def test_multiecho(self):
me = {'MultiEcho': {'TR': 10, 'TE1': 0.01, 'ESP': 0.01, 'ETL': 5}}
me_file = 'sim_me.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 1.0),
out_file='PD.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=2,
grad_vals=(0.04, 0.1),
out_file='T2.nii.gz',
verbose=vb).run()
MultiechoSim(sequence=me,
in_file=me_file,
PD='PD.nii.gz',
T2='T2.nii.gz',
noise=noise,
verbose=vb).run()
Multiecho(sequence=me, in_file=me_file, verbose=vb).run()
diff_T2 = Diff(in_file='ME_T2.nii.gz',
baseline='T2.nii.gz',
noise=noise,
verbose=vb).run()
diff_PD = Diff(in_file='ME_PD.nii.gz',
baseline='PD.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_T2.outputs.out_diff, 3)
self.assertLessEqual(diff_PD.outputs.out_diff, 2)
def test_asl(self):
seq = {
'CASL': {
'TR': 4.0,
'label_time': 3.0,
'post_label_delay': [0.3]
}
}
asl_file = 'sim_asl.nii.gz'
NewImage(img_size=[32, 32, 32, 2],
grad_dim=3,
grad_vals=(1, 1.06),
grad_steps=1,
out_file=asl_file,
verbose=vb).run()
NewImage(img_size=[32, 32, 32],
fill=147.355,
out_file='ref_cbf.nii.gz',
verbose=vb).run()
ASL(sequence=seq, in_file=asl_file, verbose=vb).run()
diff_CBF = Diff(in_file='CASL_CBF.nii.gz',
baseline='ref_cbf.nii.gz',
verbose=vb).run()
self.assertLessEqual(diff_CBF.outputs.out_diff, 0.1)
def test_planet(self):
ellipse_seq = {"SSFP": {
"FA": [15, 15, 15, 15, 15, 15],
"PhaseInc": [180, 240, 300, 0, 60, 120],
"TR": 0.01
}
}
planet_seq = {
"SSFP": {
"FA": [15],
"PhaseInc": [0],
"TR": 0.01
}
}
ellipse_file = 'planet_ellipse.nii.gz'
planet_G = 'planet_G.nii.gz'
planet_a = 'planet_a.nii.gz'
planet_b = 'planet_b.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(out_file='PD.nii.gz', verbose=vb, img_size=img_sz,
fill=1).run()
NewImage(out_file='T1.nii.gz', verbose=vb, img_size=img_sz,
grad_dim=0, grad_vals=(0.8, 1.3)).run()
NewImage(out_file='T2.nii.gz', verbose=vb, img_size=img_sz,
grad_dim=1, grad_vals=(0.05, 0.1)).run()
NewImage(out_file='zero.nii.gz', verbose=vb, img_size=img_sz,
fill=0).run()
PLANETSim(sequence=planet_seq, G_file=planet_G, a_file=planet_a, b_file=planet_b,
noise=0, verbose=vb,
PD='PD.nii.gz',
T1='T1.nii.gz',
T2='T2.nii.gz').run()
EllipseSim(sequence=ellipse_seq, in_file=ellipse_file,
noise=noise, verbose=vb,
G=planet_G, a=planet_a, b=planet_b, theta_0='zero.nii.gz', phi_rf='zero.nii.gz').run()
Ellipse(sequence=ellipse_seq, in_file=ellipse_file, verbose=vb).run()
PLANET(sequence=planet_seq, G_map=planet_G,
a_map=planet_a, b_map=planet_b, verbose=vb).run()
diff_G = Diff(in_file='ES_G.nii.gz', baseline=planet_G,
noise=noise, verbose=vb).run()
diff_a = Diff(in_file='ES_a.nii.gz', baseline=planet_a,
noise=noise, verbose=vb).run()
diff_b = Diff(in_file='ES_b.nii.gz', baseline=planet_b,
noise=noise, verbose=vb).run()
diff_PD = Diff(in_file='PLANET_PD.nii.gz', baseline='PD.nii.gz',
noise=noise, verbose=vb).run()
