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

interfaces.dtitk.registration
=============================


.. _nipype.interfaces.dtitk.registration.AffineTask:


.. index:: AffineTask

AffineTask
----------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L99>`__

Wraps command **dti_affine_reg**

Performs affine registration between two tensor volumes

    Example
    ~~~~~~~

    >>> import nipype.interfaces.dtitk as dtitk
    >>> node = dtitk.AffineTask()
    >>> node.inputs.fixed_file = 'diffusion.nii.gz'
    >>> node.inputs.moving_file = 'diffusion2.nii.gz'
    >>> node.inputs.similarity_metric = 'EDS'
    >>> node.inputs.samplingX = 4
    >>> node.inputs.samplingY = 4
    >>> node.inputs.samplingZ = 4
    >>> node.inputs.ftol = 0.01
    >>> node.inputs.useInTrans = 1
    >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        fixed_file: (a unicode string)
                fixed diffusion tensor image
                flag: %s, position: 0
        ftol: (a float)
                cost function tolerance
                flag: %s, position: 6
        moving_file: (a unicode string)
                diffusion tensor image path
                flag: %s, position: 1
        samplingX: (a float)
                dist between samp points (mm)
                flag: %s, position: 3
        samplingY: (a float)
                dist between samp points (mm)
                flag: %s, position: 4
        samplingZ: (a float)
                dist between samp points (mm)
                flag: %s, position: 5
        similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI')
                similarity metric
                flag: %s, position: 2

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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
        useInTrans: (a float)
                to initialize with existing xfm set as 1
                flag: %s, position: 7

Outputs::

        out_file: (a file name)
        out_file_xfm: (a file name)

.. _nipype.interfaces.dtitk.registration.ComposeXfmTask:


.. index:: ComposeXfmTask

ComposeXfmTask
--------------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L200>`__

Wraps command **dfRightComposeAffine**

Combines diffeomorphic and affine transforms

           Example
           ~~~~~~~

           >>> import nipype.interfaces.dtitk as dtitk
           >>> node = dtitk.ComposeXfmTask()
           >>> node.inputs.in_df = 'ants_Warp.nii.gz'
           >>> node.inputs.in_aff= 'ants_Affine.txt'
           >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        in_aff: (a unicode string)
                affine file.aff
                flag: -aff %s, position: 0
        in_df: (a unicode string)
                diffeomorphic file.df.nii.gz
                flag: -df %s, position: 1
        out_file: (a unicode string)
                output_path
                flag: -out %s, position: 2
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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::

        out_file: (a file name)
                cheese

.. _nipype.interfaces.dtitk.registration.DiffeoTask:


.. index:: DiffeoTask

DiffeoTask
----------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L156>`__

Wraps command **dti_diffeomorphic_reg**

Performs diffeomorphic registration between two tensor volumes

    Example
    ~~~~~~~

    >>> import nipype.interfaces.dtitk as dtitk
    >>> node = dtitk.DiffeoTask()
    >>> node.inputs.fixed_file = 'diffusion.nii.gz'
    >>> node.inputs.moving_file = 'diffusion2.nii.gz'
    >>> node.inputs.mask = 'mask.nii.gz'
    >>> node.inputs.legacy = 1
    >>> node.inputs.n_iters = 6
    >>> node.inputs.ftol = 0.002
    >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        ftol: (a float)
                iteration for the optimization to stop
                flag: %s, position: 5
        legacy: (a float)
                legacy parameter; always set to 1
                flag: %s, position: 3
        n_iters: (a float)
                number of iterations
                flag: %s, position: 4

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        fixed_file: (a unicode string)
                fixed diffusion tensor image
                flag: %s, position: 0
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        mask: (a unicode string)
                mask
                flag: %s, position: 2
        moving_file: (a unicode string)
                moving diffusion tensor image
                flag: %s, position: 1
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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::

        out_file: (a file name)
        out_file_xfm: (a file name)

.. _nipype.interfaces.dtitk.registration.RigidTask:


.. index:: RigidTask

RigidTask
---------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L37>`__

Wraps command **dti_rigid_reg**

Performs rigid registration between two tensor volumes

    Example
    ~~~~~~~

    >>> import nipype.interfaces.dtitk as dtitk
    >>> node = dtitk.RigidTask()
    >>> node.inputs.fixed_file = 'diffusion.nii.gz'
    >>> node.inputs.moving_file = 'diffusion2.nii.gz'
    >>> node.inputs.similarity_metric = 'EDS'
    >>> node.inputs.samplingX = 4
    >>> node.inputs.samplingY = 4
    >>> node.inputs.samplingZ = 4
    >>> node.inputs.ftol = 0.01
    >>> node.inputs.useInTrans = 1
    >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        fixed_file: (a unicode string)
                fixed diffusion tensor image
                flag: %s, position: 0
        ftol: (a float)
                cost function tolerance
                flag: %s, position: 6
        moving_file: (a unicode string)
                diffusion tensor image path
                flag: %s, position: 1
        samplingX: (a float)
                dist between samp points (mm)
                flag: %s, position: 3
        samplingY: (a float)
                dist between samp points (mm)
                flag: %s, position: 4
        samplingZ: (a float)
                dist between samp points (mm)
                flag: %s, position: 5
        similarity_metric: ('EDS' or 'GDS' or 'DDS' or 'NMI')
                similarity metric
                flag: %s, position: 2

