def alignImage(static, moving, level_iters):
"""The Symmetric Normalization algorithm uses a multi-resolution approach by building a Gaussian Pyramid.
The static image is used a reference; a transformation that transforms the moving image into the
static image is found and applied to the static image. Returns overlay images, error image, and transformation matrix.
Uses CrossCorrelation metric which makes sense for aligning AFM topography.
INPUT: static and moving are both 2d arrays of the same dimension.
Level_iters is a list (typically 4 entries) defines
the number of iterations a user wants at each level of the pyramid, with the 0th entry referring to the
finest resolution.
OUTPUT: overlayimages: an image with the static, moving, and overlay images
errorimage: the difference between the warped_moving image and the static reference. THe flatter
the better.
transformmatrix: the matrix corresponding to the forward transformation of a matrix."""
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.metrics import SSDMetric, CCMetric, EMMetric
from dipy.viz import regtools
dim = static.ndim
metric = CCMetric(dim)
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters, inv_iter = 50)
mapping = sdr.optimize(static, moving)
warped_moving = mapping.transform(moving, 'linear')
overlayimages = regtools.overlay_images(static, warped_moving, 'Static','Overlay','Warped moving',
'direct_warp_result.png')
errorimage = plt.matshow(warped_moving-static, cmap='viridis')
transformmatrix=mapping.forward
return overlayimages, errorimage, transformmatrix
def register_diffeo(t_masked, m_masked, start_affine, registration=None):
""" Run non-linear registration between `t_masked` and `m_masked`
Parameters
----------
t_masked : image
Template image object, with image data masked to set out-of-brain
voxels to zero.
m_masked : image
Moving (individual) image object, with image data masked to set
out-of-brain voxels to zero.
start_affine : shape (4, 4) ndarray
Affine mapping from voxels in `t_masked` to voxels in `m_masked`.
registration : None or SymmetricDiffeoMorphicRegistration instance
Registration instance we will use to register `t_masked` and
`m_masked`. If None, make a default registration object.
Returns
-------
mapping : mapping instance
Instance giving affine + non-linear mapping between voxels in
`t_masked` and voxels in `m_masked`.
"""
if registration is None:
registration = SymmetricDiffeomorphicRegistration(
metric=CCMetric(3), level_iters=[10, 10, 5])
return registration.optimize(t_masked.get_data().astype(float),
m_masked.get_data().astype(float),
t_masked.affine, m_masked.affine,
start_affine)
def syn_registration(static_data, static_affine, moving_data, moving_affine):
# Terminology for comments:
# 1. Static image = Reference image
# 2. Moving image = Image that will be registered to the static image
# Prealignment has been done using FLIRT, so the identity matrix is used since
# no further transformation is necessary
pre_align = np.array([[1, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]])
# We want to find an invertible map that transforms the moving image into the
# static image. We will use the Cross Correlation metric.
metric = CCMetric(3)
# Now we define an instance of the registration class. The SyN algorithm uses
# a multi-resolution approach by building a Gaussian Pyramid. We instruct the
# registration object to perform at most [n_0, n_1, ..., n_k] iterations at
# each level of the pyramid. The 0-th level corresponds to the finest resolution.
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
# Execute the optimization, which returns a DiffeomorphicMap object,
# that can be used to register images back and forth between the static and
# moving domains. We provide the pre-aligning matrix that brings the moving
# image closer to the static image
mapping = sdr.optimize(static_data, moving_data,
static_affine, moving_affine, pre_align)
# Warp the moving image and see if it gets similar to the static image
warped_moving = mapping.transform(moving_data)
return warped_moving, mapping
def test_plot_2d_diffeomorphic_map():
# Test the regtools plotting interface (lightly).
mv_shape = (11, 12)
moving = np.random.rand(*mv_shape)
st_shape = (13, 14)
static = np.random.rand(*st_shape)
dim = static.ndim
metric = SSDMetric(dim)
level_iters = [200, 100, 50, 25]
sdr = SymmetricDiffeomorphicRegistration(metric,
level_iters,
inv_iter=50)
mapping = sdr.optimize(static, moving)
# Smoke testing of plots
ff = regtools.plot_2d_diffeomorphic_map(mapping, 10)
# Defualt shape is static shape, moving shape
npt.assert_equal(ff[0].shape, st_shape)
npt.assert_equal(ff[1].shape, mv_shape)
# Can specify shape
ff = regtools.plot_2d_diffeomorphic_map(mapping,
delta = 10,
direct_grid_shape=(7, 8),
inverse_grid_shape=(9, 10))
npt.assert_equal(ff[0].shape, (7, 8))
npt.assert_equal(ff[1].shape, (9, 10))
def syn_registration(moving,
static,
moving_affine=None,
static_affine=None,
step_length=0.25,
metric='CC',
dim=3,
level_iters=[10, 10, 5],
sigma_diff=2.0,
prealign=None):
"""Register a source image (moving) to a target image (static).
Parameters
----------
moving : ndarray
The source image data to be registered
moving_affine : array, shape (4,4)
The affine matrix associated with the moving (source) data.
static : ndarray
The target image data for registration
static_affine : array, shape (4,4)
The affine matrix associated with the static (target) data
metric : string, optional
The metric to be optimized. One of `CC`, `EM`, `SSD`,
Default: CCMetric.
dim: int (either 2 or 3), optional
The dimensions of the image domain. Default: 3
level_iters : list of int, optional
the number of iterations at each level of the Gaussian Pyramid (the
length of the list defines the number of pyramid levels to be
used).
Returns
-------
warped_moving : ndarray
The data in `moving`, warped towards the `static` data.
forward : ndarray (..., 3)
The vector field describing the forward warping from the source to the
target.
backward : ndarray (..., 3)
The vector field describing the backward warping from the target to the
source.
"""
use_metric = syn_metric_dict[metric](dim, sigma_diff=sigma_diff)
sdr = SymmetricDiffeomorphicRegistration(use_metric,
level_iters,
step_length=step_length)
mapping = sdr.optimize(static,
moving,
static_grid2world=static_affine,
moving_grid2world=moving_affine,
prealign=prealign)
warped_moving = mapping.transform(moving)
return warped_moving, mapping
def exampleDipy():
# example obtained from: http://nipy.org/dipy/examples_built/syn_registration_2d.html
import ssl
if hasattr(ssl, '_create_unverified_context'):
ssl._create_default_https_context = ssl._create_unverified_context
from dipy.data import fetch_stanford_hardi, read_stanford_hardi
fetch_stanford_hardi()
nib_stanford, gtab_stanford = read_stanford_hardi()
stanford_b0 = np.squeeze(nib_stanford.get_data())[..., 0]
from dipy.data.fetcher import fetch_syn_data, read_syn_data
fetch_syn_data()
nib_syn_t1, nib_syn_b0 = read_syn_data()
syn_b0 = np.array(nib_syn_b0.get_data())
from dipy.segment.mask import median_otsu
stanford_b0_masked, stanford_b0_mask = median_otsu(stanford_b0, 4, 4)
syn_b0_masked, syn_b0_mask = median_otsu(syn_b0, 4, 4)
static = stanford_b0_masked
static_affine = nib_stanford.affine
moving = syn_b0_masked
moving_affine = nib_syn_b0.affine
pre_align = np.array(
[[1.02783543e+00, -4.83019053e-02, -6.07735639e-02, -2.57654118e+00],
[4.34051706e-03, 9.41918267e-01, -2.66525861e-01, 3.23579799e+01],
[5.34288908e-02, 2.90262026e-01, 9.80820307e-01, -1.46216651e+01],
[0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])
from dipy.align.imaffine import AffineMap
affine_map = AffineMap(pre_align,
static.shape, static_affine,
moving.shape, moving_affine)
resampled = affine_map.transform(moving)
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving, static_affine, moving_affine,
pre_align)
warped_moving = mapping.transform(moving)
for slice in range(41 - 12, 41 + 13):
regtools.overlay_slices(static, resampled, slice, 1, 'Static',
'Pre Moving',
'GIFexample1/' + str(slice) + 'T1pre.png')
regtools.overlay_slices(static, warped_moving, slice, 1, 'Static',
'Post moving',
'GIFexample1/' + str(slice) + 'T1post.png')
def syn_registration(moving, static,
moving_affine=None,
static_affine=None,
step_length=0.25,
metric='CC',
dim=3,
level_iters=[10, 10, 5],
sigma_diff=2.0,
prealign=None):
"""Register a source image (moving) to a target image (static).
Parameters
----------
moving : ndarray
The source image data to be registered
moving_affine : array, shape (4,4)
The affine matrix associated with the moving (source) data.
static : ndarray
The target image data for registration
static_affine : array, shape (4,4)
The affine matrix associated with the static (target) data
metric : string, optional
The metric to be optimized. One of `CC`, `EM`, `SSD`,
Default: CCMetric.
dim: int (either 2 or 3), optional
The dimensions of the image domain. Default: 3
level_iters : list of int, optional
the number of iterations at each level of the Gaussian Pyramid (the
length of the list defines the number of pyramid levels to be
used).
Returns
-------
warped_moving : ndarray
The data in `moving`, warped towards the `static` data.
forward : ndarray (..., 3)
The vector field describing the forward warping from the source to the
target.
backward : ndarray (..., 3)
The vector field describing the backward warping from the target to the
source.
"""
use_metric = syn_metric_dict[metric](dim, sigma_diff=sigma_diff)
sdr = SymmetricDiffeomorphicRegistration(use_metric, level_iters,
step_length=step_length)
mapping = sdr.optimize(static, moving,
static_grid2world=static_affine,
moving_grid2world=moving_affine,
prealign=prealign)
warped_moving = mapping.transform(moving)
return warped_moving, mapping
def dipy_work(self, uncorrected, worker_progress_signal):
radius = 4
sigma_diff = 3.0
metric = CCMetric(2, sigma_diff, radius)
level_iters = [25]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
corrected = np.zeros_like(uncorrected)
corrected[0] = uncorrected[0]
for i in range(1, len(uncorrected)):
mapping = sdr.optimize(corrected[0], uncorrected[i])
corrected[i] = mapping.transform(uncorrected[i])
worker_progress_signal.emit(i)
return {'corrected': corrected}
def get_params(self):
level_iters = [
np.random.randint(i, j)
for i, j in zip(self.iter_limits[0], self.iter_limits[1])
]
sdr = SymmetricDiffeomorphicRegistration(self.metric,
level_iters,
inv_iter=50)
return {"sdr": sdr}
def abstractExample():
numBlobs = 4
shape = np.array([81, 106, 76])
static = np.zeros(shape)
resampled = np.zeros(shape)
size_blob = 3
for blob in range(numBlobs):
jitter = np.random.randint(5)
randIndX = 41 + 2 * blob
randIndY = np.random.randint(shape[1] - 2 * size_blob)
randIndZ = np.random.randint(shape[2] - 2 * size_blob)
static[randIndX - size_blob:randIndX + size_blob,
randIndY - size_blob:randIndY + size_blob,
randIndZ - size_blob:randIndZ + size_blob] = 1
randIndY = randIndY + jitter
randIndZ = randIndZ + jitter + np.random.randint(-1, 2)
resampled[randIndX - size_blob:randIndX + size_blob,
randIndY - size_blob:randIndY + size_blob,
randIndZ - size_blob:randIndZ + size_blob] = 1
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, resampled)
warped_moving = mapping.transform(resampled)
for slice in range(41 - 3 * size_blob, 41 + 3 * size_blob + 1):
regtools.overlay_slices(static, resampled, slice, 0, 'Static',
'Pre Moving',
'GIFexample1/' + str(slice) + 'preMov.png')
regtools.overlay_slices(static, warped_moving, slice, 0, 'Static',
'Post moving',
'GIFexample1/' + str(slice) + 'postMov.png')
def get_elastic_transform(subject_fa, atlas_fa, subject_path=".."):
'''
:param subject_fa: the FA (nibabel img) of a static image of a subject (static)
:param atlas_fa: the FA (nibabel img) of an atlas (Atlas will be warped onto subject) (moving)
:return: elastic transformation map
'''
if isfile(subject_path + "/FAReg_elastic_transform.pklz"):
logging.debug("Load existing elastic transform...")
return Utils.load_pkl_compressed(subject_path +
"/FAReg_elastic_transform.pklz")
static_img = subject_fa
static = static_img.get_data()
moving_img = atlas_fa
moving = moving_img.get_data()
# Optional (affine transformation of moving image to static coordinate system) -> needed if on very different ones!
affine_map = AffineMap(np.eye(4), static.shape,
static_img.get_affine(), moving.shape,
moving_img.get_affine())
moving = affine_map.transform(moving)
start_time = time.time()
metric = CCMetric(3)
level_iters = [10, 10, 5] # better
# level_iters = [2, 2, 2] #fast -> not much
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving)
# mapping = sdr.optimize(static, moving, Utils.invert_x_and_y(static_img.get_affine()), Utils.invert_x_and_y(moving_img.get_affine())) #not needed
logging.debug("elastic transform took {0:.2f}s".format(time.time() -
start_time))
logging.debug("write elastic transform...")
