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

interfaces.c3
=============


.. _nipype.interfaces.c3.C3d:


.. index:: C3d

C3d
---

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/c3.py#L126>`__

Wraps the executable command ``c3d``.

Convert3d is a command-line tool for converting 3D (or 4D) images between
common file formats. The tool also includes a growing list of commands for
image manipulation, such as thresholding and resampling. The tool can also
be used to obtain information about image files. More information on
Convert3d can be found at:
https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md


Example
~~~~~~~

>>> from nipype.interfaces.c3 import C3d
>>> c3 = C3d()
>>> c3.inputs.in_file = "T1.nii"
>>> c3.inputs.pix_type = "short"
>>> c3.inputs.out_file = "T1.img"
>>> c3.cmdline
'c3d T1.nii -type short -o T1.img'
>>> c3.inputs.is_4d = True
>>> c3.inputs.in_file = "epi.nii"
>>> c3.inputs.out_file = "epi.img"
>>> c3.cmdline
'c4d epi.nii -type short -o epi.img'

Inputs::

        [Mandatory]
        in_file: (a list of items which are a file name)
                Input file (wildcard and multiple are supported).
                argument: ``%s``, position: 1

        [Optional]
        is_4d: (a boolean, nipype default value: False)
                Changes command to support 4D file operations (default is false).
        scale: (an integer (int or long) or a float)
                Multiplies the intensity of each voxel in the last image on the
                stack by the given factor.
                argument: ``-scale %s``
        out_file: (a file name)
                Output file of last image on the stack.
                argument: ``-o %s``, position: -1
                mutually_exclusive: out_files
        shift: (an integer (int or long) or a float)
                Adds the given constant to every voxel.
                argument: ``-shift %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        interp: (u'Linear' or u'NearestNeighbor' or u'Cubic' or u'Sinc' or
                  u'Gaussian')
                Specifies the interpolation used with -resample and other commands.
                Default is Linear.
                argument: ``-interpolation %s``
        multicomp_split: (a boolean, nipype default value: False)
                Enable reading of multi-component images.
                argument: ``-mcr``, 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
        smooth: (a unicode string)
                Applies Gaussian smoothing to the image. The parameter vector
                specifies the standard deviation of the Gaussian kernel.
                argument: ``-smooth %s``
        resample: (a unicode string)
                Resamples the image, keeping the bounding box the same, but changing
                the number of voxels in the image. The dimensions can be specified
                as a percentage, for example to double the number of voxels in each
                direction. The -interpolation flag affects how sampling is
                performed.
                argument: ``-resample %s``
        out_files: (a list of items which are a file name)
                Write all images on the convert3d stack as multiple files. Supports
                both list of output files or a pattern for the output filenames
                (using %d substituion).
                argument: ``-oo %s``, position: -1
                mutually_exclusive: out_file
        pix_type: (u'float' or u'char' or u'uchar' or u'short' or u'ushort'
                  or u'int' or u'uint' or u'double')
                Specifies the pixel type for the output image. By default, images
                are written in floating point (float) format
                argument: ``-type %s``

Outputs::

        out_files: (a list of items which are a file name)

.. _nipype.interfaces.c3.C3dAffineTool:


.. index:: C3dAffineTool

C3dAffineTool
-------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/c3.py#L37>`__

Wraps the executable command ``c3d_affine_tool``.

Converts fsl-style Affine registration into ANTS compatible itk format

Example
~~~~~~~

>>> from nipype.interfaces.c3 import C3dAffineTool
>>> c3 = C3dAffineTool()
>>> c3.inputs.source_file = 'cmatrix.mat'
>>> c3.inputs.itk_transform = 'affine.txt'
>>> c3.inputs.fsl2ras = True
>>> c3.cmdline
'c3d_affine_tool -src cmatrix.mat -fsl2ras -oitk affine.txt'

Inputs::

        [Optional]
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        fsl2ras: (a boolean)
                argument: ``-fsl2ras``, position: 4
        source_file: (an existing file name)
                argument: ``-src %s``, position: 2
        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
        reference_file: (an existing file name)
                argument: ``-ref %s``, position: 1
        transform_file: (an existing file name)
                argument: ``%s``, position: 3
        itk_transform: (a boolean or a file name)
                Export ITK transform.
                argument: ``-oitk %s``, position: 5

Outputs::

        itk_transform: (an existing file name)
