brains:BayesianClassifier

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Summary

This program generates a Bayesian tissue classification from multiple input images. The number of images provided as input is specified by the user. The number of classes is also specified by the user. The class exemplars and prior image should be provided by the user. The class exemplars are provided as a label map and the number of labels should be equal to the number of classes. The labels should begin at 1 and be continuous. The prior image is also a label map that corresponds to each class. The labels are then extracted and filtered to generate the prior probabilities.

DEFINE the Output Label values

Authors

• Vincent A. Magnotta
• Peter Pelligrino

Usage

  BayesianClassifier  [--returnparameterfile <std::string>]
                      [--processinformationaddress <std::string>] 
                      [--xml] [--echo]
                      [--OutputStatsFile <std::string>]
                      [--outputClassifiedImage <std::string>] 
                      [--smoothingSigma <double>] 
                      [--numberOfClasses <int>]
                      [--numberOfImages <int>]
                      [--InputClassValues <std::vector<int>>]
                      [--InputPriorLabelImage <std::string>] 
                      [--InputMaskFileName <std::string>]
                      [--InputImageFileNames <std::vector<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)

--OutputStatsFile <std::string>
Output Image Statistics (default: BayesianClassStats.txt)

--outputClassifiedImage <std::string>
Output Classified Image

--smoothingSigma <double>
Smoothing Sigma (default: 1)

--numberOfClasses <int>
Number of Classes (default: 1)

--numberOfImages <int>
Number of Input Images (default: 1)

--InputClassValues <std::vector<int>>
Label map values for tissue plugs

--InputPriorLabelImage <std::string> Input label image for prior image

--InputMaskFileName <std::string>
Input label image for class examplars

--InputImageFileNames <std::vector<std::string>>
Input images for classification

--, --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

This work was developed by the University of Iowa Departments of Radiology and Psychiatry. This software was supported in part of NIH/NINDS award NS050568.