Utils.save_pkl_compressed(
subject_path + "/FAReg_elastic_transform.pklz", mapping)
return mapping
affine = affreg.optimize(t1_s,
t1_m,
AffineTransform3D(),
None,
t1_s_grid2world,
t1_m_grid2world,
starting_affine=rigid.affine)
# apply affine transformation
t1_m_affine = affine.transform(t1_m)
###############################################################################
# Compute Symmetric Diffeomorphic Registration
# set up Symmetric Diffeomorphic Registration (metric, iterations per level)
sdr = SymmetricDiffeomorphicRegistration(CCMetric(3), niter_sdr)
# compute mapping
mapping = sdr.optimize(t1_s, t1_m_affine)
###############################################################################
# Apply transformations and plot
# morph img data
img_sdr_affine = mapping.transform(affine.transform(img))
# make transformed ndarray a nifti
img_vol_sdr_affine = nib.Nifti1Image(img_sdr_affine, affine=t1_s_grid2world)
# save morphed grid
nib.save(img_vol_sdr_affine, 'lcmv_inverse_fsavg.nii.gz')
hardi_affine = ni.get_affine()
b0 = hardi_data[..., gtab.b0s_mask]
mean_b0 = np.mean(b0, -1)
ni_b0 = nib.Nifti1Image(mean_b0, hardi_affine)
ni_b0.to_filename('mean_b0.nii')
plt.matshow(mean_b0[:,:,mean_b0.shape[-1]//2], cmap=cm.bone)
MNI_T2 = dpd.read_mni_template()
MNI_T2_data = MNI_T2.get_data()
MNI_T2_affine = MNI_T2.get_affine()
level_iters = [10, 10, 5]
dim = 3
metric = CCMetric(dim)
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters, step_length=0.25)
sdr.verbosity = VerbosityLevels.DIAGNOSE
mapping = sdr.optimize(MNI_T2_data, mean_b0, MNI_T2_affine, hardi_affine)
warped_b0 = mapping.transform(mean_b0)
plt.matshow(warped_b0[:,:,warped_b0.shape[-1]//2], cmap=cm.bone)
plt.matshow(MNI_T2_data[:, :, MNI_T2_data.shape[-1]//2], cmap=cm.bone)
new_ni = nib.Nifti1Image(warped_b0, MNI_T2_affine)
new_ni.to_filename('./warped_b0.nii.gz')
afqpath = 'D:/opt/AFQ/'
LOCC_ni = nib.load(os.path.join(afqpath,'templates/callosum2/L_Occipital.nii.gz'))
ROCC_ni = nib.load(os.path.join(afqpath,'templates/callosum2/R_Occipital.nii.gz'))
midsag_ni = nib.load(os.path.join(afqpath,'templates/callosum2/Callosum_midsag.nii.gz'))
LOCC_data = LOCC_ni.get_data()
ROCC_data = ROCC_ni.get_data()
def img_reg(moving_img, target_img, reg='non-lin'):
m_img = nib.load(moving_img)
t_img = nib.load(target_img)
m_img_data = m_img.get_data()
t_img_data = t_img.get_data()
m_img_affine = m_img.affine
t_img_affine = t_img.affine
identity = np.eye(4)
affine_map = AffineMap(identity, t_img_data.shape, t_img_affine,
m_img_data.shape, m_img_affine)
m_img_resampled = affine_map.transform(m_img_data)
c_of_mass = transform_centers_of_mass(t_img_data, t_img_affine, m_img_data,
m_img_affine)
tf_m_img_c_mass = c_of_mass.transform(m_img_data)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10, 10, 5]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine
translation = affreg.optimize(t_img_data,
m_img_data,
transform,
params0,
t_img_affine,
m_img_affine,
starting_affine=starting_affine)
tf_m_img_translat = translation.transform(m_img_data)
transform = RigidTransform3D()
params0 = None
starting_affine = translation.affine
rigid = affreg.optimize(t_img_data,
m_img_data,
transform,
params0,
t_img_affine,
m_img_affine,
starting_affine=starting_affine)
tf_m_img_rigid = rigid.transform(m_img_data)
transform = AffineTransform3D()
affreg.level_iters = [10, 10, 10]
affine = affreg.optimize(t_img_data,
m_img_data,
transform,
params0,
t_img_affine,
m_img_affine,
starting_affine=rigid.affine)
if reg is None or reg == 'non-lin':
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(t_img_data, m_img_data, t_img_affine,
m_img_affine, affine.affine)
tf_m_img = mapping.transform(m_img_data)
elif reg == 'affine':
tf_m_img_aff = affine.transform(m_img_data)
return tf_m_img
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(t_img_data,
m_img_data,
t_img_affine,
m_img_affine,
starting_affine=affine.affine)
tf_m_img = mapping.transform(m_img_data)
.. figure:: input.png
:align: center
Input images before alignment.
"""
"""
Let's the use the general Registration function with some naive parameters,
such as set `step_length` as 1 assuming maximal step 1 pixel and reasonable
small number of iteration since the deformation with already aligned images
should be minimal.
"""
sdr = SymmetricDiffeomorphicRegistration(metric=SSDMetric(img_ref.ndim),
step_length=1.0,
level_iters=[50, 100],
inv_iter=50,
ss_sigma_factor=0.1,
opt_tol=1.e-3)
"""
Perform the registration with equal images.
"""
mapping = sdr.optimize(img_ref.astype(float), img_ref.astype(float))
img_warp = mapping.transform(img_ref, 'linear')
show_images(img_ref, img_warp, 'output-0')
regtools.plot_2d_diffeomorphic_map(mapping, 5, 'map-0.png')
"""
.. figure:: output-0.png
:align: center
of Squared Differences (SSD) is a good choice. """ dim = static.ndim metric = SSDMetric(dim) """ Now we define an instance of the registration class. The SyN algorithm uses a multi-resolution approach by building a Gaussian Pyramid. We instruct the registration instance to perform at most $[n_0, n_1, ..., n_k]$ iterations at each level of the pyramid. The 0-th level corresponds to the finest resolution. """ level_iters = [200, 100, 50, 25] sdr = SymmetricDiffeomorphicRegistration(metric, level_iters, inv_iter = 50) """ Now we execute the optimization, which returns a DiffeomorphicMap object, that can be used to register images back and forth between the static and moving domains """ mapping = sdr.optimize(static, moving) """ It is a good idea to visualize the resulting deformation map to make sure the result is reasonable (at least, visually) """ regtools.plot_2d_diffeomorphic_map(mapping, 10, 'diffeomorphic_map.png')
'allen_annotation_invsynned_to_' + subject + '_adjusted.nii.gz')
# Load images
reference_image = nib.load(reference_image_path)
reference = reference_image.get_fdata()
annotation_image = nib.load(annotation_image_path)
annotation = annotation_image.get_fdata()
input_image = nib.load(input_image_path)
input = input_image.get_fdata()
# syn
metric = CCMetric(3)
level_iters = [10, 10, 5, 5, 5]
print(iSubject)
print(datetime.datetime.now())
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static=reference,
moving=input,
static_grid2world=reference_image.get_qform(),
moving_grid2world=input_image.get_qform())
warped_image = mapping.transform(input)
warped_reference = mapping.transform_inverse(reference)
warped_annotation = mapping.transform_inverse(annotation,
interpolation='nearest')
# save warps
input_invwarped_image = nib.Nifti1Image(warped_image, np.eye(4))
def affine_registration(reference, reference_grid2world, scan,
scan_grid2world):
#get first b0 volumes for both scans
reference_b0 = reference[:, :, :, 0]
scan_b0 = scan[:, :, :, 0]
#In this function we use multiple stages to register the 2 scans
#providng previous results as initialisation to the next stage,
#the reason we do this is because registration is a non-convex
#problem thus it is important to initialise as close to the
#optiaml value as possible
#Stage1: we obtain a very rough (and fast) registration by just aligning
#the centers of mass of the two images
center_of_mass = transform_centers_of_mass(reference_b0,
reference_grid2world, scan_b0,
scan_grid2world)
#create the similarity metric (Mutual Information) to be used:
nbins = 32
sampling_prop = None #use all voxels to perform registration
metric = MutualInformationMetric(nbins, sampling_prop)
#We use a multi-resolution stratergy to accelerate convergence and avoid
#getting stuck at local optimas (below are the parameters)
level_iters = [10000, 1000, 100]
sigmas = [3.0, 1.0, 0.0
] #parameters for gaussian kernel smoothing at each resolution
factors = [4, 2, 1] #subsampling factor
#optimisation algorithm used is L-BFGS-B
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
#Stage2: Perform a basic translation transform
transform = TranslationTransform3D()
translation = affreg.optimize(reference_b0,
scan_b0,
transform,
None,
reference_grid2world,
scan_grid2world,
starting_affine=center_of_mass.affine)
#Stage3 : optimize previous result with a rigid transform
#(Includes translation, rotation)
transform = RigidTransform3D()
rigid = affreg.optimize(reference_b0,
scan_b0,
transform,
None,
reference_grid2world,
scan_grid2world,
starting_affine=translation.affine)
#Stage4 : optimize previous result with a affine transform
#(Includes translation, rotation, scale, shear)
transform = AffineTransform3D()
affine = affreg.optimize(reference_b0,
scan_b0,
transform,
None,
reference_grid2world,
scan_grid2world,
starting_affine=rigid.affine)
if params.reg_type == "SDR":
#Stage 5 : Symmetric Diffeomorphic Registration
metric = CCMetric(3)
level_iters = [400, 200, 100]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(reference_b0, scan_b0, reference_grid2world,
scan_grid2world, affine.affine)
else:
mapping = affine
#Once this is completed we can perform the affine transformation on each
#volume of scan2
for volume in range(0, scan.shape[3]):
#note affine is an AffineMap object,
#The transform method transforms the input image from co-domain to domain space
#By default, the transformed image is sampled at a grid defined by the shape of the domain
#The sampling is performed using linear interpolation (refer to comp vision lab on homographies)
scan[:, :, :, volume] = mapping.transform(scan[:, :, :, volume])
return scan
""" We want to find an invertible map that transforms the moving image into the static image. We will use the Cross Correlation metric """ metric = CCMetric(3) """ Now we define an instance of the registration class. The SyN algorithm uses a multi-resolution approach by building a Gaussian Pyramid. We instruct the registration object to perform at most [n_0, n_1, ..., n_k] iterations at each level of the pyramid. The 0-th level corresponds to the finest resolution. """ level_iters = [10, 10, 5] sdr = SymmetricDiffeomorphicRegistration(metric, level_iters) """ Execute the optimization, which returns a DiffeomorphicMap object, that can be used to register images back and forth between the static and moving domains. We provide the pre-aligning matrix that brings the moving image closer to the static image """ mapping = sdr.optimize(static, moving, static_affine, moving_affine, pre_align) """ Now let's warp the moving image and see if it gets similar to the static image """ warped_moving = mapping.transform(moving)
if os.path.isfile(config_fname):
with open(config_fname,'r') as f:
options = [tuple(line.strip().split()) for line in f.readlines()]
options = {opt[0]:opt[1] for opt in options}
else:
options = {}
step_length = float(options.get('step_length', '0.25'))
inv_tol = float(options.get('inv_tol', '1e-3'))
inv_iter = int(options.get('inv_iter', '20'))
experiment_name = options.get('experiment_name')
level_iters = [400, 200, 100, 50, 25]
dim = 3
metric = SSDMetric(dim, smooth=3)
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters, inv_iter=inv_iter, inv_tol=inv_tol, opt_tol=1e-6, step_length=step_length, ss_sigma_factor=1.0)
sdr.verbosity = VerbosityLevels.DIAGNOSE
start = time.time()
mapping = sdr.optimize(cup, sphere)
end = time.time()
elapsed = end - start
print('Elapsed: %e'%(elapsed,))
fwd = np.array(mapping.forward)
bwd = np.array(mapping.backward)
# Get deformed mid slices
z0 = fwd.shape[2]//2
whlines, wvlines = get_deformed_grid(fwd, [z0])
fwd_fname = 'fwd_lines_%s.p'%(experiment_name,)
def wm_syn(template_path, fa_path, working_dir):
"""
A function to perform ANTS SyN registration
Parameters
----------
template_path : str
File path to the template reference image.
