ApplyTransforms brick¶

Using ANTs ApplyTransforms, transforms an input image according to a reference image and a transform (or a set of transforms)¶

Mandatory inputs parameters:

input_image (a string representing an existing file)
Input file to apply transformation to (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/T1w.nii'
reference_image (a string representing an existing file)
Reference image space that you wish to warp into (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/ref_T1w.nii'
transforms (multiples string representing existing files)
Transform files that will be applied in reverse order (the last specified transform will be applied first).
ex. ['/home/username/data/raw_data/post_n4c_T1w_clipped_masked_InverseComposite.h5']

Optional inputs parameters with a default value:

default_value (a float, optional, default value is 0.0)
ex. 0.0
dimension (2 or 3 or 4, optional, default value is 3)
This option forces the image to be treated as a specified-dimensional image (2 or 3 or 4).
ex. 3
float (a boolean, optional, default value is False)
Use float instead of double for computations.
ex. False
input_image_type (0 or 1 or 2 or 3, optional, default value is 0)
Option specifying the input image type of scalar (0), vector (1), tensor(2), or time series(3).
ex. 0
interpolation (Linear or NearestNeighbor or CosineWindowedSinc or WelchWindowedSinc or HammingWindowedSinc or LanczosWindowedSinc or MultiLabel or Gaussian or BSpline, optional, default value is Linear)
Interpolation model.
ex. 'Linear'
out_prefix (a string, optional, default value is ‘t’)
Prefix of the output image.
ex. 't_'
print_out_composite_warp_file (a boolean, optional, default value is False)
Output a composite warp file instead of a transformed image. Default is False.
ex. False

Optional inputs parameters:

interpolation_parameters (a tuple of the form: (an integer) or a tuple of the form: (a float, a float), optional)
Interpolation parameters. For example for BSpline order or for sigma/alphaparameters for Gaussian/Multilabel Default is Undefined (ie parameter not used).
ex. (5,) (if interpolation = 'BSpline')
invert_transform_flags (a list of boolean, optional)
Invert transform flags. For example if transforms parameter is equal to [‘ants_Warp.nii.gz’, ‘trans.mat’] and invert_transform_flags is [False, True], the following transform will be applied: –transform ants_Warp.nii.gz –transform [ trans.mat, 1 ] Default is Undefined (ie parameter not used).
ex. [False, True]

Outputs parameters:

out_file (a strings representing a file)
Out image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/t_T1w.nii'

Useful links: