Package com.xinapse.image.template

Class TissueNormaliser

java.lang.Object

com.xinapse.image.template.TissueNormaliser

public class TissueNormaliser
extends Object

A class for normalising image intensities.

Constructor Summary

Constructors

Constructor	Description
TissueNormaliser()

Method Summary

Modifier and Type	Method	Description
static float[]	getMeanSD(float[] t1Pix, float[] flairPix, float[] tissueProb, int nCols, int nRows, int nSlices)	Returns mean and standard deviation statistics about a T1-weighted image and a FLAIR image.
static float[]	getMeanSD(ReadableImage t1Image, ReadableImage flairImage, ReadableImage tissueProb)	Returns mean and standard deviation statistics about a T1-weighted image and a FLAIR image.
static float[]	getMedian(float[] t1Pix, float[] flairPix, float[] tissueProb, int nCols, int nRows, int nSlices)	Returns median intensities for a T1-weighted image and a FLAIR image.
static float[]	getMedian(ReadableImage t1Image, ReadableImage flairImage, ReadableImage tissueProb)	Returns median intensity statistics for a T1-weighted image and a FLAIR image.
static void	main(String[] args)	Runs the self-test of this class.
static WritableImage[]	normalise(ReadableImage t1Image, ReadableImage flairImage, ReadableImage gmProb, ReadableImage wmProb, ReadableImage lvProb)	Normalise the intensities of a T1-weighted image and a co-registered FLAIR image, using two particular tissues as a reference.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TissueNormaliser

public TissueNormaliser()

Method Details

normalise

public static WritableImage[] normalise(ReadableImage t1Image,
 ReadableImage flairImage,
 ReadableImage gmProb,
 ReadableImage wmProb,
 ReadableImage lvProb)
                                 throws InvalidImageException,
IOException,
NumericalException

Normalise the intensities of a T1-weighted image and a co-registered FLAIR image, using two particular tissues as a reference. After normalisation:

• The T1 image will have mean intensities intensities in the GM on the order of 0, and mean intensities in the WM on the order of 1.
• The FLAIR image will have mean intensities intensities in the WM on the order of 1, and mean intensities in the CSF on the order of 0.

Parameters:

t1Image - the T1-weighted image.

flairImage - the FLAIR image.

gmProb - an image of the probability of GM.

wmProb - an image of the probability of WM.

lvProb - an image of the probability of lateral ventricle.

Returns:

normalised versions of the input t1Image and the input flairImage.

Throws:

InvalidImageException - if any of the input images is invalid.

IOException - if an I/O error occurs while reading any of the input images.

NumericalException - if a numerical error prevents normalisation.

getMeanSD

public static float[] getMeanSD(ReadableImage t1Image,
 ReadableImage flairImage,
 ReadableImage tissueProb)
                         throws InvalidImageException,
IOException,
NumericalException

Returns mean and standard deviation statistics about a T1-weighted image and a FLAIR image.

Parameters:

t1Image - the T1-weighted image.

flairImage - the FLAIR image.

tissueProb - the tissue probabilities for which to return the stats.

Returns:

the T1 mean and SD, the FLAIR mean and SD in that order.

Throws:

InvalidImageException - if any of the input images is invalid.

IOException - if the images can't be read.

NumericalException - if a numerical error occurs while calculating the mean and SD.

getMeanSD

public static float[] getMeanSD(float[] t1Pix,
 float[] flairPix,
 float[] tissueProb,
 int nCols,
 int nRows,
 int nSlices)
                         throws InvalidImageException,
NumericalException

Returns mean and standard deviation statistics about a T1-weighted image and a FLAIR image.

Parameters:

t1Pix - the T1-weighted image pixel values.

flairPix - the FLAIR image pixel values.

tissueProb - the tissue probability pixel values.

nCols - the number of image columns.

nRows - the number of image rows.

nSlices - the number of image slices.

Returns:

the T1 mean and SD, the FLAIR mean and SD in that order.

Throws:

InvalidImageException - if any of the input images is invalid.

NumericalException - if a numerical error occurs while calculating the mean and SD.

getMedian

public static float[] getMedian(ReadableImage t1Image,
 ReadableImage flairImage,
 ReadableImage tissueProb)
                         throws InvalidImageException,
IOException,
NumericalException

Returns median intensity statistics for a T1-weighted image and a FLAIR image.

Parameters:

t1Image - the T1-weighted image.

flairImage - the FLAIR image.

tissueProb - the tissue probabilities for which to return the medians.

Returns:

the T1 median and FLAIR median in that order.

Throws:

InvalidImageException - if any of the input images is invalid.

IOException - if the images can't be read.

NumericalException - if a numerical error occurs while calculating the medians.

getMedian

public static float[] getMedian(float[] t1Pix,
 float[] flairPix,
 float[] tissueProb,
 int nCols,
 int nRows,
 int nSlices)
                         throws InvalidImageException,
NumericalException

Returns median intensities for a T1-weighted image and a FLAIR image.

Parameters:

t1Pix - the T1-weighted image pixel values.

flairPix - the FLAIR image pixel values.

tissueProb - the tissue probability pixel values.

nCols - the number of image columns.

nRows - the number of image rows.

nSlices - the number of image slices.

Returns:

the T1 median and the FLAIR median in that order.

Throws:

InvalidImageException - if any of the input images is invalid.

NumericalException - if a numerical error occurs while calculating the median and SD.

main

public static void main(String[] args)

Runs the self-test of this class.

Parameters:

args - the program arguments. Five are expected: T1, FLAIR, gmProb, wmProb, lvProb.