Registration¶
- ants.registration(fixed, moving, type_of_transform='SyN', initial_transform=None, outprefix='', mask=None, moving_mask=None, mask_all_stages=False, grad_step=0.2, flow_sigma=3, total_sigma=0, aff_metric='mattes', aff_sampling=32, aff_random_sampling_rate=0.2, syn_metric='mattes', syn_sampling=32, reg_iterations=(40, 20, 0), aff_iterations=(2100, 1200, 1200, 10), aff_shrink_factors=(6, 4, 2, 1), aff_smoothing_sigmas=(3, 2, 1, 0), write_composite_transform=False, random_seed=None, verbose=False, multivariate_extras=None, restrict_transformation=None, smoothing_in_mm=False, **kwargs)[source]¶
Register a pair of images either through the full or simplified interface to the ANTs registration method.
ANTsR function: antsRegistration
- Parameters:
fixed (ANTsImage) – fixed image to which we register the moving image.
moving (ANTsImage) – moving image to be mapped to fixed space.
type_of_transform (string) – A linear or non-linear registration type. Mutual information metric by default. See Notes below for more.
initial_transform (list of strings (optional)) – transforms to prepend
outprefix (string) – output will be named with this prefix.
mask (ANTsImage (optional)) – Registration metric mask in the fixed image space.
moving_mask (ANTsImage (optional)) – Registration metric mask in the moving image space.
mask_all_stages (boolean) – If true, apply metric mask(s) to all registration stages, instead of just the final stage.
grad_step (scalar) – gradient step size (not for all tx)
flow_sigma (scalar) – smoothing for update field
total_sigma (scalar) – smoothing for total field
aff_metric (string) – the metric for the affine part (GC, mattes, meansquares)
aff_sampling (scalar) – the nbins or radius parameter for the syn metric
aff_random_sampling_rate (scalar) – the fraction of points used to estimate the metric. this can impact speed but also reproducibility and/or accuracy.
syn_metric (string) – the metric for the syn part (CC, mattes, meansquares, demons)
syn_sampling (scalar) – the nbins or radius parameter for the syn metric
reg_iterations (list/tuple of python:integers) – vector of iterations for syn. we will set the smoothing and multi-resolution parameters based on the length of this vector.
aff_iterations (list/tuple of python:integers) – vector of iterations for low-dimensional (translation, rigid, affine) registration.
aff_shrink_factors (list/tuple of python:integers) – vector of multi-resolution shrink factors for low-dimensional (translation, rigid, affine) registration.
aff_smoothing_sigmas (list/tuple of python:integers) – vector of multi-resolution smoothing factors for low-dimensional (translation, rigid, affine) registration.
random_seed (python:integer) – random seed to improve reproducibility. note that the number of ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS should be 1 if you want perfect reproducibility.
write_composite_transform (boolean) – Boolean specifying whether or not the composite transform (and its inverse, if it exists) should be written to an hdf5 composite file. This is false by default so that only the transform for each stage is written to file.
verbose (boolean) – request verbose output (useful for debugging)
multivariate_extras (additional metrics for multi-metric registration) –
list of additional images and metrics which will trigger the use of multiple metrics in the registration process in the deformable stage. Each multivariate metric needs 5 entries: name of metric, fixed, moving, weight, samplingParam. the list of lists should be of the form ( ( “nameOfMetric2”, img, img, weight, metricParam ) ). Another example would be ( ( “MeanSquares”, f2, m2, 0.5, 0
), ( “CC”, f2, m2, 0.5, 2 ) ) . This is only compatible
with the SyNOnly or antsRegistrationSyN* transformations.
restrict_transformation (This option allows the user to restrict the) – optimization of the displacement field, translation, rigid or affine transform on a per-component basis. For example, if one wants to limit the deformation or rotation of 3-D volume to the first two dimensions, this is possible by specifying a weight vector of ‘(1,1,0)’ for a 3D deformation field or ‘(1,1,0,1,1,0)’ for a rigid transformation. Restriction currently only works if there are no preceding transformations.
smoothing_in_mm (boolean ; currently only impacts low dimensional registration) –
kwargs (keyword args) – extra arguments
- Returns:
warpedmovout: Moving image warped to space of fixed image. warpedfixout: Fixed image warped to space of moving image. fwdtransforms: Transforms to move from moving to fixed image. invtransforms: Transforms to move from fixed to moving image.
- Return type:
dict containing follow key/value pairs
Notes
- type_of_transform can be one of:
“Translation”: Translation transformation.