diff_T1 = Diff(in_file='PLANET_T1.nii.gz', baseline='T1.nii.gz',
noise=noise, verbose=vb).run()
diff_T2 = Diff(in_file='PLANET_T2.nii.gz', baseline='T2.nii.gz',
noise=noise, verbose=vb).run()
self.assertLessEqual(diff_G.outputs.out_diff, 3.5)
self.assertLessEqual(diff_a.outputs.out_diff, 3)
self.assertLessEqual(diff_b.outputs.out_diff, 7)
self.assertLessEqual(diff_PD.outputs.out_diff, 4)
self.assertLessEqual(diff_T1.outputs.out_diff, 1)
self.assertLessEqual(diff_T2.outputs.out_diff, 1)
def test_oef(self):
# Use MultiEchoFlex as a proxy for ASE
seq = {
'MultiEcho': {
'TR':
2.5,
'TE': [
-0.07, -0.06, -0.05, -0.04, -0.03, -0.02, -0.01, 0.0, 0.01,
0.02, 0.03, 0.04, 0.05, 0.06, 0.07
]
}
}
ase_file = 'sim_ase.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(img_size=img_sz,
grad_dim=0,
fill=100.,
out_file='S0.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(-0.01, 0.01),
out_file='dT.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=1,
grad_vals=(1.0, 3.0),
out_file='R2p.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=2,
grad_vals=(0.005, 0.025),
out_file='DBV.nii.gz',
verbose=vb).run()
ASESim(sequence=seq,
in_file=ase_file,
noise=noise,
verbose=vb,
S0='S0.nii.gz',
dT='dT.nii.gz',
R2p='R2p.nii.gz',
DBV='DBV.nii.gz').run()
ASE(sequence=seq, in_file=ase_file, verbose=vb).run()
diff_R2p = Diff(in_file='ASE_R2p.nii.gz',
baseline='R2p.nii.gz',
noise=noise,
verbose=vb).run()
diff_DBV = Diff(in_file='ASE_DBV.nii.gz',
baseline='DBV.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_R2p.outputs.out_diff, 12)
self.assertLessEqual(diff_DBV.outputs.out_diff, 50)
def test_fm(self):
seq = {
'SSFP': {
'TR': 5e-3,
'FA': [15, 15, 60, 60],
'PhaseInc': [180, 0, 180, 0]
}
}
ssfp_file = 'sim_ssfp.nii.gz'
img_sz = [16, 16, 16]
noise = 0.001
NewImage(img_size=img_sz, fill=1.0, out_file='PD.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 1.2),
out_file='T1.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=1,
grad_vals=(0.04, 0.1),
out_file='T2.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=2,
grad_vals=(-100, 100),
out_file='f0.nii.gz',
verbose=vb).run()
FMSim(sequence=seq,
in_file=ssfp_file,
asym=False,
t1_file='T1.nii.gz',
noise=noise,
verbose=vb,
PD='PD.nii.gz',
T2='T2.nii.gz',
f0='f0.nii.gz').run()
FM(sequence=seq,
in_file=ssfp_file,
asym=False,
t1_file='T1.nii.gz',
verbose=vb,
residuals=True).run()
diff_T2 = Diff(in_file='FM_T2.nii.gz',
baseline='T2.nii.gz',
noise=noise,
verbose=vb).run()
diff_PD = Diff(in_file='FM_PD.nii.gz',
baseline='PD.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_T2.outputs.out_diff, 20)
self.assertLessEqual(diff_PD.outputs.out_diff, 10)
def test_despot2(self, gs=False, tol=20):
seq = {
'SSFP': {
'TR': 10e-3,
'FA': [15, 30, 45, 60],
'PhaseInc': [180, 180, 180, 180]
}
}
ssfp_file = 'sim_ssfp.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 1.0),
