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

interfaces.dtitk.utils
======================


.. _nipype.interfaces.dtitk.utils.BinThresh:


.. index:: BinThresh

BinThresh
---------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L286>`__

Wraps the executable command ``BinaryThresholdImageFilter``.

Binarizes an image

Example
~~~~~~~

>>> from nipype.interfaces import dtitk
>>> node = dtitk.BinThresh()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.lower_bound = 0
>>> node.inputs.upper_bound = 100
>>> node.inputs.inside_value = 1
>>> node.inputs.outside_value = 0
>>> node.cmdline
'BinaryThresholdImageFilter im1.nii im1_thrbin.nii 0 100 1 0'
>>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        lower_bound: (a float, nipype default value: 0.01)
                lower bound of binarization range
                argument: ``%g``, position: 2
        inside_value: (a float, nipype default value: 1)
                value for voxels in binarization range
                argument: ``%g``, position: 4
        upper_bound: (a float, nipype default value: 100)
                upper bound of binarization range
                argument: ``%g``, position: 3
        outside_value: (a float, nipype default value: 0)
                value for voxelsoutside of binarization range
                argument: ``%g``, position: 5
        in_file: (an existing file name)
                Image to threshold/binarize
                argument: ``%s``, position: 0

        [Optional]
        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
        out_file: (a file name)
                output path
                argument: ``%s``, position: 1

Outputs::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.BinThreshTask:


.. index:: BinThreshTask

BinThreshTask
-------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L310>`__

Wraps the executable command ``BinaryThresholdImageFilter``.

Inputs::

        [Mandatory]
        lower_bound: (a float, nipype default value: 0.01)
                lower bound of binarization range
                argument: ``%g``, position: 2
        inside_value: (a float, nipype default value: 1)
                value for voxels in binarization range
                argument: ``%g``, position: 4
        upper_bound: (a float, nipype default value: 100)
                upper bound of binarization range
                argument: ``%g``, position: 3
        outside_value: (a float, nipype default value: 0)
                value for voxelsoutside of binarization range
                argument: ``%g``, position: 5
        in_file: (an existing file name)
                Image to threshold/binarize
                argument: ``%s``, position: 0

        [Optional]
        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
        out_file: (a file name)
                output path
                argument: ``%s``, position: 1

Outputs::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.SVAdjustVoxSp:


.. index:: SVAdjustVoxSp

SVAdjustVoxSp
-------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L98>`__

Wraps the executable command ``SVAdjustVoxelspace``.

Adjusts the voxel space of a scalar volume

   Example
   ~~~~~~~

   >>> from nipype.interfaces import dtitk
   >>> node = dtitk.SVAdjustVoxSp()
   >>> node.inputs.in_file = 'im1.nii'
   >>> node.inputs.target_file = 'im2.nii'
   >>> node.cmdline
   'SVAdjustVoxelspace -in im1.nii -out im1_avs.nii -target im2.nii'
   >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                scalar volume to modify
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin (superseded by target)
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                target volume to match
                argument: ``-target %s``
                mutually_exclusive: voxel_size, origin
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        voxel_size: (a tuple of the form: (a float, a float, a float))
                xyz voxel size (superseded by target)
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.SVAdjustVoxSpTask:


.. index:: SVAdjustVoxSpTask

SVAdjustVoxSpTask
-----------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L314>`__

Wraps the executable command ``SVAdjustVoxelspace``.

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                scalar volume to modify
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin (superseded by target)
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                target volume to match
                argument: ``-target %s``
                mutually_exclusive: voxel_size, origin
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        voxel_size: (a tuple of the form: (a float, a float, a float))
                xyz voxel size (superseded by target)
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.SVResample:


.. index:: SVResample

SVResample
----------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L192>`__

Wraps the executable command ``SVResample``.

Resamples a scalar volume

    Example
    ~~~~~~~

    >>> from nipype.interfaces import dtitk
    >>> node = dtitk.SVResample()
    >>> node.inputs.in_file = 'im1.nii'
    >>> node.inputs.target_file = 'im2.nii'
    >>> node.cmdline
    'SVResample -in im1.nii -out im1_resampled.nii -target im2.nii'
    >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                image to resample
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        array_size: (a tuple of the form: (an integer (int or long), an
                  integer (int or long), an integer (int or long)))
                resampled array size
                argument: ``-size %d %d %d``
                mutually_exclusive: target_file
        align: ('center' or 'origin')
                how to align output volume to input volume
                argument: ``-align %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        target_file: (a file name)
                specs read from the target volume
                argument: ``-target %s``
                mutually_exclusive: array_size, voxel_size, origin
        voxel_size: (a tuple of the form: (a float, a float, a float))
                resampled voxel size
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.SVResampleTask:


.. index:: SVResampleTask

SVResampleTask
--------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L318>`__

Wraps the executable command ``SVResample``.

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                image to resample
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        array_size: (a tuple of the form: (an integer (int or long), an
                  integer (int or long), an integer (int or long)))
                resampled array size
                argument: ``-size %d %d %d``
                mutually_exclusive: target_file
        align: ('center' or 'origin')
                how to align output volume to input volume
                argument: ``-align %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        target_file: (a file name)
                specs read from the target volume
                argument: ``-target %s``
                mutually_exclusive: array_size, voxel_size, origin
        voxel_size: (a tuple of the form: (a float, a float, a float))
                resampled voxel size
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.TVAdjustOriginTask:


.. index:: TVAdjustOriginTask

TVAdjustOriginTask
------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L322>`__

Wraps the executable command ``TVAdjustVoxelspace``.

