nipype.interfaces.elastix.utils module

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

class nipype.interfaces.elastix.utils.EditTransform(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)

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'
>>> tfm.inputs.reference_image = 'fixed1.nii'
>>> tfm.inputs.output_type = 'unsigned char'
>>> tfm.run()
Mandatory Inputs:

transform_file (a pathlike object or string representing an existing file) – Transform-parameter file, only 1.

Optional Inputs:

  • 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.

Outputs:

output_file (a pathlike object or string representing an existing file) – Output transform file.