out_file='PD.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=1,
grad_vals=(0.8, 1.2),
out_file='T1.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=2,
grad_vals=(0.04, 0.1),
out_file='T2.nii.gz',
verbose=vb).run()
DESPOT2Sim(sequence=seq,
in_file=ssfp_file,
t1_file='T1.nii.gz',
ellipse=gs,
noise=noise,
verbose=vb,
PD='PD.nii.gz',
T2='T2.nii.gz').run()
DESPOT2(sequence=seq,
in_file=ssfp_file,
t1_file='T1.nii.gz',
ellipse=gs,
verbose=vb,
residuals=True).run()
diff_T2 = Diff(in_file='D2_T2.nii.gz',
baseline='T2.nii.gz',
noise=noise,
verbose=vb).run()
diff_PD = Diff(in_file='D2_PD.nii.gz',
baseline='PD.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_T2.outputs.out_diff, tol)
self.assertLessEqual(diff_PD.outputs.out_diff, tol)
def test_kfilter(self):
NewImage(out_file='steps.nii.gz',
img_size=[64, 64, 64],
grad_dim=0,
grad_vals=(0, 8),
grad_steps=4,
verbose=vb).run()
Filter(in_file='steps.nii.gz', filter_spec='Gauss,2.0',
verbose=vb).run()
def test_ZSpec(self):
NewImage(out_file='zspec_linear.nii.gz',
verbose=vb,
img_size=[8, 8, 8, 4],
grad_dim=3,
grad_vals=(-3, 3)).run()
NewImage(out_file='zspec_zero.nii.gz',
verbose=vb,
img_size=[8, 8, 8],
fill=0).run()
ZSpec(in_file='zspec_linear.nii.gz',
in_freqs=[-3, -1, 1, 3],
out_freqs=[0],
verbose=vb).run()
diff_zero = Diff(in_file='zspec_linear_interp.nii.gz',
abs_diff=True,
baseline='zspec_zero.nii.gz',
noise=1,
verbose=vb).run()
self.assertLessEqual(diff_zero.outputs.out_diff, 0.01)
def test_zshim(self):
nshims = 8
sz = 32
ref_val = sqrt(sum([x**2 for x in range(1, nshims + 1)]))
NewImage(out_file='zshim.nii.gz',
img_size=[sz, sz, sz, nshims],
grad_dim=3,
grad_vals=(1, nshims),
grad_steps=7,
verbose=vb).run()
NewImage(out_file='zshim_ref.nii.gz',
img_size=[sz, sz, sz],
fill=ref_val,
verbose=vb).run()
ZShim(in_file='zshim.nii.gz', zshims=nshims, verbose=vb).run()
zdiff = Diff(in_file='zshim_zshim.nii.gz',
baseline='zshim_ref.nii.gz',
noise=1,
verbose=vb).run()
self.assertLessEqual(zdiff.outputs.out_diff, 1.e-3)
def test_rfprofile(self):
NewImage(out_file='rf_b1plus.nii.gz',
img_size=[32, 32, 32],
fill=1.0,
verbose=vb).run()
RFProfile(in_file='rf_b1plus.nii.gz',
out_file='rf_slab.nii.gz',
rf={
'rf_pos': [0, 1],
'rf_vals': [0, 1]
},
verbose=vb).run()
NewImage(out_file='rf_ref.nii.gz',
img_size=[32, 32, 32],
grad_dim=2,
grad_vals=(-16, 15),
verbose=vb).run()
rf_diff = Diff(baseline='rf_ref.nii.gz',
in_file='rf_slab.nii.gz',
noise=1,
abs_diff=True,
verbose=vb).run()
self.assertLessEqual(rf_diff.outputs.out_diff, 1.e-3)
def test_despot1(self):
seq = {'SPGR': {'TR': 10e-3, 'FA': [3, 18]}}
spgr_file = 'sim_spgr.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 1.0),
out_file='PD.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=1,
grad_vals=(0.8, 1.3),
out_file='T1.nii.gz',
verbose=vb).run()
DESPOT1Sim(sequence=seq,
in_file=spgr_file,
