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'
Mandatory Inputs:

  • output_path (a pathlike object or string representing an existing directory) – Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

  • transform_file (a pathlike object or string representing an existing file) – Transform-parameter file, only 1. Maps to a command-line argument: -tp %s.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a 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_image (a pathlike object or string representing an existing file) – Input image to deform (not used). Maps to a command-line argument: -in %s.

  • num_threads (an 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)

Outputs:

  • disp_field (a pathlike object or string representing a file) – Displacements field.

  • jacdet_map (a pathlike object or string representing a file) – Det(Jacobian) map.

  • jacmat_map (a 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'
Mandatory Inputs:

  • moving_image (a pathlike object or string representing an existing file) – Input image to deform. Maps to a command-line argument: -in %s.

  • output_path (a pathlike object or string representing an existing directory) – Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

  • transform_file (a pathlike object or string representing an existing file) – Transform-parameter file, only 1. Maps to a command-line argument: -tp %s.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

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

Outputs:

warped_file (a 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'
Mandatory Inputs:

  • output_path (a pathlike object or string representing an existing directory) – Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

  • points_file (a pathlike object or string representing an existing file) – Input points (accepts .vtk triangular meshes). Maps to a command-line argument: -def %s.

  • transform_file (a pathlike object or string representing an existing file) – Transform-parameter file, only 1. Maps to a command-line argument: -tp %s.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

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

Outputs:

warped_file (a 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'
Mandatory Inputs:

  • fixed_image (a pathlike object or string representing an existing file) – Fixed image. Maps to a command-line argument: -f %s.

  • moving_image (a pathlike object or string representing an existing file) – Moving image. Maps to a command-line argument: -m %s.

  • output_path (a pathlike object or string representing an existing directory) – Output directory. Maps to a command-line argument: -out %s. (Nipype default value: ./)

  • parameters (a 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....

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a 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_mask (a pathlike object or string representing an existing file) – Mask for fixed image. Maps to a command-line argument: -fMask %s.

  • initial_transform (a pathlike object or string representing an existing file) – Parameter file for initial transform. Maps to a command-line argument: -t0 %s.

  • moving_mask (a pathlike object or string representing an existing file) – Mask for moving image. Maps to a command-line argument: -mMask %s.

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

Outputs:

  • transform (a list of items which are a pathlike object or string representing an existing file) – Output transform.

  • warped_file (a pathlike object or string representing a file) – Input moving image warped to fixed image.

  • warped_files (a 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_flags (a list of items which are a boolean) – Flag indicating if warped image was generated.