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# interfaces.slicer.filtering.n4itkbiasfieldcorrection

## N4ITKBiasFieldCorrection

Link to code

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