noise=noise,
verbose=vb,
PD='PD.nii.gz',
T1='T1.nii.gz').run()
DESPOT1(sequence=seq, in_file=spgr_file, verbose=vb,
residuals=True).run()
diff_T1 = Diff(in_file='D1_T1.nii.gz',
baseline='T1.nii.gz',
noise=noise,
verbose=vb).run()
diff_PD = Diff(in_file='D1_PD.nii.gz',
baseline='PD.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_T1.outputs.out_diff, 35)
self.assertLessEqual(diff_PD.outputs.out_diff, 35)
def test_poly(self):
sz = 16
scale = sqrt(3 * (sz / 2)**2)
poly = {
'center': [0, 0, 0],
'scale': scale,
'coeffs': [1, 1, 2, 4, 1, 0, 0, 1, 0, 1]
}
poly_sim = 'poly_sim.nii.gz'
mask_file = 'poly_mask.nii.gz'
NewImage(img_size=[sz, sz, sz],
grad_dim=0,
grad_vals=(0, 1),
grad_steps=1,
out_file=mask_file,
verbose=vb).run()
PolyImage(ref_file=mask_file,
out_file=poly_sim,
order=2,
poly=poly,
verbose=vb).run()
fit = PolyFit(in_file=poly_sim, order=2, robust=True).run()
terms_diff = sum([
abs(x - y)
for x, y in zip(poly['coeffs'], fit.outputs.poly['coeffs'])
])
self.assertLessEqual(terms_diff, 1.e-6)
PolyImage(ref_file=mask_file,
out_file='poly_sim2.nii.gz',
order=2,
poly=fit.outputs.poly,
verbose=vb).run()
img_diff = Diff(baseline=poly_sim, in_file='poly_sim2.nii.gz',
noise=1).run()
self.assertLessEqual(img_diff.outputs.out_diff, 1.e-3)
def test_lorentzian2(self):
sat_f0 = [
*np.linspace(-40, 40, 12).squeeze().tolist(), -0.5, -0.25, 0, 0.25,
0.5
]
sequence = {
'MTSat': {
'pulse': {
'p1': 0.4,
'p2': 0.3,
'bandwidth': 0.39
},
'TR': 4,
'Trf': 0.02,
'FA': 5,
'sat_f0': sat_f0,
'sat_angle': np.repeat(180.0, 17).squeeze().tolist()
}
}
pools = [{
'name': 'DS',
'df0': [0, -2.5, 2.5],
'fwhm': [1.0, 1.e-6, 3.0],
'A': [0.2, 1.e-3, 1.0],
'use_bandwidth': True
}, {
'name': 'MT',
'df0': [-2.5, -5.0, -0.5],
'fwhm': [50.0, 35.0, 200.0],
'A': [0.3, 1.e-3, 1.0]
}]
lorentz_file = 'lorentz_sim.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(out_file='PD.nii.gz', verbose=vb, img_size=img_sz,
fill=1.0).run()
NewImage(out_file='f0.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=0,
grad_vals=(-0.25, 0.25)).run()
NewImage(out_file='fwhm.nii.gz', verbose=vb, img_size=img_sz,
fill=1.8).run()
NewImage(out_file='A.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=2,
grad_vals=(0.3, 0.4)).run()
NewImage(out_file='MTf0.nii.gz',
verbose=vb,
img_size=img_sz,
fill=-2.2).run()
NewImage(out_file='MTfwhm.nii.gz',
verbose=vb,
img_size=img_sz,
fill=90).run()
NewImage(out_file='MTA.nii.gz', verbose=vb, img_size=img_sz,
fill=0.4).run()
LorentzianSim(sequence=sequence,
pools=pools,
in_file=lorentz_file,
noise=noise,
verbose=vb,
DS_f0='f0.nii.gz',
DS_fwhm='fwhm.nii.gz',
DS_A='A.nii.gz',
MT_fwhm='MTfwhm.nii.gz',
MT_f0='f0.nii.gz',
MT_A='MTA.nii.gz').run()
Lorentzian(sequence=sequence,
pools=pools,
in_file=lorentz_file,
verbose=vb).run()
diff_fwhm = Diff(in_file='LTZ_DS_fwhm.nii.gz',
baseline='fwhm.nii.gz',
