.. 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/e63e055194d62d2bdc4665688261c03a42fd0025/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: `stream` - displays to terminal
                immediately, `allatonce` - waits till command is finished to display
                output, `file` - writes output to file, `none` - output is ignored

        [Optional]
        args: (a string)
                Additional parameters to the command
                flag: %s
        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.
                flag: --bsplineorder %d
        convergencethreshold: (a float)
                Stopping criterion for the iterative bias estimation. Larger values
                will lead to smaller execution time.
                flag: --convergencethreshold %f
        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.
                flag: --histogramsharpening %s
        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
                flag: --inputimage %s
        iterations: (an integer)
                Maximum number of iterations at each level of resolution. Larger
                values will increase execution time, but may lead to better results.
                flag: --iterations %s
        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.
                flag: --maskimage %s
        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)
                flag: --meshresolution %s
        outputbiasfield: (a boolean or a file name)
                Recovered bias field (OPTIONAL)
                flag: --outputbiasfield %s
        outputimage: (a boolean or a file name)
                Result of processing
                flag: --outputimage %s
        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.
                flag: --shrinkfactor %d
        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.
                flag: --splinedistance %f
        weightimage: (an existing file name)
                Weight Image
                flag: --weightimage %s

Outputs::

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