def create_semi_synthetic(params):
r""" Create semi-synthetic image using real_mod1 as anatomy and tmp_mod2 template as intensity model
Template tmp_mod1 is registered towards real_mod1 (which are assumed of the same modality) using SyN-CC.
The transformation is applied to template tmp_mod2 (which is assumed to be perfectly aligned with tmp_mod1).
The transfer function is computed from real_mod1 to warped tmp_mod2 and applied to real_mod1.
"""
real_mod1 = params.real
base_fixed = getBaseFileName(real_mod1)
tmp_mod1 = params.template
prealign_name = params.prealign
tmp_mod2_list = [os.path.join(params.warp_dir, name) for name in os.listdir(params.warp_dir)]
tmp_mod2_list = [tmp_mod1] + tmp_mod2_list
# Check if all warpings are already done
warp_done = os.path.isfile("mask_" + base_fixed + ".nii.gz")
if warp_done:
for tmp_mod2 in tmp_mod2_list:
base_moving = getBaseFileName(tmp_mod2)
wname = "warpedDiff_" + base_moving + "_" + base_fixed
if real_mod1[-3:] == "img": # Analyze
wname += ".img"
else:
wname += ".nii.gz"
if not os.path.isfile(wname):
warp_done = False
break
# Load input images
real_nib = nib.load(real_mod1)
real_aff = real_nib.get_affine()
real = real_nib.get_data().squeeze()
if real_mod1[-3:] == "img": # Analyze: move reference from center to corner
offset = real_aff[:3, :3].dot(np.array(real.shape) // 2)
real_aff[:3, 3] += offset
t_mod1_nib = nib.load(tmp_mod1)
t_mod1_aff = t_mod1_nib.get_affine()
t_mod1 = t_mod1_nib.get_data().squeeze()
if tmp_mod1[-3:] == "img": # Analyze: move reference from center to corner
offset = t_mod1_aff[:3, :3].dot(np.array(t_mod1.shape) // 2)
t_mod1_aff[:3, 3] += offset
# Load pre-align matrix
print("Pre-align:", prealign_name)
if not prealign_name:
prealign = np.eye(4)
else:
if real_mod1[-3:] == "img": # Analyze
ref_coordinate_system = "LAS"
else: # DICOM
ref_coordinate_system = "LPS"
if tmp_mod1[-3:] == "img": # Analyze
tgt_coordinate_system = "LAS"
else: # DICOM
tgt_coordinate_system = "LPS"
prealign = readAntsAffine(prealign_name, ref_coordinate_system, tgt_coordinate_system)
# Configure CC metric
sigma_diff = 1.7
radius = 4
similarity_metric = metrics.CCMetric(3, sigma_diff, radius)
# Configure optimizer
opt_iter = [100, 100, 50]
step_length = 0.25
opt_tol = 1e-5
inv_iter = 20
inv_tol = 1e-3
ss_sigma_factor = 0.2
if not warp_done:
syn = imwarp.SymmetricDiffeomorphicRegistration(
similarity_metric, opt_iter, step_length, ss_sigma_factor, opt_tol, inv_iter, inv_tol, callback=None
)
# Run registration
syn.verbosity = VerbosityLevels.DEBUG
mapping = syn.optimize(real, t_mod1, real_aff, t_mod1_aff, prealign)
# Save the warped template (so we can visually check the registration result)
warped = mapping.transform(t_mod1)
base_moving = getBaseFileName(tmp_mod1)
oname = "warpedDiff_" + base_moving + "_" + base_fixed
if real_mod1[-3:] == "img": # Analyze
oname += ".img"
else:
oname += ".nii.gz"
real[...] = warped[...]
real_nib.to_filename(oname)
mask = (t_mod1 > 0).astype(np.int32)
wmask = mapping.transform(mask, "nearest")
wmask_nib = nib.Nifti1Image(wmask, t_mod1_aff)
wmask_nib.to_filename("mask_" + base_fixed + ".nii.gz")
else:
wmask_nib = nib.load("mask_" + base_fixed + ".nii.gz")
wmask = wmask_nib.get_data().squeeze()
# Compute and save the semi-synthetic images in different modalities
for tmp_mod2 in tmp_mod2_list:
print("Warping: " + tmp_mod2)
t_mod2_nib = nib.load(tmp_mod2)
t_mod2_aff = t_mod2_nib.get_affine()
t_mod2 = t_mod2_nib.get_data().squeeze()
base_moving = getBaseFileName(tmp_mod2)
oname = base_moving + "_" + base_fixed
if real_mod1[-3:] == "img": # Analyze
oname += ".img"
else:
oname += ".nii.gz"
if not warp_done:
# Save warped image
warped = mapping.transform(t_mod2)
wnib = nib.Nifti1Image(warped, t_mod2_aff)
wnib.to_filename("warpedDiff_" + oname)
else:
wnib = nib.load("warpedDiff_" + oname)
warped = wnib.get_data().squeeze()
real_nib = nib.load(real_mod1)
real = real_nib.get_data().squeeze()
use_density_estimation = True
nbins = 100
if use_density_estimation:
print("Using density sampling.")