noise=noise,
verbose=vb).run()
diff_A = Diff(in_file='LTZ_DS_A.nii.gz',
baseline='A.nii.gz',
noise=noise,
verbose=vb).run()
diff_MTfwhm = Diff(in_file='LTZ_MT_fwhm.nii.gz',
baseline='MTfwhm.nii.gz',
noise=noise,
verbose=vb).run()
diff_MTA = Diff(in_file='LTZ_MT_A.nii.gz',
baseline='MTA.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_fwhm.outputs.out_diff, 15)
self.assertLessEqual(diff_A.outputs.out_diff, 300)
self.assertLessEqual(diff_MTfwhm.outputs.out_diff, 15)
self.assertLessEqual(diff_MTA.outputs.out_diff, 300)
def test_qMT(self):
qmt = {
'MTSat': {
'sat_f0':
[1000, 3000, 5000, 7000, 9000, 1000, 3000, 5000, 7000, 9000],
'sat_angle':
[360, 360, 360, 360, 360, 720, 720, 720, 720, 720],
'bw':
100,
'FA':
5,
'TR':
0.03,
'Trf':
0.015,
'pulse': {
'p1': 0.416,
'p2': 0.295,
'bandwidth': 100
}
},
}
qmt_file = 'qmt_sim.nii.gz'
t1app = 'qmt_t1app.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
lineshape_file = '_qmt_lineshape.json'
Lineshape(out_file=lineshape_file,
lineshape='SuperLorentzian',
frq_start=500,
frq_space=500,
frq_count=150).run()
NewImage(out_file='PD.nii.gz', verbose=vb, img_size=img_sz,
fill=1.0).run()
NewImage(out_file='T1_f.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=0,
grad_vals=(0.5, 1.5)).run()
NewImage(out_file='T2_f.nii.gz', verbose=vb, img_size=img_sz,
fill=0.1).run()
NewImage(out_file='T2_b.nii.gz',
verbose=vb,
img_size=img_sz,
fill=12e-6).run()
NewImage(out_file='k_bf.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=1,
grad_vals=(1.0, 5.0)).run()
NewImage(out_file='f_b.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=2,
grad_vals=(0.05, 0.2)).run()
qMTSim(sequence=qmt,
in_file=qmt_file,
t1_map=t1app,
lineshape=lineshape_file,
noise=noise,
verbose=vb,
PD='PD.nii.gz',
T1_f='T1_f.nii.gz',
T2_f='T2_f.nii.gz',
T2_b='T2_b.nii.gz',
k_bf='k_bf.nii.gz',
f_b='f_b.nii.gz').run()
qMT(sequence=qmt,
in_file=qmt_file,
t1_map=t1app,
lineshape=lineshape_file,
verbose=vb).run()
diff_T1_f = Diff(in_file='QMT_T1_f.nii.gz',
baseline='T1_f.nii.gz',
noise=noise,
verbose=vb).run()
diff_k_bf = Diff(in_file='QMT_k_bf.nii.gz',
baseline='k_bf.nii.gz',
noise=noise,
verbose=vb).run()
diff_f_b = Diff(in_file='QMT_f_b.nii.gz',
baseline='f_b.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_T1_f.outputs.out_diff, 32)
self.assertLessEqual(diff_k_bf.outputs.out_diff, 32)
self.assertLessEqual(diff_f_b.outputs.out_diff, 32)
def test_lorentzian(self):
sequence = {
'MTSat': {
'pulse': {
'p1': 0.4,
'p2': 0.3,
'bandwidth': 0.39
},
'TR': 4,
'Trf': 0.02,
'FA': 5,
'sat_f0': np.linspace(-5, 5, 21).squeeze().tolist(),
'sat_angle': np.repeat(180.0, 21).squeeze().tolist()
}
}
pools = [{
'name': 'DS',
'df0': [0, -2.5, 2.5],
'fwhm': [1.0, 1.e-6, 3.0],
'A': [0.2, 1.e-3, 1.0],
'use_bandwidth': True
}]
lorentz_file = 'lorentz_sim.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(out_file='f0.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=0,