“Rigid”: Rigid transformation: Only rotation and translation.
“Similarity”: Similarity transformation: scaling, rotation and translation.
- “QuickRigid”: Rigid transformation: Only rotation and translation.
May be useful for quick visualization fixes.’
- “DenseRigid”: Rigid transformation: Only rotation and translation.
Employs dense sampling during metric estimation.’
- “BOLDRigid”: Rigid transformation: Parameters typical for BOLD to
BOLD intrasubject registration’.’
“Affine”: Affine transformation: Rigid + scaling.
“AffineFast”: Fast version of Affine.
- “BOLDAffine”: Affine transformation: Parameters typical for BOLD to
BOLD intrasubject registration’.’
- “TRSAA”: translation, rigid, similarity, affine (twice). please set
regIterations if using this option. this would be used in cases where you want a really high quality affine mapping (perhaps with mask).
“Elastic”: Elastic deformation: Affine + deformable.
- “ElasticSyN”: Symmetric normalization: Affine + deformable
transformation, with mutual information as optimization metric and elastic regularization.
- “SyN”: Symmetric normalization: Affine + deformable transformation,
with mutual information as optimization metric.
- “SyNRA”: Symmetric normalization: Rigid + Affine + deformable
transformation, with mutual information as optimization metric.
- “SyNOnly”: Symmetric normalization: no initial transformation,
with mutual information as optimization metric. Assumes images are aligned by an inital transformation. Can be useful if you want to run an unmasked affine followed by masked deformable registration.
“SyNCC”: SyN, but with cross-correlation as the metric.
“SyNabp”: SyN optimized for abpBrainExtraction.
“SyNBold”: SyN, but optimized for registrations between BOLD and T1 images.
- “SyNBoldAff”: SyN, but optimized for registrations between BOLD
and T1 images, with additional affine step.
- “SyNAggro”: SyN, but with more aggressive registration
(fine-scale matching and more deformation). Takes more time than SyN.
- “TV[n]”: time-varying diffeomorphism with where ‘n’ indicates number of
time points in velocity field discretization. The initial transform should be computed, if needed, in a separate call to ants.registration.
“TVMSQ”: time-varying diffeomorphism with mean square metric
“TVMSQC”: time-varying diffeomorphism with mean square metric for very large deformation
- “antsRegistrationSyN[x]”: recreation of the antsRegistrationSyN.sh script in ANTs
where ‘x’ is one of the transforms available (e.g., ‘t’, ‘b’, ‘s’)
- “antsRegistrationSyNQuick[x]”: recreation of the antsRegistrationSyNQuick.sh script in ANTs
where ‘x’ is one of the transforms available (e.g., ‘t’, ‘b’, ‘s’)
“antsRegistrationSyNRepro[x]”: reproducible registration. x options as above.
“antsRegistrationSyNQuickRepro[x]”: quick reproducible registration. x options as above.
Example
>>> import ants >>> fi = ants.image_read(ants.get_ants_data('r16')) >>> mi = ants.image_read(ants.get_ants_data('r64')) >>> fi = ants.resample_image(fi, (60,60), 1, 0) >>> mi = ants.resample_image(mi, (60,60), 1, 0) >>> mytx = ants.registration(fixed=fi, moving=mi, type_of_transform = 'SyN' )
- ants.affine_initializer(fixed_image, moving_image, search_factor=20, radian_fraction=0.1, use_principal_axis=False, local_search_iterations=10, mask=None, txfn=None)[source]¶
A multi-start optimizer for affine registration Searches over the sphere to find a good initialization for further registration refinement, if needed. This is a arapper for the ANTs function antsAffineInitializer.
ANTsR function: affineInitializer
- Parameters:
fixed_image (ANTsImage) – the fixed reference image
moving_image (ANTsImage) – the moving image to be mapped to the fixed space
search_factor (scalar) – degree of increments on the sphere to search
radian_fraction (scalar) – between zero and one, defines the arc to search over
use_principal_axis (boolean) – boolean to initialize by principal axis
local_search_iterations (scalar) – gradient descent iterations
mask (ANTsImage (optional)) – optional mask to restrict registration
txfn (string (optional)) – filename for the transformation
- Returns:
transformation matrix
- Return type:
ndarray
Example
>>> import ants >>> fi = ants.image_read(ants.get_ants_data('r16')) >>> mi = ants.image_read(ants.get_ants_data('r27')) >>> txfile = ants.affine_initializer( fi, mi ) >>> tx = ants.read_transform(txfile, dimension=2)
- ants.apply_transforms(fixed, moving, transformlist, interpolator='linear', imagetype=0, whichtoinvert=None, compose=None, defaultvalue=0, verbose=False, **kwargs)[source]¶
Apply a transform list to map an image from one domain to another. In image registration, one computes mappings between (usually) pairs of images. These transforms are often a sequence of increasingly complex maps, e.g. from translation, to rigid, to affine to deformation. The list of such transforms is passed to this function to interpolate one image domain into the next image domain, as below. The order matters strongly and the user is advised to familiarize with the standards established in examples.
