =========
pre_time = 1e-3
gx_pre = make_trapezoid(channel='x',
system=system,
area=-gx.area / 2,
duration=pre_time)
gz_reph = make_trapezoid(channel='z',
system=system,
area=-gz.area / 2,
duration=pre_time)
gy_pre = make_trapezoid(
channel='y',
system=system,
area=-(Ny / 2 - 0.5 - (Ny - Nyeff)) * delta_k,
duration=pre_time
) # Es -0.5 y no +0.5 porque hay que pensar en areas, no en rayas!
# =========
# Phase blip in shortest possible time
# =========
gy = make_trapezoid(channel='y', system=system, area=delta_k)
dur = math.ceil(
calc_duration(gy) / seq.grad_raster_time) * seq.grad_raster_time
#%% --- 5 - Obtain TE and diffusion-weighting gradient waveform
# =========
# Calculate some times constant throughout the process
# =========
duration_center = math.ceil(
(calc_duration(gx) * (Ny / 2 + 0.5 -
(Ny - Nyeff)) + calc_duration(gy) *
(Ny / 2 - 0.5 -
(Ny - Nyeff))) / seq.grad_raster_time) * seq.grad_raster_time
rf_center_with_delay = rf.delay + calc_rf_center(rf)[0]
rf180_center_with_delay = rf180.delay + calc_rf_center(rf180)[0]
# =========
# Find minimum TE considering the readout times.
# =========
TE = 40e-3 # [s]
delay_te2 = -1
while delay_te2 <= 0:
TE = TE + 0.02e-3 # [ms]
delay_te2 = math.ceil((TE / 2 - calc_duration(rf180) + rf180_center_with_delay - calc_duration(gz_spoil) - \
calc_duration(gx_pre,
gy_pre) - duration_center) / seq.grad_raster_time) * seq.grad_raster_time
# =========
# Find minimum TE for the target b-value
# =========
bvalue_tmp = 0
while bvalue_tmp < np.max(bvalue):
TE = TE + 2 * seq.grad_raster_time # [ms]
delay_te1 = math.ceil((TE / 2 - calc_duration(gz) + rf_center_with_delay - pre_time - calc_duration(gz_spoil) - \
rf180_center_with_delay) / seq.grad_raster_time) * seq.grad_raster_time
delay_te2 = math.ceil((TE / 2 - calc_duration(rf180) + rf180_center_with_delay - calc_duration(gz_spoil) - \
calc_duration(gx_pre,
gy_pre) - duration_center) / seq.grad_raster_time) * seq.grad_raster_time
# Waveform Ramp time
gdiff_rt = math.ceil(system.max_grad / system.max_slew /
seq.grad_raster_time) * seq.grad_raster_time
# Select the shortest available time
gdiff_delta = min(delay_te1, delay_te2)
gdiff_Delta = math.ceil(
(delay_te1 + 2 * calc_duration(gz_spoil) + calc_duration(gz180)) /
seq.grad_raster_time) * seq.grad_raster_time
gdiff = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad,
duration=gdiff_delta)
# delta only corresponds to the rectangle.
gdiff_delta = math.ceil((gdiff_delta - 2 * gdiff_rt) /
seq.grad_raster_time) * seq.grad_raster_time
bv = difunc.calc_bval(system.max_grad, gdiff_delta, gdiff_Delta,
gdiff_rt)
bvalue_tmp = bv * 1e-6
# =========
# Show final TE and b-values:
# =========
print("TE:", round(TE * 1e3, 2), "ms")
for bv in range(1, nbvals + 1):
print(
round(
difunc.calc_bval(system.max_grad * gscl[bv], gdiff_delta,
gdiff_Delta, gdiff_rt) * 1e-6, 2), "s/mm2")
# =========
# Crusher gradients
# =========
gx_crush = make_trapezoid(channel='x',
area=2 * Nx * delta_k,
system=system)
gz_crush = make_trapezoid(channel='z',
area=4 / slice_thickness,
system=system)
#%% --- 6 - Delays
# =========
# TR delay - Takes everything into account
# EPI reading time:
# Distance between the center of the RF90s must be TR
# =========
EPI_time = calc_duration(gx) * Nyeff + calc_duration(gy) * (Nyeff - 1)
if fatsat_enable:
tr_delay = math.floor(
(TR - (TE - duration_center + EPI_time) - rf_center_with_delay - calc_duration(gx_crush, gz_crush) \
- calc_duration(rf_fs, gz_fs)) \
/ seq.grad_raster_time) * seq.grad_raster_time
else:
tr_delay = math.floor(
(TR - (TE - duration_center + EPI_time) - rf_center_with_delay - calc_duration(gx_crush, gz_crush)) \
/ seq.grad_raster_time) * seq.grad_raster_time
# =========
# Check TR delay time
# =========
assert tr_delay > 0, "Such parameter configuration needs longer TR."
# =========
# Delay time
# =========
# =========
# Time between the gradient and the RF180. This time might be zero some times, although it is not normal.
# =========
gap_te1 = math.ceil((delay_te1 - calc_duration(gdiff)) /
seq.grad_raster_time) * seq.grad_raster_time
# =========
# Time between the gradient and the locate k-space gradients.
# =========
gap_te2 = math.ceil((delay_te2 - calc_duration(gdiff)) /
seq.grad_raster_time) * seq.grad_raster_time
#%% --- 9 - b-zero acquisition
for d in range(nb0s):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Delay for RF180
seq.add_block(make_delay(delay_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Delay for EPI
seq.add_block(make_delay(delay_te2))
# Locate k-space
seq.add_block(gx_pre, gy_pre)
for i in range(Nyeff):
seq.add_block(gx, adc) # Read one line of k-space
if i is not Nyeff - 1:
seq.add_block(gy) # Phase blip
gx.amplitude = -gx.amplitude # Reverse polarity of read gradient
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
#%% --- 10 - DWI acquisition
for bv in range(1, nbvals + 1):
for d in range(ndirs):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Diffusion-weighting gradient
gdiffx = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad * gscl[bv] *
gdir[d, 0],
duration=calc_duration(gdiff))
gdiffy = make_trapezoid(channel='y',
system=system,
amplitude=system.max_grad * gscl[bv] *
gdir[d, 1],
duration=calc_duration(gdiff))
gdiffz = make_trapezoid(channel='z',
system=system,
amplitude=system.max_grad * gscl[bv] *
gdir[d, 2],
duration=calc_duration(gdiff))
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for RF180
seq.add_block(make_delay(gap_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Diffusion-weighting gradient
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for EPI
seq.add_block(make_delay(gap_te2))
# Locate k-space
seq.add_block(gx_pre, gy_pre)
for i in range(Nyeff):
seq.add_block(gx, adc) # Read one line of k-space
if i is not Nyeff - 1:
seq.add_block(gy) # Phase blip
gx.amplitude = -gx.amplitude # Reverse polarity of read gradient
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq, TE, TR, fatsat_str