oname = "ssds_" + oname
# Compute marginal distributions
densities = np.array(compute_densities(real.astype(np.int32), warped.astype(np.float64), nbins, wmask))
# Sample the marginal distributions
real[...] = create_ss_de(real.astype(np.int32), densities)
else:
print("Using mean transfer.")
oname = "ssmt_" + oname
# Compute transfer function
means, vars = get_mean_transfer(real, warped)
# Apply transfer to real
real[...] = means[real]
# Save semi_synthetic
real_nib.to_filename(oname)
def register_3d(params):
r'''
Runs the non-linear registration with the parsed parameters
'''
print('Registering %s to %s'%(params.target, params.reference))
sys.stdout.flush()
metric_name=params.metric[0:params.metric.find('[')]
metric_params_list=params.metric[params.metric.find('[')+1:params.metric.find(']')].split(',')
moving_mask = None
static_mask = None
#Initialize the appropriate metric
if metric_name == 'SSD':
smooth=float(metric_params_list[0])
inner_iter=int(metric_params_list[1])
iter_type = metric_params_list[2]
similarity_metric = metrics.SSDMetric(
3, smooth, inner_iter, iter_type)
elif metric_name=='EM':
smooth=float(metric_params_list[0])
q_levels=int(metric_params_list[1])
inner_iter=int(metric_params_list[2])
iter_type = metric_params_list[3]
double_gradient=False if params.single_gradient else True
similarity_metric = metrics.EMMetric(
3, smooth, inner_iter, q_levels, double_gradient, iter_type)
similarity_metric.mask0 = params.mask0
elif metric_name=='POLY':
print('>>>>>>>>>>>>>>>>OK<<<<<<<<<<<<<')
from dipy.align.polynomial import PolynomialTransfer
degree=int(metric_params_list[0])
smooth=float(metric_params_list[1])
q_levels=int(metric_params_list[2])
cprop=float(metric_params_list[3])
drop_zeros=int(metric_params_list[4])!=0
similarity_metric = PolynomialTransfer(3, degree, smooth, q_levels, cprop, drop_zeros)
similarity_metric.mask0 = params.mask0
elif metric_name=='CC':
sigma_diff = float(metric_params_list[0])
radius = int(metric_params_list[1])
similarity_metric = metrics.CCMetric(3, sigma_diff, radius)
elif metric_name=='ECC':
from dipy.align.ECCMetric import ECCMetric
sigma_diff = float(metric_params_list[0])
radius = int(metric_params_list[1])
q_levels = int(metric_params_list[2])
similarity_metric = ECCMetric(3, sigma_diff, radius, q_levels)
if params.target_mask is not None and os.path.isfile(params.target_mask):
moving_mask = nib.load(params.target_mask)
moving_mask = moving_mask.get_data().squeeze()
moving_mask = (moving_mask>0).astype(np.int32)
if params.reference_mask is not None and os.path.isfile(params.reference_mask):
static_mask = nib.load(params.reference_mask)
static_mask = static_mask.get_data().squeeze()
static_mask = (static_mask>0).astype(np.int32)
#Initialize the optimizer
opt_iter = [int(i) for i in params.iter.split(',')]
step_length = float(params.step_length)
opt_tol = 1e-5
inv_iter = int(params.inversion_iter)
inv_tol = float(params.inversion_tolerance)
ss_sigma_factor = float(params.ss_sigma_factor)
registration_optimizer = imwarp.SymmetricDiffeomorphicRegistration(
similarity_metric, opt_iter, step_length, ss_sigma_factor, opt_tol, inv_iter, inv_tol, None)
if hasattr(registration_optimizer, 'inv_type'):
print('Inversion type: %s'%(registration_optimizer.inv_type,))
#Load the data
moving, moving_affine = load_nifti(params.target)
fixed, fixed_affine = load_nifti(params.reference)
# If internediate is not None, we need to run two registrations
if params.intermediate is not None:
intermediate, intermediate_affine = load_nifti(params.intermediate)
inter_to_reference_aff = readAntsAffine(params.inter_to_reference_aff,
'LPS', 'LPS')
inter_to_target_aff = readAntsAffine(params.inter_to_target_aff,
'LPS', 'LPS')
registration_optimizer.verbosity = VerbosityLevels.DEBUG
inter_to_ref = registration_optimizer.optimize(fixed, intermediate,
fixed_affine,
intermediate_affine,
inter_to_reference_aff)
inter_to_moving = registration_optimizer.optimize(moving, intermediate,
moving_affine,
intermediate_affine,
inter_to_target_aff)
save_registration_results(inter_to_ref, params, inter_to_moving)
else:
print('Affine:', params.affine)
if not params.affine:
transform = np.eye(4)
else:
#http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined
if params.reference[:-3] == 'img': # Analyze
ref_coordinate_system = 'LAS'
else: # DICOM
ref_coordinate_system = 'LPS'
if params.target[:-3] == 'img': # Analyze
tgt_coordinate_system = 'LAS'
else: # DICOM
tgt_coordinate_system = 'LPS'
transform = readAntsAffine(params.affine, ref_coordinate_system, tgt_coordinate_system)
init_affine = np.linalg.inv(moving_affine).dot(transform.dot(fixed_affine))
#Preprocess the data
moving = (moving-moving.min())/(moving.max()-moving.min())
fixed = (fixed-fixed.min())/(fixed.max()-fixed.min())
#Run the registration
if params.output_list is not None and 'affine_only' in params.output_list:
print('Applying affine only')
sh_direct=fixed.shape + (3,)
sh_inv=moving.shape + (3,)
direct = np.zeros(shape = sh_direct, dtype=np.float32)
inv = np.zeros(shape = sh_inv, dtype=np.float32)
mapping=imwarp.DiffeomorphicMap(3, direct, inv, None, init_affine)
else:
registration_optimizer.verbosity = VerbosityLevels.DEBUG
mapping = registration_optimizer.optimize(fixed, moving, fixed_affine, moving_affine, transform)
del registration_optimizer
del similarity_metric
save_registration_results(mapping, params)
# Result using CC
wt1_cc_name = basedir + "\\warp\\SyNCC\\warpedDiff_SCIL_01_t1_strip_SCIL_01_b0_down_strip.nii.gz"
wt1_cc, wt1_aff = load_nib(wt1_cc_name)
wb0_cc_name = basedir + "\\warp\\SyNCC\\warpedDiff_SCIL_01_b0_down_strip_SCIL_01_t1_strip.nii.gz"
wb0_cc, wb0_aff = load_nib(wb0_cc_name)
# Result using MI
wt1_mi_name = basedir + "\\warp\\SyNMI\\warpedDiff_SCIL_01_t1_strip_SCIL_01_b0_down_strip.nii.gz"
wt1_mi, wt1_aff = load_nib(wt1_mi_name)
wt1_b0up_mi_name = basedir + "\\warp\\SyNMI\\warpedDiff_SCIL_01_t1_strip_SCIL_01_b0_up_strip.nii.gz"
wt1_b0up_mi, wt1_aff = load_nib(wt1_b0up_mi_name)
wb0_mi_name = basedir + "\\warp\\SyNMI\\warpedDiff_SCIL_01_b0_down_strip_SCIL_01_t1_strip.nii.gz"
wb0_mi, wb0_aff = load_nib(wb0_mi_name)
wb0_up_mi_name = basedir + "\\warp\\SyNMI\\warpedDiff_SCIL_01_b0_up_strip_SCIL_01_t1_strip.nii.gz"
wb0_up_mi, wb0_up_aff = load_nib(wb0_up_mi_name)
A = readAntsAffine(basedir + reg_t1_toward_b0)
T = np.linalg.inv(t1_aff).dot(A.dot(b0_aff))
shape = np.array(b0.shape, dtype=np.int32)
wb0_mi_aligned = np.array(
vfu.warp_3d_affine(wb0_mi.astype(np.float32), shape, T))
A = readAntsAffine(basedir + reg_t1_toward_b0_up)
T = np.linalg.inv(t1_aff).dot(A.dot(b0up_aff))
shape = np.array(b0.shape, dtype=np.int32)
wb0_up_mi_aligned = np.array(
vfu.warp_3d_affine(wb0_up_mi.astype(np.float32), shape, T))
# Result using ECC
wt1_ecc_name = basedir + "\\warp\\SyNECC\\warpedDiff_SCIL_01_t1_strip_SCIL_01_b0_down_strip.nii.gz"
wt1_ecc, wt1_aff = load_nib(wt1_ecc_name)
wt1_b0up_ecc_name = basedir + "\\warp\\SyNECC\\warpedDiff_SCIL_01_t1_strip_SCIL_01_b0_up_strip.nii.gz"