ANTsR function: antsApplyTransforms
- Parameters:
fixed (ANTsImage) – fixed image defining domain into which the moving image is transformed.
moving (AntsImage) – moving image to be mapped to fixed space.
transformlist (list of strings) – list of transforms generated by ants.registration where each transform is a filename.
interpolator (string) –
- Choice of interpolator. Supports partial matching.
linear nearestNeighbor multiLabel for label images (deprecated, prefer genericLabel) gaussian bSpline cosineWindowedSinc welchWindowedSinc hammingWindowedSinc lanczosWindowedSinc genericLabel use this for label images
imagetype (python:integer) – choose 0/1/2/3 mapping to scalar/vector/tensor/time-series
whichtoinvert (list of booleans (optional)) – Must be same length as transformlist. whichtoinvert[i] is True if transformlist[i] is a matrix, and the matrix should be inverted. If transformlist[i] is a warp field, whichtoinvert[i] must be False. If the transform list is a matrix followed by a warp field, whichtoinvert defaults to (True,False). Otherwise it defaults to [False]*len(transformlist)).
compose (string (optional)) – if it is a string pointing to a valid file location, this will force the function to return a composite transformation filename.
defaultvalue (scalar) – Default voxel value for mappings outside the image domain.
verbose (boolean) – print command and run verbose application of transform.
kwargs (keyword arguments) – extra parameters
- Return type:
ANTsImage or string (transformation filename)
Example
>>> import ants >>> fixed = ants.image_read( ants.get_ants_data('r16') ) >>> moving = ants.image_read( ants.get_ants_data('r64') ) >>> fixed = ants.resample_image(fixed, (64,64), 1, 0) >>> moving = ants.resample_image(moving, (64,64), 1, 0) >>> mytx = ants.registration(fixed=fixed , moving=moving , type_of_transform = 'SyN' ) >>> mywarpedimage = ants.apply_transforms( fixed=fixed, moving=moving, transformlist=mytx['fwdtransforms'] )
- ants.create_jacobian_determinant_image(domain_image, tx, do_log=False, geom=False)[source]¶
Compute the jacobian determinant from a transformation file
ANTsR function: createJacobianDeterminantImage
- Parameters:
domain_image (ANTsImage) – image that defines transformation domain
tx (string) – deformation transformation file name
do_log (boolean) – return the log jacobian
geom (bolean) – use the geometric jacobian calculation (boolean)
- Return type:
Example
>>> import ants >>> fi = ants.image_read( ants.get_ants_data('r16')) >>> mi = ants.image_read( ants.get_ants_data('r64')) >>> fi = ants.resample_image(fi,(128,128),1,0) >>> mi = ants.resample_image(mi,(128,128),1,0) >>> mytx = ants.registration(fixed=fi , moving=mi, type_of_transform = ('SyN') ) >>> jac = ants.create_jacobian_determinant_image(fi,mytx['fwdtransforms'][0],1)
- ants.create_warped_grid(image, grid_step=10, grid_width=2, grid_directions=(True, True), fixed_reference_image=None, transform=None, foreground=1, background=0)[source]¶
Deforming a grid is a helpful way to visualize a deformation field. This function enables a user to define the grid parameters and apply a deformable map to that grid.