grad_vals=(-0.5, 0.5)).run()
NewImage(out_file='fwhm.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=1,
grad_vals=(0.5, 2.5)).run()
NewImage(out_file='A.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=2,
grad_vals=(0.5, 1)).run()
LorentzianSim(sequence=sequence,
pools=pools,
in_file=lorentz_file,
noise=noise,
verbose=vb,
DS_f0='f0.nii.gz',
DS_fwhm='fwhm.nii.gz',
DS_A='A.nii.gz').run()
Lorentzian(sequence=sequence,
pools=pools,
in_file=lorentz_file,
verbose=vb).run()
diff_f0 = Diff(in_file='LTZ_DS_f0.nii.gz',
baseline='f0.nii.gz',
noise=noise,
verbose=vb).run()
diff_fwhm = Diff(in_file='LTZ_DS_fwhm.nii.gz',
baseline='fwhm.nii.gz',
noise=noise,
verbose=vb).run()
diff_A = Diff(in_file='LTZ_DS_A.nii.gz',
baseline='A.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_f0.outputs.out_diff, 60)
self.assertLessEqual(diff_fwhm.outputs.out_diff, 20)
self.assertLessEqual(diff_A.outputs.out_diff, 25)
def test_hifi(self):
seqs = {
'SPGR': {
'TR': 5e-3,
'FA': [3, 18]
},
'MPRAGE': {
'FA': 5,
'TR': 5e-3,
'TI': 0.45,
'TD': 0,
'eta': 1,
'ETL': 64,
'k0': 0
},
}
spgr_file = 'sim_spgr.nii.gz'
mprage_file = 'sim_mprage.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(out_file='PD.nii.gz',
img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 1.0),
verbose=vb).run()
NewImage(out_file='T1.nii.gz',
img_size=img_sz,
grad_dim=1,
grad_vals=(0.5, 1.5),
verbose=vb).run()
NewImage(out_file='B1.nii.gz',
img_size=img_sz,
grad_dim=2,
grad_vals=(0.8, 1.2),
verbose=vb).run()
HIFISim(sequence=seqs,
spgr_file=spgr_file,
mprage_file=mprage_file,
noise=noise,
verbose=vb,
PD='PD.nii.gz',
T1='T1.nii.gz',
B1='B1.nii.gz').run()
HIFI(sequence=seqs,
spgr_file=spgr_file,
mprage_file=mprage_file,
verbose=vb,
residuals=True).run()
diff_T1 = Diff(in_file='HIFI_T1.nii.gz',
baseline='T1.nii.gz',
noise=noise,
verbose=vb).run()
diff_PD = Diff(in_file='HIFI_PD.nii.gz',
baseline='PD.nii.gz',
noise=noise,
verbose=vb).run()
diff_B1 = Diff(in_file='HIFI_B1.nii.gz',
baseline='B1.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_T1.outputs.out_diff, 60)
self.assertLessEqual(diff_PD.outputs.out_diff, 35)
self.assertLessEqual(diff_B1.outputs.out_diff, 60)
def test_MUPA(self):
seq = {
'MUPA': {
'TR':
0.002786,
'Tramp':
0.01,
'SPS':
64,
'FA':
2,
"prep_type": [
"inversion", "delay", "delay", "delay", "t2-prep",
"t2-prep", "t2-prep"
],
"prep_time": [0.03, 0, 0, 0, 0.04, 0.08, 0.16]
}
}
sim_file = 'sim_mupa.nii.gz'
img_sz = [16, 16, 16]
noise = 0.01
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(80, 120),
out_file='PD.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 3.0),
out_file='T1.nii.gz',
verbose=vb).run()
NewImage(img_size=img_sz,
grad_dim=0,
grad_vals=(0.04, 1.0),
out_file='T2.nii.gz',
verbose=vb).run()
MUPASim(sequence=seq,
in_file=sim_file,
