niftkKMeansWindowWithLinearRegressionNormalisationBSI.cxx File Reference

Include dependency graph for niftkKMeansWindowWithLinearRegressionNormalisationBSI.cxx:

Typedefs
typedef itk::Image< int, 3 >	IntImageType
typedef itk::Image< double, 3 >	DoubleImageType
typedef itk::Image< short, 3 >	ShortImageType
typedef itk::ImageFileReader < ShortImageType >	ShortReaderType
typedef itk::ImageFileWriter < ShortImageType >	ShortWriterType
typedef itk::ImageFileReader < DoubleImageType >	DoubleReaderType
typedef itk::ImageFileWriter < DoubleImageType >	DoubleWriterType
typedef itk::ImageFileReader < IntImageType >	IntReaderType
typedef itk::ImageFileWriter < IntImageType >	IntWriterType
typedef itk::IntensityNormalisationCalculator < DoubleImageType, IntImageType >	IntensityNormalisationCalculatorType
typedef itk::BoundaryShiftIntegralCalculator < DoubleImageType, DoubleImageType, IntImageType >	BoundaryShiftIntegralFilterType
typedef itk::SimpleKMeansClusteringImageFilter < DoubleImageType, IntImageType, IntImageType >	SimpleKMeansClusteringImageFilterType
typedef itk::MultipleDilateImageFilter < IntImageType >	MultipleDilateImageFilterType
typedef itk::MultipleErodeImageFilter < IntImageType >	MultipleErodeImageFilterType
typedef itk::BinariseUsingPaddingImageFilter < IntImageType, IntImageType >	BinariseUsingPaddingType
typedef itk::SubtractImageFilter < IntImageType, IntImageType >	SubtractImageFilterType

Functions
void	estimateCSFGMWMIntensityFromDilatedMask (char *imageName, char *maskName, double &csfMean, double &csfSd, double &gmMean, double &gmSd, double &wmMean, double &wmSd, int dilations, const char *outCSF, const char *outGM, const char *outWM)
void	KMeansClassification (SimpleKMeansClusteringImageFilterType::ParametersType &means, SimpleKMeansClusteringImageFilterType::ParametersType &stds, const DoubleImageType *image, const IntImageType *mask, int numberOfDilations, int numberOfClasses, const char *outputImageName, const char *tissueToRemoveMASKFilename)
double	calculateBSI (char *baselineImageName, char *repeatImageName, char *baselineMaskName, char *repeatMaskName, char *subROIMaskName, int numberOfErosion, int numberOfDilation, double userLowerWindow, double userUpperWindow, 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 numberOfClasses, double numberOfWmSdForIntensityExclusion, char *resultFileName, char *xorFileName, unsigned int pBSIComputation, bool t1_images_mode)
void	saveNormalisedImage (char *repeatImageName, char *outputImageName, double slope, double intercept)
void	saveBSIImage (char *forward, char *backward, char *resultBSIFilename, bool t1_image_mode)
double	getVolume (char *image)
void	flipOrder (SimpleKMeansClusteringImageFilterType::ParametersType &in, int numberOfClasses)
int	main (int argc, char *argv[])

Typedef Documentation

typedef itk::BinariseUsingPaddingImageFilter<IntImageType,IntImageType> BinariseUsingPaddingType

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

typedef itk::Image<double, 3> DoubleImageType

typedef itk::ImageFileReader<DoubleImageType> DoubleReaderType

typedef itk::ImageFileWriter<DoubleImageType> DoubleWriterType

typedef itk::IntensityNormalisationCalculator<DoubleImageType, IntImageType> IntensityNormalisationCalculatorType

typedef itk::Image<int, 3> IntImageType

Typedefs.

typedef itk::ImageFileReader<IntImageType> IntReaderType

typedef itk::ImageFileWriter<IntImageType> IntWriterType

typedef itk::MultipleDilateImageFilter<IntImageType> MultipleDilateImageFilterType

typedef itk::MultipleErodeImageFilter<IntImageType> MultipleErodeImageFilterType

typedef itk::Image<short, 3> ShortImageType

typedef itk::ImageFileReader<ShortImageType> ShortReaderType

typedef itk::ImageFileWriter<ShortImageType> ShortWriterType

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

typedef itk::SubtractImageFilter<IntImageType, IntImageType> SubtractImageFilterType

Function Documentation

double calculateBSI	(	char *	baselineImageName,
		char *	repeatImageName,
		char *	baselineMaskName,
		char *	repeatMaskName,
		char *	subROIMaskName,
		int	numberOfErosion,
		int	numberOfDilation,
		double	userLowerWindow,
		double	userUpperWindow,
		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	numberOfClasses,
		double	numberOfWmSdForIntensityExclusion,
		char *	resultFileName,
		char *	xorFileName,
		unsigned int	pBSIComputation,
		bool	t1_images_mode
	)

Calculate BSI using the linear regression results.

void estimateCSFGMWMIntensityFromDilatedMask	(	char *	imageName,
		char *	maskName,
		double &	csfMean,
		double &	csfSd,
		double &	gmMean,
		double &	gmSd,
		double &	wmMean,
		double &	wmSd,
		int	dilations,
		const char *	outCSF,
		const char *	outGM,
		const char *	outWM
	)

Roughly estimate the CSF intensity using the dilated mask.

void flipOrder	(	SimpleKMeansClusteringImageFilterType::ParametersType &	in,
		int	numberOfClasses
	)

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.

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

Start main program

void saveBSIImage	(	char *	forward,
		char *	backward,
		char *	resultBSIFilename,
		bool	t1_image_mode
	)

Save BSI image.

void saveNormalisedImage	(	char *	repeatImageName,
		char *	outputImageName,
		double	slope,
		double	intercept
	)

Save normalised repeat image.