fa_path : str
File path to the FA moving image.
working_dir : str
Path to the working directory to perform SyN and save outputs.
"""
import uuid
from time import strftime
from dipy.align.imaffine import MutualInformationMetric, AffineRegistration, transform_origins
from dipy.align.transforms import TranslationTransform3D, RigidTransform3D, AffineTransform3D
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.metrics import CCMetric
from dipy.viz import regtools
fa_img = nib.load(fa_path)
template_img = nib.load(template_path)
static = np.asarray(template_img.dataobj)
static_affine = template_img.affine
moving = np.asarray(fa_img.dataobj).astype(np.float32)
moving_affine = fa_img.affine
affine_map = transform_origins(static, static_affine, moving,
moving_affine)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10, 10, 5]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affine_reg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
translation = affine_reg.optimize(static, moving, transform, params0,
static_affine, moving_affine)
transform = RigidTransform3D()
rigid_map = affine_reg.optimize(static,
moving,
transform,
params0,
static_affine,
moving_affine,
starting_affine=translation.affine)
transform = AffineTransform3D()
# We bump up the iterations to get a more exact fit:
affine_reg.level_iters = [1000, 1000, 100]
affine_opt = affine_reg.optimize(static,
moving,
transform,
params0,
static_affine,
moving_affine,
starting_affine=rigid_map.affine)
# We now perform the non-rigid deformation using the Symmetric Diffeomorphic Registration(SyN) Algorithm:
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving, static_affine, moving_affine,
affine_opt.affine)
warped_moving = mapping.transform(moving)
# Save warped FA image
run_uuid = '%s_%s' % (strftime('%Y%m%d_%H%M%S'), uuid.uuid4())
warped_fa = '{}/warped_fa_{}.nii.gz'.format(working_dir, run_uuid)
nib.save(nib.Nifti1Image(warped_moving, affine=static_affine), warped_fa)
# We show the registration result with:
regtools.overlay_slices(
static, warped_moving, None, 0, "Static", "Moving",
"%s%s%s%s" % (working_dir, "/transformed_sagittal_", run_uuid, ".png"))
regtools.overlay_slices(
static, warped_moving, None, 1, "Static", "Moving",
"%s%s%s%s" % (working_dir, "/transformed_coronal_", run_uuid, ".png"))
regtools.overlay_slices(
static, warped_moving, None, 2, "Static", "Moving",
"%s%s%s%s" % (working_dir, "/transformed_axial_", run_uuid, ".png"))
return mapping, affine_map, warped_fa
of Squared Differences (SSD) is a good choice. """ dim = static.ndim metric = SSDMetric(dim) """ Now we define an instance of the registration class. The SyN algorithm uses a multi-resolution approach by building a Gaussian Pyramid. We instruct the registration instance to perform at most $[n_0, n_1, ..., n_k]$ iterations at each level of the pyramid. The 0-th level corresponds to the finest resolution. """ level_iters = [200, 100, 50, 25] sdr = SymmetricDiffeomorphicRegistration(metric, level_iters, inv_iter = 50) """ Now we execute the optimization, which returns a DiffeomorphicMap object, that can be used to register images back and forth between the static and moving domains """ mapping = sdr.optimize(static, moving) """ It is a good idea to visualize the resulting deformation map to make sure the result is reasonable (at least, visually) """ regtools.plot_2d_diffeomorphic_map(mapping, 10, 'diffeomorphic_map.png')
def generate_warp_field(self, static, moving, static_axis_units,
moving_axis_units):
from numpy import eye
from dipy.align.imaffine import AffineRegistration
from dipy.align.transforms import (
TranslationTransform3D,
RigidTransform3D,
AffineTransform3D,
)
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration as SDR
static_g2w = eye(1 + static.ndim)
moving_g2w = static_g2w.copy()
params0 = None
static_g2w[range(static.ndim), range(static.ndim)] = static_axis_units
moving_g2w[range(moving.ndim), range(moving.ndim)] = moving_axis_units
self.affreg = AffineRegistration(
metric=self.metric_lin,
level_iters=self.level_iters_lin,
sigmas=self.sigmas,
factors=self.factors,
verbosity=self.verbosity,
ss_sigma_factor=self.ss_sigma_factor,
)
self.sdreg = SDR(
metric=self.metric_syn,
level_iters=self.level_iters_syn,
ss_sigma_factor=self.ss_sigma_factor,
)
self.translation_tx = self.affreg.optimize(
static,
moving,
TranslationTransform3D(),
params0,
static_g2w,
moving_g2w,
starting_affine="mass",
)
self.rigid_tx = self.affreg.optimize(
static,
moving,
RigidTransform3D(),
params0,
static_g2w,
moving_g2w,
starting_affine=self.translation_tx.affine,
)
self.affine_tx = self.affreg.optimize(
static,
moving,
AffineTransform3D(),
params0,
static_g2w,
moving_g2w,
starting_affine=self.rigid_tx.affine,
)
self.sdr_tx = self.sdreg.optimize(static, moving, static_g2w,
moving_g2w, self.affine_tx.affine)
class SYNreg(object):
"""
Wrap full linear + nonlinear(syn) registration, with the assumption that affine params and warp field are
estimated from spatially downsampled data.
"""
def __init__(
self,
level_iters_lin,
sigmas,
factors,
level_iters_syn,
metric_lin=None,
metric_syn=None,
ss_sigma_factor=1.0,
verbosity=0,
):
from dipy.align.metrics import CCMetric
from dipy.align.imaffine import MutualInformationMetric
self.level_iters_lin = level_iters_lin
self.sigmas = sigmas
self.factors = factors
self.level_iters_syn = level_iters_syn
self.ss_sigma_factor = ss_sigma_factor
self.verbosity = verbosity
if metric_lin is None:
nbins = 32
self.metric_lin = MutualInformationMetric(nbins, None)
if metric_syn is None:
self.metric_syn = CCMetric(3)
self.affreg = None
self.sdreg = None
self.translation_tx = None
self.rigid_tx = None
self.affine_tx = None
self.sdr_tx = None
def generate_warp_field(self, static, moving, static_axis_units,
moving_axis_units):
from numpy import eye
from dipy.align.imaffine import AffineRegistration
from dipy.align.transforms import (
TranslationTransform3D,
RigidTransform3D,
AffineTransform3D,
)
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration as SDR
static_g2w = eye(1 + static.ndim)
moving_g2w = static_g2w.copy()
params0 = None
static_g2w[range(static.ndim), range(static.ndim)] = static_axis_units
moving_g2w[range(moving.ndim), range(moving.ndim)] = moving_axis_units
self.affreg = AffineRegistration(
metric=self.metric_lin,
level_iters=self.level_iters_lin,
sigmas=self.sigmas,
factors=self.factors,
verbosity=self.verbosity,
ss_sigma_factor=self.ss_sigma_factor,
)
self.sdreg = SDR(
metric=self.metric_syn,
level_iters=self.level_iters_syn,
ss_sigma_factor=self.ss_sigma_factor,
)
self.translation_tx = self.affreg.optimize(
static,
moving,
TranslationTransform3D(),
params0,
static_g2w,
moving_g2w,
starting_affine="mass",
)
self.rigid_tx = self.affreg.optimize(
static,
moving,
RigidTransform3D(),
params0,
static_g2w,
moving_g2w,
starting_affine=self.translation_tx.affine,
)
self.affine_tx = self.affreg.optimize(
static,
moving,
AffineTransform3D(),
params0,
static_g2w,
moving_g2w,
starting_affine=self.rigid_tx.affine,
)
self.sdr_tx = self.sdreg.optimize(static, moving, static_g2w,
moving_g2w, self.affine_tx.affine)
def apply_transform(self, moving, moving_axis_units, desired_transform):
from numpy import eye
from numpy.linalg import inv
moving_g2w = eye(1 + moving.ndim)
moving_g2w[range(moving.ndim), range(moving.ndim)] = moving_axis_units
txs = dict(affine=self.affine_tx, sdr=self.sdr_tx)
tx = txs[desired_transform]
if desired_transform == "sdr":
result = tx.transform(
moving,
image_world2grid=inv(moving_g2w),
out_shape=moving.shape,
out_grid2world=moving_g2w,
)
else:
result = tx.transform(
moving,
image_grid2world=moving_g2w,
sampling_grid_shape=moving.shape,
sampling_grid2world=moving_g2w,
)
return result
import nibabel as nib from dipy.align.imwarp import SymmetricDiffeomorphicRegistration from dipy.align.metrics import CCMetric f_t1 = '/home/eleftherios/Data/reg/t1_fa.nii.gz' f_fa = '/home/eleftherios/Data/reg/fa.nii.gz' t1 = nib.load(f_t1).get_data() img = nib.load(f_fa) fa = img.get_data() fa_aff = img.get_affine() cc = CCMetric(3) sdr = SymmetricDiffeomorphicRegistration(metric=cc) sdr.verbosity = 2 sdm = sdr.optimize(static=fa, moving=t1) t1_warped = sdm.transform(t1) f_t1_warped = '/home/eleftherios/Data/reg/t1_fa_warped.nii.gz' nib.save(nib.Nifti1Image(t1_warped, fa_aff), f_t1_warped)
def warp_syn_dipy(static_fname, moving_fname):
import os
import numpy as np
import nibabel as nb
from dipy.align.metrics import CCMetric
from dipy.align.imaffine import (transform_centers_of_mass, AffineMap,
MutualInformationMetric,
AffineRegistration)
from dipy.align.transforms import (TranslationTransform3D,
RigidTransform3D, AffineTransform3D)
from dipy.align.imwarp import (DiffeomorphicMap,
SymmetricDiffeomorphicRegistration)
from nipype.utils.filemanip import fname_presuffix
static = nb.load(static_fname)
moving = nb.load(moving_fname)
c_of_mass = transform_centers_of_mass(static.get_data(), static.affine,
moving.get_data(), moving.affine)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10000, 1000, 100]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine
translation = affreg.optimize(static.get_data(),
moving.get_data(),
transform,
params0,
static.affine,
moving.affine,
starting_affine=starting_affine)
transform = RigidTransform3D()
params0 = None
starting_affine = translation.affine
rigid = affreg.optimize(static.get_data(),
moving.get_data(),
transform,
params0,
static.affine,
moving.affine,
starting_affine=starting_affine)
transform = AffineTransform3D()
params0 = None
starting_affine = rigid.affine
affine = affreg.optimize(static.get_data(),
moving.get_data(),
transform,
params0,
static.affine,
moving.affine,
starting_affine=starting_affine)
metric = CCMetric(3, sigma_diff=3.)
