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

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


.. _nipype.interfaces.c3.C3d:


.. index:: C3d

C3d
---

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/c3.py#L132>`__

Wraps 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).
                flag: %s, position: 1

        [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
        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.
                flag: -interpolation %s
        is_4d: (a boolean, nipype default value: False)
                Changes command to support 4D file operations (default is false).
        multicomp_split: (a boolean, nipype default value: False)
                Enable reading of multi-component images.
                flag: -mcr, position: 0
        out_file: (a file name)
                Output file of last image on the stack.
                flag: -o %s, position: -1
                mutually_exclusive: out_files
        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).
                flag: -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
                flag: -type %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.
                flag: -resample %s
        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.
                flag: -scale %s
        shift: (an integer (int or long) or a float)
                Adds the given constant to every voxel.
                flag: -shift %s
        smooth: (a unicode string)
                Applies Gaussian smoothing to the image. The parameter vector
                specifies the standard deviation of the Gaussian kernel.
                flag: -smooth %s
        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_files: (a list of items which are a file name)

.. _nipype.interfaces.c3.C3dAffineTool:


.. index:: C3dAffineTool

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

`Link to code <file:///build/nipype-fj7ofr/nipype-1.0.0+git69-gdb2670326/nipype/interfaces/c3.py#L43>`__

Wraps 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::

        [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
        fsl2ras: (a boolean)
                flag: -fsl2ras, position: 4
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        itk_transform: (a boolean or a file name)
                Export ITK transform.
                flag: -oitk %s, position: 5
        reference_file: (an existing file name)
                flag: -ref %s, position: 1
        source_file: (an existing file name)
                flag: -src %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
        transform_file: (an existing file name)
                flag: %s, position: 3

Outputs::

        itk_transform: (an existing file name)
