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# interfaces.slicer.filtering.n4itkbiasfieldcorrection

## N4ITKBiasFieldCorrection

Link to code

Wraps command **/home/raid3/gorgolewski/software/slicer/Slicer –launch 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]

    [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