brains:N4ITK

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Summary

Performs Bias Field Correction using the non-uniform intensity normalization N4 (Nick's N3 ITK Implementation For MRI Bias Field Correction) approach. The algorithm is described in this Insight Journal article. We have wrapped the provided methods using 3D Slicer's Command line module.

Authors

• Hans Johnson
• Nick Tustison
• Jim Gee

Usage

N4ITK  [--returnparameterfile <std::string>]
       [--processinformationaddress <std::string>] [--xml]
       [--echo] [--biasVolume <std::string>] 
       [--fittingLevels <std::vector<int>>] 
       [--numberOfControlPoints <std::vector<int>>] 
       [--splineDistance <float>]
       [--useSplineDistance] [--sigmoidNormalizedBeta <float>]
       [--sigmoidNormalizedAlpha <float>] [--splineOrder <int>]
       [--convergenceThreshold <float>] [--force2D]
       [--maximumNumberOfIterations <std::vector<int>>]
       [--biasFieldFullWidthAtHalfMaximum <float>]
       [--weinerFilterNoise <float>] 
       [--numberOfHistogramBins <int>] 
       [--shrinkFactor <int>] 
       [--weightVolume <std::string>] 
       [--maskVolume <std::string>]
       [--outputVolume <std::string>] 
       [--inputVolume <std::string>] 
       [--] [--version] [-h]

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float, int-vector, etc.) as opposed to bulk return parameters (image, geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort, etc.). (default: 0)

--xml

    Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--biasVolume <std::string>
Filename of computed bias field volume

--fittingLevels <std::vector<int>>
The number of parameters in the estimated bspline grid (default: 1,1,1)

--numberOfControlPoints <std::vector<int>>
number of spline control points (default: 4,4,4)

--splineDistance <float>
Sigmoid Normalized Beta (default: 0)

--useSplineDistance
Specify parameters in terms of spline distance (default: 0)

--sigmoidNormalizedBeta <float>
Sigmoid Normalized Beta (default: 0.5)

--sigmoidNormalizedAlpha <float>
Sigmoid Normalized Alpha (default: 0)

--splineOrder <int>
order of BSpline (default: 3)

--convergenceThreshold <float>
Convergence threshold (default: 0.001)

--force2D
If true, process in 2D. (default: 0)

--maximumNumberOfIterations <std::vector<int>>
For each fitting level, give the maximum number of iterations (default: 50,50,50,50)

--biasFieldFullWidthAtHalfMaximum <float>
Bias Field Full Width At Half Maximum (default: 0.15)

--weinerFilterNoise <float>
Weiner Filter Noise (default: 0.01)

--numberOfHistogramBins <int>
Number of Histogram Bins (default: 200)

--shrinkFactor <int>
Factor for Image shrinking/resampling before bias correction (default: 1)

--weightVolume <std::string>
Weight Volume

--maskVolume <std::string>
Filename of binary image used to mask volume in input image to correct

--outputVolume <std::string>
Bias Corrected Output Filename

--inputVolume <std::string>
Filename of Image to which Bias Field Correction is applied

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

Figures

References

Acknowledgements