level_iters = [25, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
starting_affine = affine.affine
mapping = sdr.optimize(static.get_data(), moving.get_data(), static.affine,
moving.affine, starting_affine)
warped_filename = os.path.abspath(
fname_presuffix(moving_fname,
newpath='./',
suffix='_warped',
use_ext=True))
warped = nb.Nifti1Image(mapping.transform(moving.get_data()),
static.affine)
warped.to_filename(warped_filename)
warp_filename = os.path.abspath(
fname_presuffix(moving_fname,
newpath='./',
suffix='_warp.npz',
use_ext=False))
np.savez(warp_filename,
prealign=mapping.prealign,
forward=mapping.forward,
backward=mapping.backward)
return warp_filename, warped_filename
def wm_syn(template_path, fa_path, working_dir):
"""A function to perform ANTS SyN registration using dipy functions
Parameters
----------
template_path : str
File path to the template reference FA image.
fa_path : str
File path to the FA moving image (image to be fitted to reference)
working_dir : str
Path to the working directory to perform SyN and save outputs.
Returns
-------
DiffeomorphicMap
An object that can be used to register images back and forth between static (template) and moving (FA) domains
AffineMap
An object used to transform the moving (FA) image towards the static image (template)
"""
fa_img = nib.load(fa_path)
template_img = nib.load(template_path)
static = template_img.get_data()
static_affine = template_img.affine
moving = fa_img.get_data().astype(np.float32)
moving_affine = fa_img.affine
affine_map = transform_origins(static, static_affine, moving,
moving_affine)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10, 10, 5]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affine_reg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
translation = affine_reg.optimize(static, moving, transform, params0,
static_affine, moving_affine)
transform = RigidTransform3D()
rigid_map = affine_reg.optimize(
static,
moving,
transform,
params0,
static_affine,
moving_affine,
starting_affine=translation.affine,
)
transform = AffineTransform3D()
# We bump up the iterations to get a more exact fit:
affine_reg.level_iters = [1000, 1000, 100]
affine_opt = affine_reg.optimize(
static,
moving,
transform,
params0,
static_affine,
moving_affine,
starting_affine=rigid_map.affine,
)
# We now perform the non-rigid deformation using the Symmetric Diffeomorphic Registration(SyN) Algorithm:
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving, static_affine, moving_affine,
affine_opt.affine)
warped_moving = mapping.transform(moving)
# We show the registration result with:
regtools.overlay_slices(
static,
warped_moving,
None,
0,
"Static",
"Moving",
f"{working_dir}/transformed_sagittal.png",
)
regtools.overlay_slices(
static,
warped_moving,
None,
1,
"Static",
"Moving",
f"{working_dir}/transformed_coronal.png",
)
regtools.overlay_slices(
static,
warped_moving,
None,
2,
"Static",
"Moving",
f"{working_dir}/transformed_axial.png",
)
return mapping, affine_map
def ROI_registration(datapath, template, t1, b0, roi):
t1_path = datapath + '/' + t1
b0_path = datapath + '/' + b0
roi_path = datapath + '/' + roi
template_path = datapath + '/' + template
template_img, template_affine = load_nifti(template_path)
t1_img, t1_affine = load_nifti(t1_path)
b0_img, b0_affine = load_nifti(b0_path)
roi_img, roi_affine = load_nifti(roi_path)
#diff2struct affine registartion
moving = b0_img
moving_grid2world = b0_affine
static = t1_img
static_grid2world = t1_affine
affine_path = datapath + '/' + 'diff2struct_affine.mat'
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
sigmas = [3.0, 1.0, 0.0]
level_iters = [10000, 1000, 100]
factors = [4, 2, 1]
affreg_diff2struct = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = AffineTransform3D()
params0 = None
affine_diff2struct = affreg_diff2struct.optimize(static,
moving,
transform,
params0,
static_grid2world,
moving_grid2world,
starting_affine=None)
saveAffineMat(affine_diff2struct, affine_path)
# struct2standard affine registartion
moving = t1_img
moving_grid2world = t1_affine
static = template_img
static_grid2world = template_affine
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
sigmas = [3.0, 1.0, 0.0]
level_iters = [10000, 1000, 100]
factors = [4, 2, 1]
affreg_struct2standard = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = AffineTransform3D()
params0 = None
affine_struct2standard = affreg_struct2standard.optimize(
static,
moving,
transform,
params0,
static_grid2world,
moving_grid2world,
starting_affine=None)
# struct2standard SyN registartion
pre_align = affine_struct2standard.get_affine()
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving, static_grid2world,
moving_grid2world, pre_align)
warped = mapping.transform_inverse(template_img)
warped = affine_diff2struct.transform_inverse(warped)
template_diff_path = datapath + '/' + 'MNI152_diff'
save_nifti(template_diff_path, warped, b0_affine)
warped_roi = mapping.transform_inverse(roi_img)
warped_roi = affine_diff2struct.transform_inverse(warped_roi)
roi_diff_path = datapath + '/' + roi + '_diff.nii.gz'
save_nifti(roi_diff_path, warped_roi, b0_affine)
print(" Done! ")
def wm_syn(t1w_brain,
ap_path,
working_dir,
fa_path=None,
template_fa_path=None):
"""
A function to perform SyN registration
Parameters
----------
t1w_brain : str
File path to the skull-stripped T1w brain Nifti1Image.
ap_path : str
File path to the AP moving image.
working_dir : str
Path to the working directory to perform SyN and save outputs.
fa_path : str
File path to the FA moving image.
template_fa_path : str
File path to the T1w-connformed template FA reference image.
"""
import uuid
from time import strftime
from dipy.align.imaffine import (
MutualInformationMetric,
AffineRegistration,
transform_origins,
)
from dipy.align.transforms import (
TranslationTransform3D,
RigidTransform3D,
AffineTransform3D,
)
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.metrics import CCMetric
# from dipy.viz import regtools
# from nilearn.image import resample_to_img
ap_img = nib.load(ap_path)
t1w_brain_img = nib.load(t1w_brain)
static = np.asarray(t1w_brain_img.dataobj, dtype=np.float32)
static_affine = t1w_brain_img.affine
moving = np.asarray(ap_img.dataobj, dtype=np.float32)
moving_affine = ap_img.affine
affine_map = transform_origins(static, static_affine, moving,
moving_affine)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10, 10, 5]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affine_reg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
translation = affine_reg.optimize(static, moving, transform, params0,
static_affine, moving_affine)
transform = RigidTransform3D()
rigid_map = affine_reg.optimize(
static,
moving,
transform,
params0,
static_affine,
moving_affine,
starting_affine=translation.affine,
)
transform = AffineTransform3D()
# We bump up the iterations to get a more exact fit:
affine_reg.level_iters = [1000, 1000, 100]
affine_opt = affine_reg.optimize(
static,
moving,
transform,
params0,
static_affine,
moving_affine,
starting_affine=rigid_map.affine,
)
# We now perform the non-rigid deformation using the Symmetric
# Diffeomorphic Registration(SyN) Algorithm:
metric = CCMetric(3)
level_iters = [10, 10, 5]
# Refine fit
if template_fa_path is not None:
from nilearn.image import resample_to_img
fa_img = nib.load(fa_path)
template_img = nib.load(template_fa_path)
template_img_res = resample_to_img(template_img, t1w_brain_img)
static = np.asarray(template_img_res.dataobj, dtype=np.float32)
static_affine = template_img_res.affine
moving = np.asarray(fa_img.dataobj, dtype=np.float32)
moving_affine = fa_img.affine
else:
static = np.asarray(t1w_brain_img.dataobj, dtype=np.float32)
static_affine = t1w_brain_img.affine
moving = np.asarray(ap_img.dataobj, dtype=np.float32)
moving_affine = ap_img.affine
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving, static_affine, moving_affine,
affine_opt.affine)
warped_moving = mapping.transform(moving)
# Save warped FA image
run_uuid = f"{strftime('%Y%m%d_%H%M%S')}_{uuid.uuid4()}"
warped_fa = f"{working_dir}/warped_fa_{run_uuid}.nii.gz"
nib.save(nib.Nifti1Image(warped_moving, affine=static_affine), warped_fa)
# # We show the registration result with:
# regtools.overlay_slices(static, warped_moving, None, 0,
# "Static", "Moving",
# "%s%s%s%s" % (working_dir,
# "/transformed_sagittal_", run_uuid, ".png"))
# regtools.overlay_slices(static, warped_moving, None,
# 1, "Static", "Moving",
# "%s%s%s%s" % (working_dir,
# "/transformed_coronal_", run_uuid, ".png"))
# regtools.overlay_slices(static, warped_moving,
# None, 2, "Static", "Moving",
# "%s%s%s%s" % (working_dir,
# "/transformed_axial_", run_uuid, ".png"))
return mapping, affine_map, warped_fa
