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_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.
args : a unicode 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 (int or long)
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_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'
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.
args : a unicode 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 (int or long)
Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)
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'
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.
args : a unicode 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 (int or long)
Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)
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'
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....
args : a unicode 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 (int or long)
Set the maximum number of threads of elastix. Maps to a command-line argument: -threads %01d. (Nipype default value: 1)
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.