nipype.interfaces.slicer.filtering.histogrammatching module

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HistogramMatching

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: HistogramMatching.

title: Histogram Matching

category: Filtering

description: Normalizes the grayscale values of a source image based on the grayscale values of a reference image. This filter uses a histogram matching technique where the histograms of the two images are matched only at a specified number of quantile values.

The filter was originally designed to normalize MR images of the sameMR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms. A simple background exclusion method is to exclude all pixels whose grayscale values are smaller than the mean grayscale value. ThresholdAtMeanIntensity switches on this simple background exclusion method.

Number of match points governs the number of quantile values to be matched.

The filter assumes that both the source and reference are of the same type and that the input and output image type have the same number of dimension and have scalar pixel types.

version: 0.1.0.$Revision: 19608 $(alpha)

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

contributor: Bill Lorensen (GE)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • inputVolume (a pathlike object or string representing an existing file) – Input volume to be filtered. Maps to a command-line argument: %s (position: -3).

  • numberOfHistogramLevels (an integer) – The number of hisogram levels to use. Maps to a command-line argument: --numberOfHistogramLevels %d.

  • numberOfMatchPoints (an integer) – The number of match points to use. Maps to a command-line argument: --numberOfMatchPoints %d.

  • outputVolume (a boolean or a pathlike object or string representing a file) – Output volume. This is the input volume with intensities matched to the reference volume. Maps to a command-line argument: %s (position: -1).

  • referenceVolume (a pathlike object or string representing an existing file) – Input volume whose histogram will be matched. Maps to a command-line argument: %s (position: -2).

  • threshold (a boolean) – If on, only pixels above the mean in each volume are thresholded. Maps to a command-line argument: --threshold.

Outputs:

outputVolume (a pathlike object or string representing an existing file) – Output volume. This is the input volume with intensities matched to the reference volume.