Package gov.nih.mipav.model.algorithms

Class AlgorithmTwoMRIImagesSNR

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTwoMRIImagesSNR

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmTwoMRIImagesSNR
extends AlgorithmBase

This module implements the National Electrical Manufacturers Association (NEMA) standard for SNR estimation in diagnostic MRI. This method requires a perfect geometrical registration of 2 MRI images scanned sequentailly with less than five minutes elapsed time from the end of the first scan to the beginning of the second scan. A simple 2 step process is used: 1.) Determine the standard deviation of the difference image over the same VOI region used for the signal mean difference variance = (1/(VOI pixel number - 1)) * sum over VOI region of (image[i] - image2[i])**2 difference standard deviation = square root(difference variance)

2.) SNR for a signal VOI = square root(2) * (voi mean)/difference standard deviation The factor square root(2) is required because the standard deviation used is from the difference image rather than one of the original images The contrast to noise ratio is simply SNR for VOI 1 - SNR for VOI 2.

An optional registration may be performed before SNR. In this registration image2 is registered to image. AlgorithmRegOAR2D is used with the cost function being the only registration parameter the user can vary in the dialog box. Correlation ratio is the default cost function, but the user can also select least squares, normalized cross correlation, or normalized mutual information. The SNR will be performed with the registered image2 rather than on the original prebleached image.

Note that even for 2 perfectly aligned images the results differ substantially for processing without and with registration. In 1 example for 2 aligned images without registration the standard deviation equalled 12.3 and the SNR equalled 8.44. With registration the standard deviation equalled 7.66 and the SNR equalled 13.6.

The code here assumes the presence of 1 or 2 VOI regions - a required signal region and optional second signal region. The VOIs must all be placed in the the same image. Radio buttons in the dialog box are used to select a red signal 1 or a green signal 2 VOI. Either an ellipse VOI, rectangle VOI, or polyline VOI will be selected from the top MIPAV toolbar. There is no need to hit the NEW_VOI button.

Reference: 1.) PhD. Thesis Signal and Noise Estimation From Magnetic Resonance Images by Jan Sijbers, Universiteit Antwerpen, Department Natuurkunde, Section 7.1.2 The NEMA standard, p. 49.

2.) Acceptance Testing of Magnetic Resonance Imaging Systems, AAPM Report No. 34, Published by the American Assoication of Physicists in Medicine by the American Institute of Physics, March, 1992 (Reprinted from Medical Physics, Vol. 19, Issue 1, 1992).

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private int	cost	DOCUMENT ME!
private boolean	createRegImage	DOCUMENT ME!
private ModelImage	image2	private ModelImage srcImage;.
private boolean	register	DOCUMENT ME!
private int	signal2Index	DOCUMENT ME!
private int	signalImage	DOCUMENT ME!
private int	signalIndex	DOCUMENT ME!
private ViewUserInterface	UI	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmTwoMRIImagesSNR(ModelImage image, ModelImage image2, int signalIndex, int signalImage, int signal2Index, boolean register, int cost, boolean createRegImage)	Creates a new AlgorithmTwoMRIImagesSNR object.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for destruction.
void	runAlgorithm()	starts the algorithm.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

cost

private int cost

DOCUMENT ME!

createRegImage

private boolean createRegImage

DOCUMENT ME!

image2

private ModelImage image2

private ModelImage srcImage;.

register

private boolean register

DOCUMENT ME!

signal2Index

private int signal2Index

DOCUMENT ME!

signalImage

private int signalImage

DOCUMENT ME!

signalIndex

private int signalIndex

DOCUMENT ME!

UI

private ViewUserInterface UI

DOCUMENT ME!

Constructor Details

AlgorithmTwoMRIImagesSNR

public AlgorithmTwoMRIImagesSNR(ModelImage image,
 ModelImage image2,
 int signalIndex,
 int signalImage,
 int signal2Index,
 boolean register,
 int cost,
 boolean createRegImage)

Creates a new AlgorithmTwoMRIImagesSNR object.

Parameters:

image - First MRI image

image2 - Second MRI image

signalIndex - the index of the signal VOI

signalImage - image the signal VOI belongs to; 1 if image, 2 if image 2

signal2Index - the index of the second signal VOI if >= 0

register - If true register the image2 to the image before SNR

cost - Cost function used in registration

createRegImage - If register = true and createRegImage = true, then create a frame with the registered image

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

starts the algorithm.

Specified by:

runAlgorithm in class AlgorithmBase