nipype.interfaces.elastix.utils module

Generic interfaces to manipulate registration parameters files, including transform files (to configure warpings)

EditTransform

Link to code

Bases: BaseInterface

Manipulates an existing transform file generated with elastix

Example

>>> from nipype.interfaces.elastix import EditTransform
>>> tfm = EditTransform()
>>> tfm.inputs.transform_file = 'TransformParameters.0.txt'  # doctest: +SKIP
>>> tfm.inputs.reference_image = 'fixed1.nii'  # doctest: +SKIP
>>> tfm.inputs.output_type = 'unsigned char'
>>> tfm.run() # doctest: +SKIP

transform_file : a pathlike object or string representing an existing file

Transform-parameter file, only 1.

interpolation : ‘cubic’ or ‘linear’ or ‘nearest’

Set a new interpolator for transformation. Maps to a command-line argument: FinalBSplineInterpolationOrder. (Nipype default value: cubic)

output_file : a pathlike object or string representing a file

The filename for the resulting transform file.

output_format : ‘nii.gz’ or ‘nii’ or ‘mhd’ or ‘hdr’ or ‘vtk’

Set a new image format for resampled images. Maps to a command-line argument: ResultImageFormat.

output_type : ‘float’ or ‘unsigned char’ or ‘unsigned short’ or ‘short’ or ‘unsigned long’ or ‘long’ or ‘double’

Set a new output pixel type for resampled images. Maps to a command-line argument: ResultImagePixelType.

reference_image : a pathlike object or string representing an existing file

Set a new reference image to change the target coordinate system.

output_file : a pathlike object or string representing an existing file

Output transform file.