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                tensor volume to modify
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin (superseded by target)
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                target volume to match
                argument: ``-target %s``
                mutually_exclusive: voxel_size, origin
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        voxel_size: (a tuple of the form: (a float, a float, a float))
                xyz voxel size (superseded by target)
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.TVAdjustVoxSp:


.. index:: TVAdjustVoxSp

TVAdjustVoxSp
-------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L57>`__

Wraps the executable command ``TVAdjustVoxelspace``.

 Adjusts the voxel space of a tensor volume

Example
~~~~~~~

>>> from nipype.interfaces import dtitk
>>> node = dtitk.TVAdjustVoxSp()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.target_file = 'im2.nii'
>>> node.cmdline
'TVAdjustVoxelspace -in im1.nii -out im1_avs.nii -target im2.nii'
>>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                tensor volume to modify
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin (superseded by target)
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                target volume to match
                argument: ``-target %s``
                mutually_exclusive: voxel_size, origin
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        voxel_size: (a tuple of the form: (a float, a float, a float))
                xyz voxel size (superseded by target)
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.TVAdjustVoxSpTask:


.. index:: TVAdjustVoxSpTask

TVAdjustVoxSpTask
-----------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L326>`__

Wraps the executable command ``TVAdjustVoxelspace``.

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                tensor volume to modify
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin (superseded by target)
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                target volume to match
                argument: ``-target %s``
                mutually_exclusive: voxel_size, origin
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        voxel_size: (a tuple of the form: (a float, a float, a float))
                xyz voxel size (superseded by target)
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.TVResample:


.. index:: TVResample

TVResample
----------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L146>`__

Wraps the executable command ``TVResample``.

Resamples a tensor volume

    Example
    ~~~~~~~

    >>> from nipype.interfaces import dtitk
    >>> node = dtitk.TVResample()
    >>> node.inputs.in_file = 'im1.nii'
    >>> node.inputs.target_file = 'im2.nii'
    >>> node.cmdline
    'TVResample -in im1.nii -out im1_resampled.nii -target im2.nii'
    >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                tensor volume to resample
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                specs read from the target volume
                argument: ``-target %s``
                mutually_exclusive: array_size, voxel_size, origin
        align: ('center' or 'origin')
                how to align output volume to input volume
                argument: ``-align %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        array_size: (a tuple of the form: (an integer (int or long), an
                  integer (int or long), an integer (int or long)))
                resampled array size
                argument: ``-size %d %d %d``
                mutually_exclusive: target_file
        voxel_size: (a tuple of the form: (a float, a float, a float))
                resampled voxel size
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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
        interpolation: ('LEI' or 'EI')
                Log Euclidean Euclidean Interpolation
                argument: ``-interp %s``

Outputs::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.TVResampleTask:


.. index:: TVResampleTask

TVResampleTask
--------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L330>`__

Wraps the executable command ``TVResample``.

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                tensor volume to resample
                argument: ``-in %s``

        [Optional]
        origin: (a tuple of the form: (a float, a float, a float))
                xyz origin
                argument: ``-origin %g %g %g``
                mutually_exclusive: target_file
        out_file: (a file name)
                output path
                argument: ``-out %s``
        target_file: (a file name)
                specs read from the target volume
                argument: ``-target %s``
                mutually_exclusive: array_size, voxel_size, origin
        align: ('center' or 'origin')
                how to align output volume to input volume
                argument: ``-align %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        array_size: (a tuple of the form: (an integer (int or long), an
                  integer (int or long), an integer (int or long)))
                resampled array size
                argument: ``-size %d %d %d``
                mutually_exclusive: target_file
        voxel_size: (a tuple of the form: (a float, a float, a float))
                resampled voxel size
                argument: ``-vsize %g %g %g``
                mutually_exclusive: target_file
        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
        interpolation: ('LEI' or 'EI')
                Log Euclidean Euclidean Interpolation
                argument: ``-interp %s``

Outputs::

        out_file: (an existing file name)

.. _nipype.interfaces.dtitk.utils.TVtool:


.. index:: TVtool

TVtool
------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L225>`__

Wraps the executable command ``TVtool``.

Calculates a tensor metric volume from a tensor volume

    Example
    ~~~~~~~

    >>> from nipype.interfaces import dtitk
    >>> node = dtitk.TVtool()
    >>> node.inputs.in_file = 'im1.nii'
    >>> node.inputs.in_flag = 'fa'
    >>> node.cmdline
    'TVtool -in im1.nii -fa -out im1_fa.nii'
    >>> node.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                scalar volume to resample
                argument: ``-in %s``

        [Optional]
        in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
                argument: ``-%s``
        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
        out_file: (a file name)
                argument: ``-out %s``

Outputs::

        out_file: (a file name)

.. _nipype.interfaces.dtitk.utils.TVtoolTask:


.. index:: TVtoolTask

TVtoolTask
----------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/dtitk/utils.py#L334>`__

Wraps the executable command ``TVtool``.

Inputs::

        [Mandatory]
        in_file: (an existing file name)
                scalar volume to resample
                argument: ``-in %s``

        [Optional]
        in_flag: ('fa' or 'tr' or 'ad' or 'rd' or 'pd' or 'rgb')
                argument: ``-%s``
        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
        out_file: (a file name)
                argument: ``-out %s``

Outputs::

        out_file: (a file name)
