niftkKNDoubleWindowBSI.cxx File Reference

Include dependency graph for niftkKNDoubleWindowBSI.cxx:

Typedefs
typedef itk::Image< double, 3 >	DoubleImageType
typedef itk::Image< float, 3 >	FloatImageType
typedef itk::Image< int, 3 >	IntImageType
typedef itk::ImageFileReader < DoubleImageType >	DoubleReaderType
typedef itk::ImageFileReader < IntImageType >	IntReaderType
typedef itk::ImageFileWriter < IntImageType >	WriterType
typedef itk::IntensityNormalisationCalculator < DoubleImageType, IntImageType >	IntensityNormalisationCalculatorType
typedef itk::BoundaryShiftIntegralCalculator < DoubleImageType, DoubleImageType, IntImageType >	BoundaryShiftIntegralFilterType
typedef itk::DoubleWindowBoundaryShiftIntegralCalculator < DoubleImageType, DoubleImageType, FloatImageType >	DoubleWindowBoundaryShiftIntegralFilterType
typedef itk::SimpleKMeansClusteringImageFilter < DoubleImageType, IntImageType, IntImageType >	SimpleKMeansClusteringImageFilterType
typedef itk::MultipleDilateImageFilter < IntImageType >	MultipleDilateImageFilterType
typedef itk::BinariseUsingPaddingImageFilter < IntImageType, IntImageType >	BinariseUsingPaddingImageFilterType

Functions
void	KMeansClassification (SimpleKMeansClusteringImageFilterType::ParametersType &means, SimpleKMeansClusteringImageFilterType::ParametersType &stds, const DoubleImageType *image, const IntImageType *mask, int numberOfDilations, int numberOfClasses, const char *outputImageName, const char *tissueToRemoveMASKFilename)
void	LocalKMeansClassification (SimpleKMeansClusteringImageFilterType::ParametersType &means, SimpleKMeansClusteringImageFilterType::ParametersType &stds, const DoubleImageType *image, const IntImageType *localGMNormalisationMask, int numberOfDilations, int numberOfClasses)
double	calculateKNBSI (const char *baselineImageName, const char *repeatImageName, const char *baselineMaskName, const char *repeatMaskName, const char *subROIMaskName, const char *weightImageName, const char *bsiMaskName, double csfGreyWindowFactor, double greyWhiteWindowFactor, int numberOfErosion, int numberOfDilation, const itk::Array< double > &baselineFinalMeans, const itk::Array< double > &repeatFinalMeans, const itk::Array< double > &baselineFinalStds, const itk::Array< double > &repeatFinalStds, double slope, double intercept, int windowAverageMode, double minSecondWindowWidth, const char *firstBSIMapName, const char *secondBSIMapName, double userLowerCSFGMWindowValue, double userUpperCSFGMWindowValue, double userLowerGMWMWindowValue, double userUpperGMWMWindowValue, char *resultFileName, unsigned int pBSIComputation)
void	saveBSIImage (char *forward, char *backward, char *resultBSIFilename)
double	getVolume (char *image)
int	main (int argc, char *argv[])

Typedef Documentation

typedef itk::BinariseUsingPaddingImageFilter<IntImageType,IntImageType> BinariseUsingPaddingImageFilterType

typedef itk::BoundaryShiftIntegralCalculator<DoubleImageType,DoubleImageType,IntImageType> BoundaryShiftIntegralFilterType

typedef itk::Image<double, 3> DoubleImageType

Typedefs.

typedef itk::ImageFileReader<DoubleImageType> DoubleReaderType

typedef itk::DoubleWindowBoundaryShiftIntegralCalculator<DoubleImageType,DoubleImageType,FloatImageType> DoubleWindowBoundaryShiftIntegralFilterType

typedef itk::Image<float, 3> FloatImageType

typedef itk::IntensityNormalisationCalculator<DoubleImageType, IntImageType> IntensityNormalisationCalculatorType

typedef itk::Image<int, 3> IntImageType

typedef itk::ImageFileReader<IntImageType> IntReaderType

typedef itk::MultipleDilateImageFilter<IntImageType> MultipleDilateImageFilterType

typedef itk::SimpleKMeansClusteringImageFilter< DoubleImageType, IntImageType, IntImageType > SimpleKMeansClusteringImageFilterType

typedef itk::ImageFileWriter<IntImageType> WriterType

Function Documentation

double calculateKNBSI	(	const char *	baselineImageName,
		const char *	repeatImageName,
		const char *	baselineMaskName,
		const char *	repeatMaskName,
		const char *	subROIMaskName,
		const char *	weightImageName,
		const char *	bsiMaskName,
		double	csfGreyWindowFactor,
		double	greyWhiteWindowFactor,
		int	numberOfErosion,
		int	numberOfDilation,
		const itk::Array< double > &	baselineFinalMeans,
		const itk::Array< double > &	repeatFinalMeans,
		const itk::Array< double > &	baselineFinalStds,
		const itk::Array< double > &	repeatFinalStds,
		double	slope,
		double	intercept,
		int	windowAverageMode,
		double	minSecondWindowWidth,
		const char *	firstBSIMapName,
		const char *	secondBSIMapName,
		double	userLowerCSFGMWindowValue,
		double	userUpperCSFGMWindowValue,
		double	userLowerGMWMWindowValue,
		double	userUpperGMWMWindowValue,
		char *	resultFileName,
		unsigned int	pBSIComputation
	)

Calculate BSI using the linear regression results.

int windowAverageMode: 0 - baseline and repeat, 1 - use baseline only, 2 - use repeat only.

double getVolume

(

char *

image

)

void KMeansClassification	(	SimpleKMeansClusteringImageFilterType::ParametersType &	means,
		SimpleKMeansClusteringImageFilterType::ParametersType &	stds,
		const DoubleImageType *	image,
		const IntImageType *	mask,
		int	numberOfDilations,
		int	numberOfClasses,
		const char *	outputImageName,
		const char *	tissueToRemoveMASKFilename
	)

Use K-means clustering to get the means of the tissues.

void LocalKMeansClassification	(	SimpleKMeansClusteringImageFilterType::ParametersType &	means,
		SimpleKMeansClusteringImageFilterType::ParametersType &	stds,
		const DoubleImageType *	image,
		const IntImageType *	localGMNormalisationMask,
		int	numberOfDilations,
		int	numberOfClasses
	)

Use K-means clustering to get the local means of the tissues.

int main	(	int	argc,
		char *	argv[]
	)

Main program.

void saveBSIImage	(	char *	forward,
		char *	backward,
		char *	resultBSIFilename
	)

Save BSI image.