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# interfaces.elastix.registration

## AnalyzeWarp

Link to code

Wraps command transformix -def all -jac all -jacmat all

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 -out ./ -tp TransformParameters.0.txt'

Inputs:

    [Mandatory]
    output_path: (an existing directory name, nipype default value: ./)
            output directory
            flag: -out %s
    transform_file: (an existing file name)
            transform-parameter file, only 1
            flag: -tp %s

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    num_threads: (an integer)
            set the maximum number of threads of elastix
            flag: -threads %01d
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    disp_field: (a file name)
            displacements field
    jacdet_map: (a file name)
            det(Jacobian) map
    jacmat_map: (a file name)
            Jacobian matrix map

## ApplyWarp

Link to code

Wraps command 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 -out ./ -tp TransformParameters.0.txt'

Inputs:

    [Mandatory]
    moving_image: (an existing file name)
            input image to deform
            flag: -in %s
    output_path: (an existing directory name, nipype default value: ./)
            output directory
            flag: -out %s
    transform_file: (an existing file name)
            transform-parameter file, only 1
            flag: -tp %s

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    num_threads: (an integer)
            set the maximum number of threads of elastix
            flag: -threads %01d
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    warped_file: (a file name)
            input moving image warped to fixed image

## PointsWarp

Link to code

Wraps command 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 -out ./ -def surf1.vtk -tp TransformParameters.0.txt'

Inputs:

    [Mandatory]
    output_path: (an existing directory name, nipype default value: ./)
            output directory
            flag: -out %s
    points_file: (an existing file name)
            input points (accepts .vtk triangular meshes).
            flag: -def %s
    transform_file: (an existing file name)
            transform-parameter file, only 1
            flag: -tp %s

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    num_threads: (an integer)
            set the maximum number of threads of elastix
            flag: -threads %01d
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    warped_file: (a file name)
            input points displaced in fixed image domain

## Registration

Link to code

Wraps command 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 -out ./ -p elastix.txt'

Inputs:

    [Mandatory]
    fixed_image: (an existing file name)
            fixed image
            flag: -f %s
    moving_image: (an existing file name)
            moving image
            flag: -m %s
    output_path: (an existing directory name, nipype default value: ./)
            output directory
            flag: -out %s
    parameters: (a list of items which are an existing file name)
            parameter file, elastix handles 1 or more -p
            flag: -p %s...

    [Optional]
    args: (a string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a value of type 'str' and
             with values which are a value of type 'str', nipype default value:
             {})
            Environment variables
    fixed_mask: (an existing file name)
            mask for fixed image
            flag: -fMask %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    initial_transform: (an existing file name)
            parameter file for initial transform
            flag: -t0 %s
    moving_mask: (an existing file name)
            mask for moving image
            flag: -mMask %s
    num_threads: (an integer)
            set the maximum number of threads of elastix
            flag: -threads %01d
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    transform: (a list of items which are an existing file name)
            output transform
    warped_file: (a file name)
            input moving image warped to fixed image
    warped_files: (a list of items which are a file name)
            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