.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.elastix.registration
===============================


.. _nipype.interfaces.elastix.registration.AnalyzeWarp:


.. index:: AnalyzeWarp

AnalyzeWarp
-----------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/elastix/registration.py#L210>`__

Wraps the executable command ``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'

Inputs::

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

        [Optional]
        num_threads: (an integer (int or long), nipype default value: 1)
                set the maximum number of threads of elastix
                argument: ``-threads %01d``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        moving_image: (an existing file name)
                input image to deform (not used)
                argument: ``-in %s``
        points: (u'all', nipype default value: all)
                transform all points from the input-image, which effectively
                generates a deformation field.
                argument: ``-def %s``, position: 0
        environ: (a dictionary with keys which are a newbytes or None or a
                  newstr or None and with values which are a newbytes or None or a
                  newstr or None, nipype default value: {})
                Environment variables
        jac: (u'all', nipype default value: all)
                generate an image with the determinant of the spatial Jacobian
                argument: ``-jac %s``
        jacmat: (u'all', nipype default value: all)
                generate an image with the spatial Jacobian matrix at each voxel
                argument: ``-jacmat %s``

Outputs::

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

.. _nipype.interfaces.elastix.registration.ApplyWarp:


.. index:: ApplyWarp

ApplyWarp
---------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/elastix/registration.py#L152>`__

Wraps the executable 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 -threads 1 -out ./ -tp TransformParameters.0.txt'

Inputs::

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

        [Optional]
        num_threads: (an integer (int or long), nipype default value: 1)
                set the maximum number of threads of elastix
                argument: ``-threads %01d``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        environ: (a dictionary with keys which are a newbytes or None or a
                  newstr or None and with values which are a newbytes or None or a
                  newstr or None, nipype default value: {})
                Environment variables

Outputs::

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

.. _nipype.interfaces.elastix.registration.PointsWarp:


.. index:: PointsWarp

PointsWarp
----------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/elastix/registration.py#L257>`__

Wraps the executable 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 -threads 1 -out ./ -def surf1.vtk -tp TransformParameters.0.txt'

Inputs::

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

        [Optional]
        num_threads: (an integer (int or long), nipype default value: 1)
                set the maximum number of threads of elastix
                argument: ``-threads %01d``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        environ: (a dictionary with keys which are a newbytes or None or a
                  newstr or None and with values which are a newbytes or None or a
                  newstr or None, nipype default value: {})
                Environment variables

Outputs::

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

.. _nipype.interfaces.elastix.registration.Registration:


.. index:: Registration

Registration
------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/elastix/registration.py#L55>`__

Wraps the executable 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 -threads 1 -out ./ -p elastix.txt'

Inputs::

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

        [Optional]
        num_threads: (an integer (int or long), nipype default value: 1)
                set the maximum number of threads of elastix
                argument: ``-threads %01d``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        moving_mask: (an existing file name)
                mask for moving image
                argument: ``-mMask %s``
        fixed_mask: (an existing file name)
                mask for fixed image
                argument: ``-fMask %s``
        environ: (a dictionary with keys which are a newbytes or None or a
                  newstr or None and with values which are a newbytes or None or a
                  newstr or None, nipype default value: {})
                Environment variables
        initial_transform: (an existing file name)
                parameter file for initial transform
                argument: ``-t0 %s``

Outputs::

        warped_file: (a file name)
                input moving image warped to fixed image
        warped_files_flags: (a list of items which are a boolean)
                flag indicating if warped image was generated
        transform: (a list of items which are an existing file name)
                output transform
        warped_files: (a list of items which are a file name)
                input moving image warped to fixed image at each level