ANTsR function: createWarpedGrid
- Parameters:
image (ANTsImage) – input image
grid_step (scalar) – width of grid blocks
grid_width (scalar) – width of grid lines
grid_directions (tuple of booleans) – directions in which to draw grid lines, boolean vector
fixed_reference_image (ANTsImage (optional)) – reference image space
transform (list/tuple of strings (optional)) – vector of transforms
foreground (scalar) – intensity value for grid blocks
background (scalar) – intensity value for grid lines
- Return type:
Example
>>> import ants >>> fi = ants.image_read( ants.get_ants_data( 'r16' ) ) >>> mi = ants.image_read( ants.get_ants_data( 'r64' ) ) >>> mygr = ants.create_warped_grid( mi ) >>> mytx = ants.registration(fixed=fi, moving=mi, type_of_transform = ('SyN') ) >>> mywarpedgrid = ants.create_warped_grid( mi, grid_directions=(False,True), transform=mytx['fwdtransforms'], fixed_reference_image=fi )
- ants.fsl2antstransform(matrix, reference, moving)[source]¶
Convert an FSL linear transform to an antsrTransform
ANTsR function: fsl2antsrtransform
- Parameters:
- Return type:
Examples
>>> import ants >>> import numpy as np >>> fslmat = np.zeros((4,4)) >>> np.fill_diagonal(fslmat, 1) >>> img = ants.image_read(ants.get_ants_data('ch2')) >>> tx = ants.fsl2antstransform(fslmat, img, img)
- ants.image_mutual_information(image1, image2)[source]¶
Compute mutual information between two ANTsImage types
ANTsR function: antsImageMutualInformation
Example
>>> import ants >>> fi = ants.image_read( ants.get_ants_data('r16') ).clone('float') >>> mi = ants.image_read( ants.get_ants_data('r64') ).clone('float') >>> mival = ants.image_mutual_information(fi, mi) # -0.1796141
- ants.reflect_image(image, axis=None, tx=None, metric='mattes')[source]¶
Reflect an image along an axis
ANTsR function: reflectImage
- Parameters:
image (ANTsImage) – image to reflect
axis (python:integer (optional)) – which dimension to reflect across, numbered from 0 to imageDimension-1
tx (string (optional)) – transformation type to estimate after reflection
metric (string) – similarity metric for image registration. see antsRegistration.
- Return type:
Example
>>> import ants >>> fi = ants.image_read( ants.get_ants_data('r16'), 'float' ) >>> axis = 2 >>> asym = ants.reflect_image(fi, axis, 'Affine')['warpedmovout'] >>> asym = asym - fi
- ants.reorient_image()¶
- ants.get_center_of_mass(image)[source]¶
Compute an image center of mass in physical space which is defined as the mean of the intensity weighted voxel coordinate system.
ANTsR function: getCenterOfMass
- Parameters:
image (ANTsImage) – image from which center of mass will be computed
- Return type:
scalar
Example
>>> fi = ants.image_read( ants.get_ants_data("r16")) >>> com1 = ants.get_center_of_mass( fi ) >>> fi = ants.image_read( ants.get_ants_data("r64")) >>> com2 = ants.get_center_of_mass( fi )
- ants.resample_image(image, resample_params, use_voxels=False, interp_type=1)[source]¶
Resample image by spacing or number of voxels with various interpolators. Works with multi-channel images.
ANTsR function: resampleImage
- Parameters:
image (ANTsImage) – input image
resample_params (tuple/list) – vector of size dimension with numeric values
use_voxels (boolean) – True means interpret resample params as voxel counts
interp_type (python:integer) – one of 0 (linear), 1 (nearest neighbor), 2 (gaussian), 3 (windowed sinc), 4 (bspline)
- Return type:
Example
>>> import ants >>> fi = ants.image_read( ants.get_ants_data("r16")) >>> finn = ants.resample_image(fi,(50,60),True,0) >>> filin = ants.resample_image(fi,(1.5,1.5),False,1)
- ants.resample_image_to_target(image, target, interp_type='linear', imagetype=0, verbose=False, **kwargs)[source]¶
Resample image by using another image as target reference. This function uses ants.apply_transform with an identity matrix to achieve proper resampling.
ANTsR function: resampleImageToTarget
- Parameters:
image (ANTsImage) – image to resample
target (ANTsImage) – image of reference, the output will be in this space
interp_type (string) –
- Choice of interpolator. Supports partial matching.
linear nearestNeighbor multiLabel for label images but genericlabel is preferred gaussian bSpline cosineWindowedSinc welchWindowedSinc hammingWindowedSinc lanczosWindowedSinc genericLabel use this for label images
imagetype (python:integer) – choose 0/1/2/3 mapping to scalar/vector/tensor/time-series
verbose (boolean) – print command and run verbose application of transform.
kwargs (keyword arguments) – additional arugment passed to antsApplyTransforms C code
- Return type:
Example
>>> import ants >>> fi = ants.image_read(ants.get_ants_data('r16')) >>> fi2mm = ants.resample_image(fi, (2,2), use_voxels=0, interp_type='linear') >>> resampled = ants.resample_image_to_target(fi2mm, fi, verbose=True)