Modules:HistogramMatching-Documentation-3.6

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Gallery of New Features

Module Name

Histogram Matching

Histogram Matching UI

Reference image: MR Acquisition 1

Source image: MR Acquisition 2

Output image: MR Acquisition 2 matched to MR Acquisition 1

General Information

Module Type & Category

Type: CLI

Category: Filtering

Authors, Collaborators & Contact

• Author: Bill Lorensen
• Contact: bill.lorensen at gmail.com

Module 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 orginally designed to normalize MR images of the same MR 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.

Usage

Examples, Use cases & Tutorials

The filter was orginally designed to normalize MR images of the same MR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms.

A command line example is:

HistogramMatching --numberOfHistogramLevels 64
   --numberOfMatchPoints 10
   ${TEST_DATA}/CTHeadAxial.nhdr
   ${TEST_DATA}/MRHeadResampled.nhdr
   ${TEMP}/HistogramMatchingTest.nhdr

Quick Tour of Features and Use

• Input/Output panel

Input/Output panels

The module takes two input volumes and generate one output volume. The Input Volume is the volume whose histogram is to be transformed. The Reference Volume is a volume that provide a target histogram for the first volume. Upon completion of execution, the result is stored in the Output Volume.

• Parameters panel

Parameters panels

The user can specify parameters for the histogram module on this panel. The Number of Histogram Level specifies how many levels the intensity range is divided. The Number of Matching Points tells the module the number of quantile points in the histogram to be matched. When Threshold at mean is checked, the module will exclude background voxels from the histogram matching process.

Development

Dependencies

Depends only on the core IO and display functionalities of Slicer.

Known Bugs

None.

Source Code and Documentation

Source Code: HistogramMatching.cxx

XML Description: HistogramMatching.xml

Test: HistogramMatchingTest.cxx

./HistogramMatching  [--processinformationaddress <std::string>] [--xml]
                     [--echo] [--threshold] [--numberOfMatchPoints
                     <int>] [--numberOfHistogramLevels <int>] [--]
                     [--version] [-h] <std::string> <std::string>
                     <std::string>


Where: 

--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)

--threshold
  If on, only pixels above the mean in each volume are thresholded.
  (default: 0)

--numberOfMatchPoints <int>
  The number of match points to use (default: 10)

--numberOfHistogramLevels <int>
  The number of hisogram levels to use (default: 128)

--,  --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.

<std::string>
  (required)  Input volume to be filtered

<std::string>
  (required)  Input volume whose histogram will be matched

<std::string>
  (required)  Output volume. This is the input volume with intensities
  matched to the reference volume.

More Information

Acknowledgement

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.

References

Internally, the module uses itk::HistogramMatchingImageFilter. More details on algorithm can be found here.