img = nib.load(ffa)
fa = img.get_data()
ffa_template = '/usr/share/data/fsl-mni152-templates/FMRIB58_FA_1mm.nii.gz'
img = nib.load(ffa_template)
fa_template = img.get_data()
fa = np.interp(fa, [fa.min(), fa.max()],
[fa_template.min(), fa_template.max()])
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.metrics import CCMetric
cc = CCMetric(3)
sdr = SymmetricDiffeomorphicRegistration(metric=cc)
sdr.verbosity = 2
sdm = sdr.optimize(static=fa_template, moving=fa)
fa_warped = sdm.transform(fa)
ffa_warped = '/home/eleftherios/Data/reg/fa_to_template_warped.nii.gz'
nib.save(nib.Nifti1Image(fa_warped, img.get_affine()), ffa_warped)
hardi_affine = ni.get_affine()
b0 = hardi_data[..., gtab.b0s_mask]
mean_b0 = np.mean(b0, -1)
ni_b0 = nib.Nifti1Image(mean_b0, hardi_affine)
ni_b0.to_filename('mean_b0.nii')
plt.matshow(mean_b0[:, :, mean_b0.shape[-1] // 2], cmap=cm.bone)
MNI_T2 = dpd.read_mni_template()
MNI_T2_data = MNI_T2.get_data()
MNI_T2_affine = MNI_T2.get_affine()
level_iters = [10, 10, 5]
dim = 3
metric = CCMetric(dim)
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters, step_length=0.25)
sdr.verbosity = VerbosityLevels.DIAGNOSE
mapping = sdr.optimize(MNI_T2_data, mean_b0, MNI_T2_affine, hardi_affine)
warped_b0 = mapping.transform(mean_b0)
plt.matshow(warped_b0[:, :, warped_b0.shape[-1] // 2], cmap=cm.bone)
plt.matshow(MNI_T2_data[:, :, MNI_T2_data.shape[-1] // 2], cmap=cm.bone)
new_ni = nib.Nifti1Image(warped_b0, MNI_T2_affine)
new_ni.to_filename('./warped_b0.nii.gz')
afqpath = 'D:/opt/AFQ/'
LOCC_ni = nib.load(
os.path.join(afqpath, 'templates/callosum2/L_Occipital.nii.gz'))
ROCC_ni = nib.load(
os.path.join(afqpath, 'templates/callosum2/R_Occipital.nii.gz'))
midsag_ni = nib.load(
else:
ibsr_bw_affmap = dipy_align(ibsr1, ibsr1_affine, brainweb, brainweb_affine)
pickle.dump(ibsr_bw_affmap, open(aff_name, "w"))
bw_on_ibsr1 = ibsr_bw_affmap.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=0) # aligned (sagital view)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=1) # aligned (axial view)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=2) # aligned (coronal view)
# Start diffeomorphic registration
diff_name = "ibsr1_to_brainweb_diff.p"
if os.path.isfile(diff_name):
ibsr_bw_diffmap = pickle.load(open(diff_name, "r"))
else:
metric = CCMetric(3)
level_iters = [50, 10]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
sdr.verbosity = VerbosityLevels.DEBUG
ibsr_bw_diffmap = sdr.optimize(ibsr1, brainweb, ibsr1_affine, brainweb_affine, ibsr_bw_affmap.affine)
pickle.dump(ibsr_bw_diffmap, open(diff_name, "w"))
bw_warped_ibsr1 = ibsr_bw_diffmap.transform(brainweb)
rt.overlay_slices(ibsr1, bw_warped_ibsr1, slice_type=0) # warped (sagital view)
rt.overlay_slices(ibsr1, bw_warped_ibsr1, slice_type=1) # warped (axial view)
rt.overlay_slices(ibsr1, bw_warped_ibsr1, slice_type=2) # warped (coronal view)
# Now the initial segmentation
bw_mask_ibsr1 = ibsr_bw_diffmap.transform(brainweb_mask)
bw_mask_ibsr1 = bw_mask_ibsr1 > 0
# Dilate
structure = np.ones((5, 5, 5))
def run(self, static_image_files, moving_image_files, prealign_file='',
inv_static=False, level_iters=[10, 10, 5], metric="cc",
mopt_sigma_diff=2.0, mopt_radius=4, mopt_smooth=0.0,
mopt_inner_iter=0.0, mopt_q_levels=256, mopt_double_gradient=True,
mopt_step_type='', step_length=0.25,
ss_sigma_factor=0.2, opt_tol=1e-5, inv_iter=20,
inv_tol=1e-3, out_dir='', out_warped='warped_moved.nii.gz',
out_inv_static='inc_static.nii.gz',
out_field='displacement_field.nii.gz'):
"""
Parameters
----------
static_image_files : string
Path of the static image file.
moving_image_files : string
Path to the moving image file.
prealign_file : string, optional
The text file containing pre alignment information via an
affine matrix.
inv_static : boolean, optional
Apply the inverse mapping to the static image (default 'False').
level_iters : variable int, optional
The number of iterations at each level of the gaussian pyramid.
By default, a 3-level scale space with iterations
sequence equal to [10, 10, 5] will be used. The 0-th
level corresponds to the finest resolution.
metric : string, optional
The metric to be used (Default cc, 'Cross Correlation metric').
metric available: cc (Cross Correlation), ssd (Sum Squared
Difference), em (Expectation-Maximization).
mopt_sigma_diff : float, optional
Metric option applied on Cross correlation (CC).
The standard deviation of the Gaussian smoothing kernel to be
applied to the update field at each iteration (default 2.0)
mopt_radius : int, optional
Metric option applied on Cross correlation (CC).
the radius of the squared (cubic) neighborhood at each voxel to
be considered to compute the cross correlation. (default 4)
mopt_smooth : float, optional
Metric option applied on Sum Squared Difference (SSD) and
Expectation Maximization (EM). Smoothness parameter, the
larger the value the smoother the deformation field.
(default 1.0 for EM, 4.0 for SSD)
mopt_inner_iter : int, optional
Metric option applied on Sum Squared Difference (SSD) and
Expectation Maximization (EM). This is number of iterations to be
performed at each level of the multi-resolution Gauss-Seidel
optimization algorithm (this is not the number of steps per
Gaussian Pyramid level, that parameter must be set for the
optimizer, not the metric). Default 5 for EM, 10 for SSD.
mopt_q_levels : int, optional
Metric option applied on Expectation Maximization (EM).
Number of quantization levels (Default: 256 for EM)
mopt_double_gradient : bool, optional
Metric option applied on Expectation Maximization (EM).
if True, the gradient of the expected static image under the moving
modality will be added to the gradient of the moving image,
similarly, the gradient of the expected moving image under the
static modality will be added to the gradient of the static image.
mopt_step_type : string, optional
Metric option applied on Sum Squared Difference (SSD) and
Expectation Maximization (EM). The optimization schedule to be
used in the multi-resolution Gauss-Seidel optimization algorithm
(not used if Demons Step is selected). Possible value:
('gauss_newton', 'demons'). default: 'gauss_newton' for EM,
'demons' for SSD.
step_length : float, optional
the length of the maximum displacement vector of the update
displacement field at each iteration.
ss_sigma_factor : float, optional
parameter of the scale-space smoothing kernel. For example, the
std. dev. of the kernel will be factor*(2^i) in the isotropic case
where i = 0, 1, ..., n_scales is the scale.
opt_tol : float, optional
the optimization will stop when the estimated derivative of the
energy profile w.r.t. time falls below this threshold.
inv_iter : int, optional
the number of iterations to be performed by the displacement field
inversion algorithm.
inv_tol : float, optional
the displacement field inversion algorithm will stop iterating
when the inversion error falls below this threshold.
out_dir : string, optional
Directory to save the transformed files (default '').
out_warped : string, optional
Name of the warped file. (default 'warped_moved.nii.gz').
out_inv_static : string, optional
Name of the file to save the static image after applying the
inverse mapping (default 'inv_static.nii.gz').
out_field : string, optional
Name of the file to save the diffeomorphic map.
(default 'displacement_field.nii.gz')
"""
io_it = self.get_io_iterator()
metric = metric.lower()
if metric not in ['ssd', 'cc', 'em']:
raise ValueError("Invalid similarity metric: Please"
" provide a valid metric like 'ssd', 'cc', 'em'")
logging.info("Starting Diffeormorphic Registration")
logging.info('Using {0} Metric'.format(metric.upper()))
# Init parameter if they are not setup
init_param = {'ssd': {'mopt_smooth': 4.0,
'mopt_inner_iter': 10,
'mopt_step_type': 'demons'
},
'em': {'mopt_smooth': 1.0,
'mopt_inner_iter': 5,
'mopt_step_type': 'gauss_newton'
}
}
mopt_smooth = mopt_smooth or init_param[metric]['mopt_smooth']
mopt_inner_iter = mopt_inner_iter or \
init_param[metric]['mopt_inner_iter']
mopt_step_type = mopt_step_type or \
init_param[metric]['mopt_step_type']
for (static_file, moving_file, owarped_file, oinv_static_file,
omap_file) in io_it:
logging.info('Loading static file {0}'.format(static_file))
logging.info('Loading moving file {0}'.format(moving_file))
# Loading the image data from the input files into object.
static_image, static_grid2world = load_nifti(static_file)
moving_image, moving_grid2world = load_nifti(moving_file)
# Sanity check for the input image dimensions.
check_dimensions(static_image, moving_image)
