nipype.interfaces.elastix.registration module¶
Interfaces to perform image registrations and to apply the resulting displacement maps to images and points.
AnalyzeWarp¶
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¶
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¶
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¶
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.