brains:BRAINSDiscreteClass

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Summary

This program will convert a continuous tissue classified image into a discrete classified image. This is simply a multi-level threshold algorithm that assigns each voxel to one of the pure tissue labels. The user is allowed to provide three threshold values. These are

• csfThreshold - Threshold between CSF and gray matter
• corticalThreshold - Threshold between gray matter and white matter
• subcorticalThreshold - Threshold between gray matter and white matter within a specified mask region. This is used to generate a better classification in the subcortical region.

The thresholds are applied as follows:

• 10 <= pixel < csfThreshold => pixel = 10
• csfThreshold <= pixel < corticalThreshold => pixel = 130
• corticalThreshold <= pixel => pixel = 250

If the pixel is within the mask region then the subcorticalThreshold replaces the corticalThreshold value. Other labels 0-9 are retained in the resulting discrete image.

Authors

• Vincent A. Magnotta
• Greg Harris

Usage

BRAINSDiscreteClass  [--returnparameterfile <std::string>]
                     [--processinformationaddress <std::string>] 
                     [--xml] [--echo]
                     [--csfThreshold <float>]
                     [--corticalThreshold <float>]
                     [--subcorticalThreshold <float>]
                     [--outputVolume <std::string>]
                     [--subcorticalMask <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)

--csfThreshold <float>
CSF/GM Threshold (default: 70)

--corticalThreshold <float>
Cortical GM/WM Threshold (default: 190)

--subcorticalThreshold <float>
Subcortical GM/WM Threshold (default: 197)

--outputVolume <std::string>
Output discrete class Image

--subcorticalMask <std::string>
Region for alternate GM/WM threshold

--inputVolume <std::string>
Continuous tissue classified image

--, --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

1. Harris G, Andreasen NC, Cizadlo T, Bailey JM, Bockholt HJ, Magnotta VA, Arndt S. Improving tissue classification in MRI: a three-dimensional multispectral discriminant analysis method with automated training class selection. J Comput Assist Tomogr. 1999 Jan-Feb;23(1):144-54.

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.