nipype.interfaces.elastix.registration module

Interfaces to perform image registrations and to apply the resulting displacement maps to images and points.

AnalyzeWarp

Link to code

Bases: ApplyWarp

Wrapped executable: transformix.

Use transformix to get details from the input transform (generate the corresponding deformation field, generate the determinant of the Jacobian map or the Jacobian map itself)

Example

>>> from nipype.interfaces.elastix import AnalyzeWarp
>>> reg = AnalyzeWarp()
>>> reg.inputs.transform_file = 'TransformParameters.0.txt'
>>> reg.cmdline
'transformix -def all -jac all -jacmat all -threads 1 -out ./ -tp TransformParameters.0.txt'
output_patha pathlike object or string representing an existing directory

Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

transform_filea pathlike object or string representing an existing file

Transform-parameter file, only 1. Maps to a command-line argument: -tp %s.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

jac‘all’

Generate an image with the determinant of the spatial Jacobian. Maps to a command-line argument: -jac %s. (Nipype default value: all)

jacmat‘all’

Generate an image with the spatial Jacobian matrix at each voxel. Maps to a command-line argument: -jacmat %s. (Nipype default value: all)

moving_imagea pathlike object or string representing an existing file

Input image to deform (not used). Maps to a command-line argument: -in %s.

num_threadsan integer

Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)

points‘all’

Transform all points from the input-image, which effectively generates a deformation field. Maps to a command-line argument: -def %s (position: 0). (Nipype default value: all)

disp_fielda pathlike object or string representing a file

Displacements field.

jacdet_mapa pathlike object or string representing a file

Det(Jacobian) map.

jacmat_mapa pathlike object or string representing a file

Jacobian matrix map.

ApplyWarp

Link to code

Bases: CommandLine

Wrapped executable: transformix.

Use transformix to apply a transform on an input image. The transform is specified in the transform-parameter file.

Example

>>> from nipype.interfaces.elastix import ApplyWarp
>>> reg = ApplyWarp()
>>> reg.inputs.moving_image = 'moving1.nii'
>>> reg.inputs.transform_file = 'TransformParameters.0.txt'
>>> reg.cmdline
'transformix -in moving1.nii -threads 1 -out ./ -tp TransformParameters.0.txt'
moving_imagea pathlike object or string representing an existing file

Input image to deform. Maps to a command-line argument: -in %s.

output_patha pathlike object or string representing an existing directory

Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

transform_filea pathlike object or string representing an existing file

Transform-parameter file, only 1. Maps to a command-line argument: -tp %s.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

num_threadsan integer

Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)

warped_filea pathlike object or string representing a file

Input moving image warped to fixed image.

PointsWarp

Link to code

Bases: CommandLine

Wrapped executable: transformix.

Use transformix to apply a transform on an input point set. The transform is specified in the transform-parameter file.

Example

>>> from nipype.interfaces.elastix import PointsWarp
>>> reg = PointsWarp()
>>> reg.inputs.points_file = 'surf1.vtk'
>>> reg.inputs.transform_file = 'TransformParameters.0.txt'
>>> reg.cmdline
'transformix -threads 1 -out ./ -def surf1.vtk -tp TransformParameters.0.txt'
output_patha pathlike object or string representing an existing directory

Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

points_filea pathlike object or string representing an existing file

Input points (accepts .vtk triangular meshes). Maps to a command-line argument: -def %s.

transform_filea pathlike object or string representing an existing file

Transform-parameter file, only 1. Maps to a command-line argument: -tp %s.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

num_threadsan integer

Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)

warped_filea pathlike object or string representing a file

Input points displaced in fixed image domain.

Registration

Link to code

Bases: CommandLine

Wrapped executable: elastix.

Elastix nonlinear registration interface

Example

>>> from nipype.interfaces.elastix import Registration
>>> reg = Registration()
>>> reg.inputs.fixed_image = 'fixed1.nii'
>>> reg.inputs.moving_image = 'moving1.nii'
>>> reg.inputs.parameters = ['elastix.txt']
>>> reg.cmdline
'elastix -f fixed1.nii -m moving1.nii -threads 1 -out ./ -p elastix.txt'
fixed_imagea pathlike object or string representing an existing file

Fixed image. Maps to a command-line argument: -f %s.

moving_imagea pathlike object or string representing an existing file

Moving image. Maps to a command-line argument: -m %s.

output_patha pathlike object or string representing an existing directory

Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

parametersa list of items which are a pathlike object or string representing an existing file

Parameter file, elastix handles 1 or more -p. Maps to a command-line argument: -p %s....

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

fixed_maska pathlike object or string representing an existing file

Mask for fixed image. Maps to a command-line argument: -fMask %s.

initial_transforma pathlike object or string representing an existing file

Parameter file for initial transform. Maps to a command-line argument: -t0 %s.

moving_maska pathlike object or string representing an existing file

Mask for moving image. Maps to a command-line argument: -mMask %s.

num_threadsan integer

Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)

transforma list of items which are a pathlike object or string representing an existing file

Output transform.

warped_filea pathlike object or string representing a file

Input moving image warped to fixed image.

warped_filesa list of items which are a pathlike object or string representing a file

Input moving image warped to fixed image at each level.

warped_files_flagsa list of items which are a boolean

Flag indicating if warped image was generated.