interfaces.c3¶
C3d¶
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 pathlike object or string
representing a file)
Input file (wildcard and multiple are supported).
argument: ``%s``, position: 1
[Optional]
out_file: (a pathlike object or string representing a file)
Output file of last image on the stack.
argument: ``-o %s``, position: -1
mutually_exclusive: out_files
out_files: (a list of items which are a pathlike object or string
representing a file)
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: ('float' or 'char' or 'uchar' or 'short' or 'ushort' or
'int' or 'uint' or 'double')
Specifies the pixel type for the output image. By default, images
are written in floating point (float) format
argument: ``-type %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.
argument: ``-scale %s``
shift: (an integer (int or long) or a float)
Adds the given constant to every voxel.
argument: ``-shift %s``
interp: ('Linear' or 'NearestNeighbor' or 'Cubic' or 'Sinc' or
'Gaussian')
Specifies the interpolation used with -resample and other commands.
Default is Linear.
argument: ``-interpolation %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``
smooth: (a unicode string)
Applies Gaussian smoothing to the image. The parameter vector
specifies the standard deviation of the Gaussian kernel.
argument: ``-smooth %s``
multicomp_split: (a boolean, nipype default value: False)
Enable reading of multi-component images.
argument: ``-mcr``, position: 0
is_4d: (a boolean, nipype default value: False)
Changes command to support 4D file operations (default is false).
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
out_files: (a list of items which are a pathlike object or string
representing a file)
C3dAffineTool¶
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]
reference_file: (a pathlike object or string representing an existing
file)
argument: ``-ref %s``, position: 1
source_file: (a pathlike object or string representing an existing
file)
argument: ``-src %s``, position: 2
transform_file: (a pathlike object or string representing an existing
file)
argument: ``%s``, position: 3
itk_transform: (a boolean or a pathlike object or string representing
a file)
Export ITK transform.
argument: ``-oitk %s``, position: 5
fsl2ras: (a boolean)
argument: ``-fsl2ras``, position: 4
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
itk_transform: (a pathlike object or string representing an existing
file)