# Loading the affine matrix.
prealign = np.loadtxt(prealign_file) if prealign_file else None
l_metric = {"ssd": SSDMetric(static_image.ndim,
smooth=mopt_smooth,
inner_iter=mopt_inner_iter,
step_type=mopt_step_type
),
"cc": CCMetric(static_image.ndim,
sigma_diff=mopt_sigma_diff,
radius=mopt_radius),
"em": EMMetric(static_image.ndim,
smooth=mopt_smooth,
inner_iter=mopt_inner_iter,
step_type=mopt_step_type,
q_levels=mopt_q_levels,
double_gradient=mopt_double_gradient)
}
current_metric = l_metric.get(metric.lower())
sdr = SymmetricDiffeomorphicRegistration(
metric=current_metric,
level_iters=level_iters,
step_length=step_length,
ss_sigma_factor=ss_sigma_factor,
opt_tol=opt_tol,
inv_iter=inv_iter,
inv_tol=inv_tol
)
mapping = sdr.optimize(static_image, moving_image,
static_grid2world, moving_grid2world,
prealign)
mapping_data = np.array([mapping.forward.T, mapping.backward.T]).T
warped_moving = mapping.transform(moving_image)
# Saving
logging.info('Saving warped {0}'.format(owarped_file))
save_nifti(owarped_file, warped_moving, static_grid2world)
logging.info('Saving Diffeormorphic map {0}'.format(omap_file))
save_nifti(omap_file, mapping_data, mapping.codomain_world2grid)
def register_save(inputpathdir, target_path, subject, outputpath, figspath,
params, registration_types, applydirs, verbose):
anat_path = get_anat(inputpathdir, subject)
#myanat = load_nifti(anat_path)
myanat = nib.load(anat_path)
anat_data = np.squeeze(myanat.get_data()[..., 0])
anat_affine = myanat.affine
anat_hdr = myanat.header
vox_size = myanat.header.get_zooms()[0]
#mynifti = load_nifti("/Volumes/Data/Badea/Lab/19abb14/N57437_nii4D.nii")
#anat_data = np.squeeze(myanat[0])[..., 0]
#anat_affine = myanat[1]
#hdr = myanat.header
mytarget = nib.load(target_path)
target_data = np.squeeze(mytarget.get_data()[..., 0])
target_affine = mytarget.affine
identity = np.eye(4)
affine_map = AffineMap(identity, target_data.shape, target_affine,
anat_data.shape, anat_affine)
resampled = affine_map.transform(anat_data)
"""
regtools.overlay_slices(target_data, resampled, None, 0,
"target_data", "anat_data", figspath + "resampled_0.png")
regtools.overlay_slices(target_data, resampled, None, 1,
"target_data", "anat_data", figspath + "resampled_1.png")
regtools.overlay_slices(target_data, resampled, None, 2,
"target_data", "anat_data", figspath + "resampled_2.png")
"""
c_of_mass = transform_centers_of_mass(target_data, target_affine,
anat_data, anat_affine)
apply_niftis = []
apply_trks = []
if inputpathdir in applydirs:
applyfiles = [anat_path]
else:
applyfiles = []
for applydir in applydirs:
apply_niftis.extend(get_niftis(applydir, subject))
apply_trks.extend(get_trks(applydir, subject))
if "center_mass" in registration_types:
if apply_trks:
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(target_data, anat_data, target_affine,
anat_affine, c_of_mass.affine)
for apply_nifti in apply_niftis:
fname = os.path.basename(apply_nifti).split(".")[0]
fpath = outputpath + fname + "_centermass.nii"
applynii = nib.load(apply_nifti)
apply_data = applynii.get_data()
apply_affine = applynii.affine
apply_hdr = myanat.header
if len(np.shape(apply_data)) == 4:
transformed_all = c_of_mass.transform(apply_data, apply4D=True)
transformed = transformed_all[:, :, :, 0]
else:
transformed_all = c_of_mass.transform(apply_data)
transformed = transformed_all
save_nifti(fpath, transformed_all, apply_affine, hdr=apply_hdr)
if figspath is not None:
regtools.overlay_slices(target_data, transformed, None, 0,
"target_data", "Transformed",
figspath + fname + "_centermass_1.png")
regtools.overlay_slices(target_data, transformed, None, 1,
"target_data", "Transformed",
figspath + fname + "_centermass_2.png")
regtools.overlay_slices(target_data, transformed, None, 2,
"target_data", "Transformed",
figspath + fname + "_centermass_3.png")
if verbose:
print("Saved the file at " + fpath)
#mapping = sdr.optimize(target_data, anat_data, target_affine, anat_affine,
# c_of_mass.affine)
#warped_moving = mapping.transform(anat_data)
for apply_trk in apply_trks:
fname = os.path.basename(apply_trk).split(".")[0]
fpath = outputpath + fname + "_centermass.trk"
sft = load_tractogram(apply_trk, 'same')
target_isocenter = np.diag(
np.array([-vox_size, vox_size, vox_size, 1]))
origin_affine = affine_map.affine.copy()
origin_affine[0][3] = -origin_affine[0][3]
origin_affine[1][3] = -origin_affine[1][3]
origin_affine[2][3] = origin_affine[2][3] / vox_size
origin_affine[1][3] = origin_affine[1][3] / vox_size**2
# Apply the deformation and correct for the extents
mni_streamlines = deform_streamlines(
sft.streamlines,
deform_field=mapping.get_forward_field(),
stream_to_current_grid=target_isocenter,
current_grid_to_world=origin_affine,
stream_to_ref_grid=target_isocenter,
ref_grid_to_world=np.eye(4))
if has_fury:
show_template_bundles(mni_streamlines,
anat_data,
show=False,
fname=figspath + fname +
'_streamlines_centermass.png')
sft = StatefulTractogram(mni_streamlines, myanat, Space.RASMM)
save_tractogram(sft, fpath, bbox_valid_check=False)
if verbose:
print("Saved the file at " + fpath)
metric = MutualInformationMetric(params.nbins, params.sampling_prop)
if "AffineRegistration" in registration_types:
affreg = AffineRegistration(metric=metric,
level_iters=params.level_iters,
sigmas=params.sigmas,
factors=params.factors)
transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine
translation = affreg.optimize(target_data,
anat_data,
transform,
params0,
target_affine,
anat_affine,
starting_affine=starting_affine)
if apply_trks:
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(target_data, anat_data, target_affine,
anat_affine, translation.affine)
for apply_nifti in apply_niftis:
fname = os.path.basename(apply_nifti).split(".")[0]
fpath = outputpath + fname + "_affinereg.nii"
applynii = nib.load(apply_nifti)
apply_data = applynii.get_data()
apply_affine = applynii.affine
apply_hdr = myanat.header
if len(np.shape(apply_data)) == 4:
transformed_all = translation.transform(apply_data,
apply4D=True)
transformed = transformed_all[:, :, :, 0]
else:
transformed_all = translation.transform(apply_data)
transformed = transformed_all
save_nifti(fpath, transformed_all, anat_affine, hdr=anat_hdr)
if figspath is not None:
regtools.overlay_slices(target_data, transformed, None, 0,
"target_data", "Transformed",
figspath + fname + "_affinereg_1.png")
regtools.overlay_slices(target_data, transformed, None, 1,
"target_data", "Transformed",
figspath + fname + "_affinereg_2.png")
regtools.overlay_slices(target_data, transformed, None, 2,
"target_data", "Transformed",
figspath + fname + "_affinereg_3.png")
if verbose:
print("Saved the file at " + fpath)
for apply_trk in apply_trks:
fname = os.path.basename(apply_trk).split(".")[0]
fpath = outputpath + fname + "_affinereg.trk"
sft = load_tractogram(apply_trk, 'same')
target_isocenter = np.diag(
np.array([-vox_size, vox_size, vox_size, 1]))
origin_affine = affine_map.affine.copy()
origin_affine[0][3] = -origin_affine[0][3]
origin_affine[1][3] = -origin_affine[1][3]
origin_affine[2][3] = origin_affine[2][3] / vox_size
origin_affine[1][3] = origin_affine[1][3] / vox_size**2
# Apply the deformation and correct for the extents
mni_streamlines = deform_streamlines(
sft.streamlines,
deform_field=mapping.get_forward_field(),
stream_to_current_grid=target_isocenter,
current_grid_to_world=origin_affine,
stream_to_ref_grid=target_isocenter,
ref_grid_to_world=np.eye(4))
if has_fury:
show_template_bundles(mni_streamlines,
anat_data,
show=False,
fname=figspath + fname +
'_streamlines_affinereg.png')
sft = StatefulTractogram(mni_streamlines, myanat, Space.RASMM)
save_tractogram(sft, fpath, bbox_valid_check=False)
if verbose:
print("Saved the file at " + fpath)
if "RigidTransform3D" in registration_types:
transform = RigidTransform3D()
params0 = None
if 'translation' not in locals():
affreg = AffineRegistration(metric=metric,
level_iters=params.level_iters,
sigmas=params.sigmas,
factors=params.factors)
translation = affreg.optimize(target_data,
anat_data,
transform,
params0,
target_affine,
anat_affine,
starting_affine=c_of_mass.affine)
starting_affine = translation.affine
rigid = affreg.optimize(target_data,
anat_data,
transform,
params0,
target_affine,
anat_affine,
starting_affine=starting_affine)
transformed = rigid.transform(anat_data)
if apply_trks:
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(target_data, anat_data, target_affine,
anat_affine, rigid.affine)
for apply_nifti in apply_niftis:
fname = os.path.basename(apply_nifti).split(".")[0]
fpath = outputpath + fname + "_rigidtransf3d.nii"
applynii = nib.load(apply_nifti)
apply_data = applynii.get_data()
apply_affine = applynii.affine
apply_hdr = myanat.header
if len(np.shape(apply_data)) == 4:
transformed_all = rigid.transform(apply_data, apply4D=True)
transformed = transformed_all[:, :, :, 0]
else:
transformed_all = rigid.transform(apply_data)
transformed = transformed_all
save_nifti(fpath, transformed_all, anat_affine, hdr=anat_hdr)
if figspath is not None:
regtools.overlay_slices(
target_data, transformed, None, 0, "target_data",
"Transformed", figspath + fname + "_rigidtransf3d_1.png")
regtools.overlay_slices(
target_data, transformed, None, 1, "target_data",
"Transformed", figspath + fname + "_rigidtransf3d_2.png")
regtools.overlay_slices(
target_data, transformed, None, 2, "target_data",
"Transformed", figspath + fname + "_rigidtransf3d_3.png")
if verbose:
print("Saved the file at " + fpath)
for apply_trk in apply_trks:
fname = os.path.basename(apply_trk).split(".")[0]
fpath = outputpath + fname + "_rigidtransf3d.trk"
sft = load_tractogram(apply_trk, 'same')
target_isocenter = np.diag(
np.array([-vox_size, vox_size, vox_size, 1]))
origin_affine = affine_map.affine.copy()
origin_affine[0][3] = -origin_affine[0][3]
origin_affine[1][3] = -origin_affine[1][3]
origin_affine[2][3] = origin_affine[2][3] / vox_size
origin_affine[1][3] = origin_affine[1][3] / vox_size**2
# Apply the deformation and correct for the extents
mni_streamlines = deform_streamlines(
sft.streamlines,
deform_field=mapping.get_forward_field(),
stream_to_current_grid=target_isocenter,
current_grid_to_world=origin_affine,
stream_to_ref_grid=target_isocenter,
ref_grid_to_world=np.eye(4))
if has_fury:
show_template_bundles(mni_streamlines,
anat_data,
show=False,
fname=figspath + fname +
'_rigidtransf3d.png')
sft = StatefulTractogram(mni_streamlines, myanat, Space.RASMM)
save_tractogram(sft, fpath, bbox_valid_check=False)
if verbose:
print("Saved the file at " + fpath)
if "AffineTransform3D" in registration_types:
transform = AffineTransform3D()
params0 = None
starting_affine = rigid.affine
affine = affreg.optimize(target_data,
anat_data,
transform,
params0,
target_affine,
anat_affine,
starting_affine=starting_affine)
transformed = affine.transform(anat_data)
if apply_trks:
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(target_data, anat_data, target_affine,
anat_affine, affine.affine)
for apply_nifti in apply_niftis:
fname = os.path.basename(apply_nifti).split(".")[0]
fpath = outputpath + fname + "_affinetransf3d.nii"
applynii = nib.load(apply_nifti)
apply_data = applynii.get_data()
apply_affine = applynii.affine
apply_hdr = myanat.header
if len(np.shape(apply_data)) == 4:
transformed_all = affine.transform(apply_data, apply4D=True)
transformed = transformed_all[:, :, :, 0]
else:
transformed_all = affine.transform(apply_data)
transformed = transformed_all
save_nifti(fpath, transformed_all, anat_affine, hdr=anat_hdr)
if figspath is not None:
regtools.overlay_slices(
target_data, transformed, None, 0, "target_data",
"Transformed", figspath + fname + "_affinetransf3d_1.png")
regtools.overlay_slices(
target_data, transformed, None, 1, "target_data",
"Transformed", figspath + fname + "_affinetransf3d_2.png")
regtools.overlay_slices(
target_data, transformed, None, 2, "target_data",
"Transformed", figspath + fname + "_affinetransf3d_3.png")
if verbose:
print("Saved the file at " + fpath)
for apply_trk in apply_trks:
fname = os.path.basename(apply_trk).split(".")[0]
fpath = outputpath + fname + "_affinetransf3d.trk"
sft = load_tractogram(apply_trk, 'same')
target_isocenter = np.diag(
np.array([-vox_size, vox_size, vox_size, 1]))
origin_affine = affine_map.affine.copy()
origin_affine[0][3] = -origin_affine[0][3]
origin_affine[1][3] = -origin_affine[1][3]
origin_affine[2][3] = origin_affine[2][3] / vox_size
origin_affine[1][3] = origin_affine[1][3] / vox_size**2
# Apply the deformation and correct for the extents
mni_streamlines = deform_streamlines(
sft.streamlines,
deform_field=mapping.get_forward_field(),
stream_to_current_grid=target_isocenter,
current_grid_to_world=origin_affine,
stream_to_ref_grid=target_isocenter,
ref_grid_to_world=np.eye(4))
if has_fury:
show_template_bundles(mni_streamlines,
anat_data,
show=False,
fname=figspath + fname +
'_streamlines_affinetransf3d.png')
sft = StatefulTractogram(mni_streamlines, myanat, Space.RASMM)
save_tractogram(sft, fpath, bbox_valid_check=False)
if verbose:
print("Saved the file at " + fpath)
def run(self,
static_image_files,
moving_image_files,
prealign_file='',
inv_static=False,
level_iters=[10, 10, 5],
metric="cc",
mopt_sigma_diff=2.0,
mopt_radius=4,
mopt_smooth=0.0,
mopt_inner_iter=0.0,
mopt_q_levels=256,
mopt_double_gradient=True,
mopt_step_type='',
step_length=0.25,
ss_sigma_factor=0.2,
opt_tol=1e-5,
inv_iter=20,
inv_tol=1e-3,
out_dir='',
out_warped='warped_moved.nii.gz',
out_inv_static='inc_static.nii.gz',
out_field='displacement_field.nii.gz'):
"""
Parameters
----------
static_image_files : string
Path of the static image file.
moving_image_files : string
Path to the moving image file.
prealign_file : string, optional
The text file containing pre alignment information via an
affine matrix.
inv_static : boolean, optional
Apply the inverse mapping to the static image (default 'False').
level_iters : variable int, optional
The number of iterations at each level of the gaussian pyramid.
