cmtklib.interfaces.ants module
The ANTs module provides Nipype interfaces for the ANTs registration toolbox missing in nipype or modified.
MultipleANTsApplyTransforms
Bases: nipype.interfaces.base.core.BaseInterface
Apply linear and deformable transforms estimated by ANTS to a list of images.
It calls the
antsApplyTransform
on a series of images.Examples
>>> apply_tf = MultipleANTsApplyTransforms() >>> apply_tf.inputs.input_images = ['/path/to/sub-01_atlas-L2018_desc-scale1_dseg.nii.gz', >>> '/path/to/sub-01_atlas-L2018_desc-scale2_dseg.nii.gz', >>> '/path/to/sub-01_atlas-L2018_desc-scale3_dseg.nii.gz', >>> '/path/to/sub-01_atlas-L2018_desc-scale4_dseg.nii.gz', >>> '/path/to/sub-01_atlas-L2018_desc-scale5_dseg.nii.gz'] >>> apply_tf.inputs.transforms = ['/path/to/final1Warp.nii.gz', >>> '/path/to/final0GenericAffine.mat'] >>> apply_tf.inputs.reference_image = File(mandatory=True, exists=True) >>> apply_tf.inputs.interpolation = 'NearestNeighbor' >>> apply_tf.inputs.default_value = 0.0 >>> apply_tf.inputs.out_postfix = "_transformed" >>> apply_tf.run()reference_image : a string or os.PathLike object referring to an existing file transforms : a list of items which are a string or os.PathLike object referring to an existing file
Transform files: will be applied in reverse order. For example, the last specified transform will be applied first.
default_value : a float input_images : a list of items which are a string or os.PathLike object referring to an existing file interpolation : ‘Linear’ or ‘NearestNeighbor’ or ‘CosineWindowedSinc’ or ‘WelchWindowedSinc’ or ‘HammingWindowedSinc’ or ‘LanczosWindowedSinc’ or ‘MultiLabel’ or ‘Gaussian’ or ‘BSpline’
(Nipype default value:
Linear
)
- out_postfixa string
(Nipype default value:
_transformed
)output_images : a list of items which are a string or os.PathLike object