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# interfaces.c3

## C3d

Link to code

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)

## C3dAffineTool

Link to code

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)