By default, a 3-level scale space with iterations
sequence equal to [10, 10, 5] will be used. The 0-th
level corresponds to the finest resolution.
metric : string, optional
The metric to be used (Default cc, 'Cross Correlation metric').
metric available: cc (Cross Correlation), ssd (Sum Squared
Difference), em (Expectation-Maximization).
mopt_sigma_diff : float, optional
Metric option applied on Cross correlation (CC).
The standard deviation of the Gaussian smoothing kernel to be
applied to the update field at each iteration (default 2.0)
mopt_radius : int, optional
Metric option applied on Cross correlation (CC).
the radius of the squared (cubic) neighborhood at each voxel to
be considered to compute the cross correlation. (default 4)
mopt_smooth : float, optional
Metric option applied on Sum Squared Difference (SSD) and
Expectation Maximization (EM). Smoothness parameter, the
larger the value the smoother the deformation field.
(default 1.0 for EM, 4.0 for SSD)
mopt_inner_iter : int, optional
Metric option applied on Sum Squared Difference (SSD) and
Expectation Maximization (EM). This is number of iterations to be
performed at each level of the multi-resolution Gauss-Seidel
optimization algorithm (this is not the number of steps per
Gaussian Pyramid level, that parameter must be set for the
optimizer, not the metric). Default 5 for EM, 10 for SSD.
mopt_q_levels : int, optional
Metric option applied on Expectation Maximization (EM).
Number of quantization levels (Default: 256 for EM)
mopt_double_gradient : bool, optional
Metric option applied on Expectation Maximization (EM).
if True, the gradient of the expected static image under the moving
modality will be added to the gradient of the moving image,
similarly, the gradient of the expected moving image under the
static modality will be added to the gradient of the static image.
mopt_step_type : string, optional
Metric option applied on Sum Squared Difference (SSD) and
Expectation Maximization (EM). The optimization schedule to be
used in the multi-resolution Gauss-Seidel optimization algorithm
(not used if Demons Step is selected). Possible value:
('gauss_newton', 'demons'). default: 'gauss_newton' for EM,
'demons' for SSD.
step_length : float, optional
the length of the maximum displacement vector of the update
displacement field at each iteration.
ss_sigma_factor : float, optional
parameter of the scale-space smoothing kernel. For example, the
std. dev. of the kernel will be factor*(2^i) in the isotropic case
where i = 0, 1, ..., n_scales is the scale.
opt_tol : float, optional
the optimization will stop when the estimated derivative of the
energy profile w.r.t. time falls below this threshold.
inv_iter : int, optional
the number of iterations to be performed by the displacement field
inversion algorithm.
inv_tol : float, optional
the displacement field inversion algorithm will stop iterating
when the inversion error falls below this threshold.
out_dir : string, optional
Directory to save the transformed files (default '').
out_warped : string, optional
Name of the warped file. (default 'warped_moved.nii.gz').
out_inv_static : string, optional
Name of the file to save the static image after applying the
inverse mapping (default 'inv_static.nii.gz').
out_field : string, optional
Name of the file to save the diffeomorphic map.
(default 'displacement_field.nii.gz')
"""
io_it = self.get_io_iterator()
metric = metric.lower()
if metric not in ['ssd', 'cc', 'em']:
raise ValueError("Invalid similarity metric: Please"
" provide a valid metric like 'ssd', 'cc', 'em'")
logging.info("Starting Diffeomorphic Registration")
logging.info('Using {0} Metric'.format(metric.upper()))
# Init parameter if they are not setup
init_param = {
'ssd': {
'mopt_smooth': 4.0,
'mopt_inner_iter': 10,
'mopt_step_type': 'demons'
},
'em': {
'mopt_smooth': 1.0,
'mopt_inner_iter': 5,
'mopt_step_type': 'gauss_newton'
}
}
mopt_smooth = mopt_smooth or init_param[metric]['mopt_smooth']
mopt_inner_iter = mopt_inner_iter or \
init_param[metric]['mopt_inner_iter']
mopt_step_type = mopt_step_type or \
init_param[metric]['mopt_step_type']
for (static_file, moving_file, owarped_file, oinv_static_file,
omap_file) in io_it:
logging.info('Loading static file {0}'.format(static_file))
logging.info('Loading moving file {0}'.format(moving_file))
# Loading the image data from the input files into object.
static_image, static_grid2world = load_nifti(static_file)
moving_image, moving_grid2world = load_nifti(moving_file)
# Sanity check for the input image dimensions.
check_dimensions(static_image, moving_image)
# Loading the affine matrix.
prealign = np.loadtxt(prealign_file) if prealign_file else None
l_metric = {
"ssd":
SSDMetric(static_image.ndim,
smooth=mopt_smooth,
inner_iter=mopt_inner_iter,
step_type=mopt_step_type),
"cc":
CCMetric(static_image.ndim,
sigma_diff=mopt_sigma_diff,
radius=mopt_radius),
"em":
EMMetric(static_image.ndim,
smooth=mopt_smooth,
inner_iter=mopt_inner_iter,
step_type=mopt_step_type,
q_levels=mopt_q_levels,
double_gradient=mopt_double_gradient)
}
current_metric = l_metric.get(metric.lower())
sdr = SymmetricDiffeomorphicRegistration(
metric=current_metric,
level_iters=level_iters,
step_length=step_length,
ss_sigma_factor=ss_sigma_factor,
opt_tol=opt_tol,
inv_iter=inv_iter,
inv_tol=inv_tol)
mapping = sdr.optimize(static_image, moving_image,
static_grid2world, moving_grid2world,
prealign)
mapping_data = np.array([mapping.forward.T, mapping.backward.T]).T
warped_moving = mapping.transform(moving_image)
# Saving
logging.info('Saving warped {0}'.format(owarped_file))
save_nifti(owarped_file, warped_moving, static_grid2world)
logging.info('Saving Diffeomorphic map {0}'.format(omap_file))
save_nifti(omap_file, mapping_data, mapping.codomain_world2grid)
-ref ' + template_path + ' \
-out ' + input_skull_flirted_path + ' \
-init ' + input_flirt_path + ' \
-verbose 0')
input_skull_flirted_image = nib.load(input_skull_flirted_path)
input_skull_flirted = input_skull_flirted_image.get_fdata()
else:
print('without skull processing')
input_skull_flirted = input_flirted
# SyN
# metric = SSDMetric(3)
# metric = EMMetric(3)
metric = CCMetric(3)
level_iters = [10, 10, 5, 5, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(
static=template,
moving=input_skull_flirted,
static_grid2world=template_image.get_qform(),
moving_grid2world=input_flirted_image.get_qform())
with open(input_flirted_syn_path, 'wb') as f:
dump([mapping, metric, level_iters, sdr],
f,
protocol=4,
compression='gzip')
forw_field = mapping.get_forward_field()
back_field = mapping.get_backward_field()
forw_SS = np.sum(np.power(forw_field, 2))
# allen template flirted cropping
allen_template_flirted_cropped, crop_index = zeroPadImage(
allen_template_flirted, allen_template_flirted, 0.1)
allen_template_flirted_cropped_image = nib.Nifti1Image(
allen_template_flirted_cropped, allen_template_flirted_image.affine)
allen_template_flirted_cropped_path = allen_template_flirted_path.split(
'.')[0] + '_cropped.nii.gz'
print(allen_template_flirted_cropped_path)
nib.save(allen_template_flirted_cropped_image,
allen_template_flirted_cropped_path)
# SyN flirted images to AMBMC
print('SyN')
metric = CCMetric(3)
level_iters = [10, 10, 5, 5, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(
static=AMBMC_template_zeropadded,
moving=allen_template_flirted,
static_grid2world=AMBMC_template_zeropadded_image.get_qform(),
moving_grid2world=allen_template_flirted_image.get_qform())
with open(allen_template_flirted_syn_path, 'wb') as f:
dump([mapping, metric, level_iters, sdr],
f,
protocol=4,
compression='gzip')
# with open(allen_template_flirted_syn_path, 'rb') as f:
# [mapping, metric, level_iters, sdr] = load(f, compression='gzip')
forw_field = mapping.get_forward_field()
back_field = mapping.get_backward_field()
def align_atlas():
neo_fname = get_neobrain('train', 1, 'T2')
neo_nib = nib.load(neo_fname)
neo = neo_nib.get_data()
neo_affine = neo_nib.get_affine()
# Load atlas (with skull)
atlas_fname = get_neobrain('atlas', 'neo-withSkull', None)
atlas_nib = nib.load(atlas_fname)
atlas = atlas_nib.get_data()
atlas_affine = atlas_nib.get_affine()
# The first training volume dimensions are about 5cm x 5cm x 8cm
# The atlas dimensions are about 7cm x 9cm x 11 cm
# Assuming isotropic scale, the atlas is about 1.5 times larger than
# the input image:
iso_scale = (float(7*9*11)/float(5*5*8))**(1.0/3)
print(iso_scale)
#We can use this to constraint the transformation to rigid
scale = np.eye(4)
scale[:3,:3] *= iso_scale
rigid_map_fname = 'atlas_towards_neo1_rigid.p'
if os.path.isfile(rigid_map_fname):
rigid_map = pickle.load(open(rigid_map_fname, 'r'))
else:
transforms = ['RIGID']
rigid_map = dipy_align(neo, neo_affine, atlas, atlas_affine,
transforms=transforms, prealign=scale)
pickle.dump(rigid_map, open(rigid_map_fname, 'w'))
atlas_resampled = rigid_map.transform(atlas)
# Compare anterior coronal slices
rt.overlay_slices(neo, atlas_resampled, slice_type=2, slice_index=10, ltitle='Neo1', rtitle='Atlas');
# Compare middle coronal slices
rt.overlay_slices(neo, atlas_resampled, slice_type=2, slice_index=25, ltitle='Neo1', rtitle='Atlas');
# Compare posterior coronal slices
rt.overlay_slices(neo, atlas_resampled, slice_type=2, slice_index=40, ltitle='Neo1', rtitle='Atlas');
# Load the peeled atlas
atlas_wcerebellum_fname = get_neobrain('atlas', 'neo-withCerebellum', None)
atlas_wcerebellum_nib = nib.load(atlas_wcerebellum_fname)
atlas_wcerebellum = atlas_wcerebellum_nib.get_data()
atlas_wcerebellum_affine = atlas_wcerebellum_nib.get_affine()
# Configure diffeomorphic registration
diff_map_name = 'atlas_towards_neo1_diff.p'
if os.path.isfile(diff_map_name):
diff_map = pickle.load(open(diff_map_name, 'r'))
else:
metric = CCMetric(3)
sdr = SymmetricDiffeomorphicRegistration(metric)
# The atlases are not aligned in physical space!! use atlas_affine instead of atlas_wcerebellum_affine
diff_map = sdr.optimize(neo, atlas_wcerebellum, neo_affine, atlas_affine, prealign=rigid_map.affine)
