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# 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.