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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
        useInTrans: (a float)
                to initialize with existing xfm set as 1
                flag: %s, position: 7

Outputs::

        out_file: (a file name)
        out_file_xfm: (a file name)

.. _nipype.interfaces.dtitk.registration.affScalarVolTask:


.. index:: affScalarVolTask

affScalarVolTask
----------------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L320>`__

Wraps command **affineScalarVolume**

Applies affine transform to a scalar volume

            Example
            ~~~~~~~

            >>> import nipype.interfaces.dtitk as dtitk
            >>> node = dtitk.affScalarVolTask()
            >>> node.inputs.in_volume = 'fa.nii.gz'
            >>> node.inputs.in_xfm = 'ants_Affine.txt'
            >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        in_target: (a unicode string)
                flag: -target %s, position: 2
        in_volume: (a unicode string)
                moving volume
                flag: -in %s, position: 0
        in_xfm: (a unicode string)
                transform to apply
                flag: -trans %s, position: 1
        out_file: (a unicode string)
                flag: -out %s, position: 3
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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::

        out_file: (a file name)
                moved volume

.. _nipype.interfaces.dtitk.registration.affSymTensor3DVolTask:


.. index:: affSymTensor3DVolTask

affSymTensor3DVolTask
---------------------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L281>`__

Wraps command **affineSymTensor3DVolume**

Applies affine transform to a tensor volume

            Example
            ~~~~~~~

            >>> import nipype.interfaces.dtitk as dtitk
            >>> node = dtitk.affSymTensor3DVolTask()
            >>> node.inputs.in_tensor = 'diffusion.nii'
            >>> node.inputs.in_xfm = 'ants_Affine.txt'
            >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        in_target: (a unicode string)
                flag: -target %s, position: 2
        in_tensor: (a unicode string)
                moving tensor
                flag: -in %s, position: 0
        in_xfm: (a unicode string)
                transform to apply
                flag: -trans %s, position: 1
        out_file: (a unicode string)
                flag: -out %s, position: 3
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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::

        out_file: (a file name)
                cheese

.. _nipype.interfaces.dtitk.registration.diffeoScalarVolTask:


.. index:: diffeoScalarVolTask

diffeoScalarVolTask
-------------------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L368>`__

Wraps command **deformationScalarVolume**

Applies diffeomorphic transform to a scalar volume

            Example
            ~~~~~~~

            >>> import nipype.interfaces.dtitk as dtitk
            >>> node = dtitk.diffeoScalarVolTask()
            >>> node.inputs.in_volume = 'fa.nii.gz'
            >>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
            >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        in_flip: (a unicode string)
                flag: -flip %s, position: 5
        in_interp: (a unicode string)
                0 trilin, 1 NN
                flag: -interp %s, position: 7
        in_target: (a unicode string)
                flag: -target %s, position: 3
        in_type: (a unicode string)
                flag: -type %s, position: 6
        in_volume: (a unicode string)
                moving volume
                flag: -in %s, position: 0
        in_vsize: (a unicode string)
                flag: -vsize %s, position: 4
        in_xfm: (a unicode string)
                transform to apply
                flag: -trans %s, position: 2
        out_file: (a unicode string)
                flag: -out %s, position: 1
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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::

        out_file: (a file name)
                moved volume

.. _nipype.interfaces.dtitk.registration.diffeoSymTensor3DVolTask:


.. index:: diffeoSymTensor3DVolTask

diffeoSymTensor3DVolTask
------------------------

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/dtitk/registration.py#L241>`__

Wraps command **deformationSymTensor3DVolume**

Applies diffeomorphic transform to a tensor volume

            Example
            ~~~~~~~

            >>> import nipype.interfaces.dtitk as dtitk
            >>> node = dtitk.diffeoSymTensor3DVolTask()
            >>> node.inputs.in_tensor = 'diffusion.nii'
            >>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
            >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                flag: %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
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        in_target: (a unicode string)
                flag: -target %s, position: 2
        in_tensor: (a unicode string)
                moving tensor
                flag: -in %s, position: 0
        in_xfm: (a unicode string)
                transform to apply
                flag: -trans %s, position: 1
        out_file: (a unicode string)
                flag: -out %s, position: 3
        terminal_output: (u'stream' or u'allatonce' or u'file' or u'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::

        out_file: (a file name)
                cheese
