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

interfaces.ants.preprocess
==========================


.. _nipype.interfaces.ants.preprocess.N4BiasFieldCorrection:


.. index:: N4BiasFieldCorrection

N4BiasFieldCorrection
---------------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/ants/preprocess.py#L36

Wraps command **N4BiasFieldCorrection**

N4 is a variant of the popular N3 (nonparameteric nonuniform normalization)
retrospective bias correction algorithm. Based on the assumption that the
corruption of the low frequency bias field can be modeled as a convolution of
the intensity histogram by a Gaussian, the basic algorithmic protocol is to
iterate between deconvolving the intensity histogram by a Gaussian, remapping
the intensities, and then spatially smoothing this result by a B-spline modeling
of the bias field itself. The modifications from and improvements obtained over
the original N3 algorithm are described in the following paper: N. Tustison et
al., N4ITK: Improved N3 Bias Correction, IEEE Transactions on Medical Imaging,
29(6):1310-1320, June 2010.

Examples
~~~~~~~~

>>> from nipype.interfaces.ants import N4BiasFieldCorrection
>>> n4 = N4BiasFieldCorrection()
>>> n4.inputs.dimension = 3
>>> n4.inputs.input_image = 'structural.nii'
>>> n4.inputs.bspline_fitting_distance = 300
>>> n4.inputs.shrink_factor = 3
>>> n4.inputs.n_iterations = [50,50,30,20]
>>> n4.inputs.convergence_threshold = 1e-6
>>> n4.cmdline
'N4BiasFieldCorrection --convergence [ 50x50x30x20 ,1e-06] --bsline-fitting [300] --image-dimension 3 --input-image structural.nii --output structural_corrected.nii --shrink-factor 3'

Inputs::

        [Mandatory]
        input_image: (a file name)
                image to apply transformation to (generally a coregistered functional)

        [Optional]
        args: (a string)
                Additional parameters to the command
        bspline_fitting_distance: (a float)
        convergence_threshold: (a float)
                requires: n_iterations
        dimension: (3 or 2, nipype default value: 3)
                image dimension (2 or 3)
        environ: (a dictionary with keys which are a value of type 'str' and with values which
                 are a value of type 'str', 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
        n_iterations: (a list of items which are an integer)
                requires: convergence_threshold
        num_threads: (an integer, nipype default value: 1)
                Number of ITK threads to use
        output_image: (a string)
                output file name
        shrink_factor: (an integer)

Outputs::

        output_image: (an existing file name)
                Warped image
