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

interfaces.slicer.filtering.n4itkbiasfieldcorrection
====================================================


.. _nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection.N4ITKBiasFieldCorrection:


.. index:: N4ITKBiasFieldCorrection

N4ITKBiasFieldCorrection
------------------------

`Link to code <http://github.com/nipy/nipype/tree/9595f272aa4086ea28f7534a8bd05690f60bf6b8/nipype/interfaces/slicer/filtering/n4itkbiasfieldcorrection.py#L29>`__

Wraps command **N4ITKBiasFieldCorrection **

title: N4ITK MRI Bias correction

category: Filtering

description: Performs image bias correction using N4 algorithm. This module is based on the ITK filters contributed in the following publication:  Tustison N, Gee J "N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction", The Insight Journal 2009 January-June, http://hdl.handle.net/10380/3053

version: 9

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/N4ITKBiasFieldCorrection

contributor: Nick Tustison (UPenn), Andrey Fedorov (SPL, BWH), Ron Kikinis (SPL, BWH)

acknowledgements: The development of this module was partially supported by NIH grants R01 AA016748-01, R01 CA111288 and U01 CA151261 as well as by NA-MIC, NAC, NCIGT and the Slicer community.

Inputs::

        [Mandatory]
        terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
                Control terminal output

        [Optional]
        args: (a string)
                Additional parameters to the command
        bsplineorder: (an integer)
                Order of B-spline used in the approximation. Larger values will lead to longer execution
                times, may result in overfitting and poor result.
        convergencethreshold: (a float)
                Stopping criterion for the iterative bias estimation. Larger values will lead to smaller
                execution time.
        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
        histogramsharpening: (a float)
                A vector of up to three values. Non-zero values correspond to Bias Field Full Width at
                Half Maximum, Wiener filter noise, and Number of histogram bins.
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run
        inputimage: (an existing file name)
                Input image where you observe signal inhomegeneity
        iterations: (an integer)
                Maximum number of iterations at each level of resolution. Larger values will increase
                execution time, but may lead to better results.
        maskimage: (an existing file name)
                Binary mask that defines the structure of your interest. NOTE: This parameter is
                OPTIONAL. If the mask is not specified, the module will use internally Otsu thresholding
                to define this mask. Better processing results can often be obtained when a meaningful
                mask is defined.
        meshresolution: (a float)
                Resolution of the initial bspline grid defined as a sequence of three numbers. The
                actual resolution will be defined by adding the bspline order (default is 3) to the
                resolution in each dimension specified here. For example, 1,1,1 will result in a 4x4x4
                grid of control points. This parameter may need to be adjusted based on your input
                image. In the multi-resolution N4 framework, the resolution of the bspline grid at
                subsequent iterations will be doubled. The number of resolutions is implicitly defined
                by Number of iterations parameter (the size of this list is the number of resolutions)
        outputbiasfield: (a boolean or a file name)
                Recovered bias field (OPTIONAL)
        outputimage: (a boolean or a file name)
                Result of processing
        shrinkfactor: (an integer)
                Defines how much the image should be upsampled before estimating the inhomogeneity
                field. Increase if you want to reduce the execution time. 1 corresponds to the original
                resolution. Larger values will significantly reduce the computation time.
        splinedistance: (a float)
                An alternative means to define the spline grid, by setting the distance between the
                control points. This parameter is used only if the grid resolution is not specified.
        weightimage: (an existing file name)
                Weight Image

Outputs::

        outputbiasfield: (an existing file name)
                Recovered bias field (OPTIONAL)
        outputimage: (an existing file name)
                Result of processing