pickle.dump(diff_map, open(diff_map_name, 'w'))
atlas_wcerebellum_deformed = diff_map.transform(atlas_wcerebellum)
# Before and after diffeomorphic registration
rt.overlay_slices(neo, atlas_resampled, slice_type=2, slice_index=10, ltitle='Neo1', rtitle='Atlas');
rt.overlay_slices(neo, atlas_wcerebellum_deformed, slice_type=2, slice_index=10, ltitle='Neo1', rtitle='Atlas');
# Before and after diffeomorphic registration
rt.overlay_slices(neo, atlas_resampled, slice_type=2, slice_index=25, ltitle='Neo1', rtitle='Atlas');
rt.overlay_slices(neo, atlas_wcerebellum_deformed, slice_type=2, slice_index=25, ltitle='Neo1', rtitle='Atlas');
# Before and after diffeomorphic registration
rt.overlay_slices(neo, atlas_resampled, slice_type=2, slice_index=40, ltitle='Neo1', rtitle='Atlas');
rt.overlay_slices(neo, atlas_wcerebellum_deformed, slice_type=2, slice_index=40, ltitle='Neo1', rtitle='Atlas');
# Now all volumes
atlas_fname = get_neobrain('atlas', 'neo-withSkull', None)
atlas_nib = nib.load(atlas_fname)
atlas = atlas_nib.get_data()
atlas_affine = atlas_nib.get_affine()
atlas_wcerebellum_fname = get_neobrain('atlas', 'neo-withCerebellum', None)
atlas_wcerebellum_nib = nib.load(atlas_wcerebellum_fname)
atlas_wcerebellum = atlas_wcerebellum_nib.get_data()
atlas_wcerebellum_affine = atlas_wcerebellum_nib.get_affine()
idx = 2
neoi_fname = get_neobrain('train', idx, 'T2')
neoi_nib = nib.load(neoi_fname)
neoi = neoi_nib.get_data()
neoi_affine = neoi_nib.get_affine()
iso_scale = (float(7*9*11)/float(5*5*8))**(1.0/3)
print(iso_scale)
#We can use this to constraint the transformation to rigid
scale = np.eye(4)
scale[:3,:3] *= iso_scale
rigid_map_fname = 'atlas_towards_neo%d_affine.p'%(idx,)
if os.path.isfile(rigid_map_fname):
rigid_map = pickle.load(open(rigid_map_fname, 'r'))
else:
transforms = ['RIGID', 'AFFINE']
level_iters = [[10000, 1000, 100], [100]]
rigid_map = dipy_align(neoi, neoi_affine, atlas, atlas_affine,
transforms=transforms,
level_iters=level_iters,
prealign=scale)
pickle.dump(rigid_map, open(rigid_map_fname, 'w'))
atlas_resampled = rigid_map.transform(atlas)
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index = 6)
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index = 10)
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index = 25)
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index = 40)
diff_map_name = 'atlas_towards_neo%d_diff.p'%(idx,)
if os.path.isfile(diff_map_name):
diff_map = pickle.load(open(diff_map_name, 'r'))
else:
metric = CCMetric(3)
sdr = SymmetricDiffeomorphicRegistration(metric)
# The atlases are not aligned in physical space!! use atlas_affine instead of atlas_wcerebellum_affine
diff_map = sdr.optimize(neoi, atlas_wcerebellum, neoi_affine, atlas_affine, prealign=rigid_map.affine)
pickle.dump(diff_map, open(diff_map_name, 'w'))
atlas_wcerebellum_deformed = diff_map.transform(atlas_wcerebellum)
# Before and after diffeomorphic registration
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index=6, ltitle='Neo%d'%(idx,), rtitle='Atlas');
rt.overlay_slices(neoi, atlas_wcerebellum_deformed, slice_type=2, slice_index=6, ltitle='Neo%d'%(idx,), rtitle='Atlas');
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index=10, ltitle='Neo%d'%(idx,), rtitle='Atlas');
rt.overlay_slices(neoi, atlas_wcerebellum_deformed, slice_type=2, slice_index=10, ltitle='Neo%d'%(idx,), rtitle='Atlas');
# Before and after diffeomorphic registration
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index=25, ltitle='Neo%d'%(idx,), rtitle='Atlas');
rt.overlay_slices(neoi, atlas_wcerebellum_deformed, slice_type=2, slice_index=25, ltitle='Neo%d'%(idx,), rtitle='Atlas');
# Before and after diffeomorphic registration
rt.overlay_slices(neoi, atlas_resampled, slice_type=2, slice_index=40, ltitle='Neo%d'%(idx,), rtitle='Atlas');
rt.overlay_slices(neoi, atlas_wcerebellum_deformed, slice_type=2, slice_index=40, ltitle='Neo%d'%(idx,), rtitle='Atlas');
moving_affine,
starting_affine=rigid_map.affine)
transformed = highres_map.transform(moving)
"""
We now perform the non-rigid deformation using the Symmetric Diffeomorphic
Registration (SyN) Algorithm proposed by Avants et al. [Avants09]_ (also
implemented in the ANTs software [Avants11]_):
"""
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.metrics import CCMetric
metric = CCMetric(3)
level_iters = [10, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
mapping = sdr.optimize(static, moving, static_affine, moving_affine,
highres_map.affine)
warped_moving = mapping.transform(moving)
"""
We show the registration result with:
"""
from dipy.viz import regtools
regtools.overlay_slices(static, warped_moving, None, 0, 'Static', 'Moving',
'transformed_sagittal.png')
regtools.overlay_slices(static, warped_moving, None, 1, 'Static', 'Moving',
'transformed_coronal.png')
"""
.. figure:: input.png
:align: center
Input images before alignment.
"""
"""
Let's use the general Registration function with some naive parameters,
such as set `step_length` as 1 assuming maximal step 1 pixel and a reasonably
small number of iterations since the deformation with already aligned images
should be minimal.
"""
sdr = SymmetricDiffeomorphicRegistration(metric=SSDMetric(img_ref.ndim),
step_length=1.0,
level_iters=[50, 100],
inv_iter=50,
ss_sigma_factor=0.1,
opt_tol=1.e-3)
"""
Perform the registration with equal images.
"""
mapping = sdr.optimize(img_ref.astype(float), img_ref.astype(float))
img_warp = mapping.transform(img_ref, 'linear')
show_images(img_ref, img_warp, 'output-0')
regtools.plot_2d_diffeomorphic_map(mapping, 5, 'map-0.png')
"""
.. figure:: output-0.png
:align: center
.. figure:: map-0.png
:align: center
def syn_registration(moving,
static,
moving_affine=None,
static_affine=None,
step_length=0.25,
metric='CC',
dim=3,
level_iters=None,
prealign=None,
**metric_kwargs):
"""Register a 2D/3D source image (moving) to a 2D/3D target image (static).
Parameters
----------
moving, static : array or nib.Nifti1Image or str.
Either as a 2D/3D array or as a nifti image object, or as
a string containing the full path to a nifti file.
moving_affine, static_affine : 4x4 array, optional.
Must be provided for `data` provided as an array. If provided together
with Nifti1Image or str `data`, this input will over-ride the affine
that is stored in the `data` input. Default: use the affine stored
in `data`.
metric : string, optional
The metric to be optimized. One of `CC`, `EM`, `SSD`,
Default: 'CC' => CCMetric.
dim: int (either 2 or 3), optional
The dimensions of the image domain. Default: 3
level_iters : list of int, optional
the number of iterations at each level of the Gaussian Pyramid (the
length of the list defines the number of pyramid levels to be
used). Default: [10, 10, 5].
metric_kwargs : dict, optional
Parameters for initialization of the metric object. If not provided,
uses the default settings of each metric.
Returns
-------
warped_moving : ndarray
The data in `moving`, warped towards the `static` data.
forward : ndarray (..., 3)
The vector field describing the forward warping from the source to the
target.
backward : ndarray (..., 3)
The vector field describing the backward warping from the target to the
source.
"""
level_iters = level_iters or [10, 10, 5]
static, static_affine, moving, moving_affine, _ = \
_handle_pipeline_inputs(moving, static,
moving_affine=moving_affine,
static_affine=static_affine,
starting_affine=None)
use_metric = syn_metric_dict[metric.upper()](dim, **metric_kwargs)
sdr = SymmetricDiffeomorphicRegistration(use_metric,
level_iters,
step_length=step_length)
mapping = sdr.optimize(static,
moving,
static_grid2world=static_affine,
moving_grid2world=moving_affine,
prealign=prealign)
warped_moving = mapping.transform(moving)
return warped_moving, mapping
def warp_syn_dipy(static_fname, moving_fname):
import os
import numpy as np
import nibabel as nb
from dipy.align.metrics import CCMetric
from dipy.align.imaffine import (transform_centers_of_mass,
AffineMap,
MutualInformationMetric,
AffineRegistration)
from dipy.align.transforms import (TranslationTransform3D,
RigidTransform3D,
AffineTransform3D)
from dipy.align.imwarp import (DiffeomorphicMap,
SymmetricDiffeomorphicRegistration)
from nipype.utils.filemanip import fname_presuffix
static = nb.load(static_fname)
moving = nb.load(moving_fname)
c_of_mass = transform_centers_of_mass(static.get_data(), static.affine,
moving.get_data(), moving.affine)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10000, 1000, 100]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine
translation = affreg.optimize(static.get_data(), moving.get_data(),
transform, params0,
static.affine, moving.affine,
starting_affine=starting_affine)
transform = RigidTransform3D()
params0 = None
starting_affine = translation.affine
rigid = affreg.optimize(static.get_data(), moving.get_data(), transform, params0,
static.affine, moving.affine,
starting_affine=starting_affine)
transform = AffineTransform3D()
params0 = None
starting_affine = rigid.affine
affine = affreg.optimize(static.get_data(), moving.get_data(), transform, params0,
static.affine, moving.affine,
starting_affine=starting_affine)
metric = CCMetric(3, sigma_diff=3.)
level_iters = [25, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
starting_affine = affine.affine
mapping = sdr.optimize(
static.get_data(), moving.get_data(),
static.affine, moving.affine,
starting_affine)
warped_filename = os.path.abspath(fname_presuffix(moving_fname, newpath='./', suffix='_warped', use_ext=True))
warped = nb.Nifti1Image(mapping.transform(moving.get_data()), static.affine)
warped.to_filename(warped_filename)
warp_filename = os.path.abspath(fname_presuffix(moving_fname, newpath='./', suffix='_warp.npz', use_ext=False))
np.savez(warp_filename,prealign=mapping.prealign,forward=mapping.forward,backward=mapping.backward)
return warp_filename, warped_filename