PD='PD.nii.gz',
T1='T1.nii.gz',
T2='T2.nii.gz',
noise=noise,
verbose=vb).run()
MUPA(sequence=seq, in_file=sim_file, verbose=vb, threads=-1).run()
diff_T2 = Diff(in_file='MUPA_T2.nii.gz',
baseline='T2.nii.gz',
noise=noise,
verbose=vb).run()
diff_PD = Diff(in_file='MUPA_PD.nii.gz',
baseline='PD.nii.gz',
noise=noise,
verbose=vb).run()
diff_T1 = Diff(in_file='MUPA_T1.nii.gz',
baseline='T1.nii.gz',
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_PD.outputs.out_diff, 10)
self.assertLessEqual(diff_T1.outputs.out_diff, 10)
self.assertLessEqual(diff_T2.outputs.out_diff, 12)
def test_emt(self):
ellipse_sim = {
"SSFP": {
"FA": [1, 1, 1, 1, 1, 1],
"PhaseInc": [180, 240, 300, 0, 60, 120],
"TR": 0.01
}
}
ellipse_fit = {
"SSFP": {
"FA": [1, 1, 1, 1, 1, 1],
"PhaseInc": [180, 240, 300, 0, 60, 120],
"TR": 0.01
}
}
emt_seq = {
"SSFPMT": {
"FA": [30],
"PhaseInc": [180, 240, 300, 0, 60, 120],
"TR": [0.01],
"Trf": [0.00025],
"pulse": {
"p1": 0.250629,
"p2": 0.201183,
"bandwidth": 2
}
}
}
ellipse_file = 'emt_ellipse.nii.gz'
emt_G = 'emt_G.nii.gz'
emt_a = 'emt_a.nii.gz'
emt_b = 'emt_b.nii.gz'
img_sz = [32, 32, 32]
noise = 0.001
NewImage(out_file='PD.nii.gz', verbose=vb, img_size=img_sz,
fill=1).run()
NewImage(out_file='T1_f.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=0,
grad_vals=(0.8, 1.3)).run()
NewImage(out_file='T2_f.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=1,
grad_vals=(0.05, 0.1)).run()
NewImage(out_file='f_b.nii.gz',
verbose=vb,
img_size=img_sz,
grad_dim=2,
grad_vals=(0.01, 0.15)).run()
NewImage(out_file='k_bf.nii.gz', verbose=vb, img_size=img_sz,
fill=2).run()
NewImage(out_file='zero.nii.gz', verbose=vb, img_size=img_sz,
fill=0).run()
eMTSim(sequence=emt_seq,
G_file=emt_G,
a_file=emt_a,
b_file=emt_b,
noise=0,
verbose=vb,
PD='PD.nii.gz',
T1_f='T1_f.nii.gz',
T2_f='T2_f.nii.gz',
f_b='f_b.nii.gz',
k_bf='k_bf.nii.gz').run()
EllipseSim(sequence=ellipse_sim,
in_file=ellipse_file,
noise=noise,
verbose=vb,
G=emt_G,
a=emt_a,
b=emt_b,
theta_0='zero.nii.gz',
phi_rf='zero.nii.gz').run()
Ellipse(sequence=ellipse_fit, in_file=ellipse_file, verbose=vb).run()
eMT(sequence=emt_seq,
G_map=emt_G,
a_map=emt_a,
b_map=emt_b,
verbose=vb).run()
# Currently the simulation framework does not support blocked algorithms
# Hence simulating a proper eMT dataset would involve individually simulating
# the different TR/Trf combinations and then merging them. I'm not doing that
# now, so a proper test will have to wait
diff_G = Diff(in_file='ES_G.nii.gz',
baseline=emt_G,
noise=noise,
verbose=vb).run()
diff_a = Diff(in_file='ES_a.nii.gz',
baseline=emt_a,
noise=noise,
verbose=vb).run()
diff_b = Diff(in_file='ES_b.nii.gz',
baseline=emt_b,
noise=noise,
verbose=vb).run()
self.assertLessEqual(diff_G.outputs.out_diff, 3.5)
self.assertLessEqual(diff_a.outputs.out_diff, 3.5)
self.assertLessEqual(diff_b.outputs.out_diff, 10)