Package gov.nih.mipav.model.algorithms

Class AlgorithmDEMRI3

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmDEMRI3

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmDEMRI3
extends AlgorithmBase

3 model parameters are fit for each voxel in 3D: 1) K_trans in [0, 0.99] 2) User choice of k_ep in [0, 0.99] or ve 3) f_vp in [0, 0.99] K_trans and k_ep default to rates per second, but the user changed select rates per minute. srcImage is a dynamic "4D volume" of MRI signal (3D over time). An optional intrinsic relaxivity map may be obtained by acquiring two acquisition scans at low and high flip angles; otherwise, a single tissue relaxivity can be assumed for the whole brain. References: 1.) "A Unified Magnetic Resonance Imaging Pharmacokinetic Theory: Intravascular and Extracellular Contrast Reagents" by Xin Li, William D. Rooney, and Charles S. Springer, Jr., Magnetic Resonance in Medicine, Vol. 54, 2005, pp. 1351-1359. 2.) Erratum: Magnetic Resonance in Medicine, Vol. 55, 2006, p.1217. 3.) Quantitative MRI of the Brain, Edited by Paul Tofts, 2003, John Wiley invalid input: '&' Sons, Ltd., ISBN: 0-47084721-2, Chapter 10, T1-w DCE-MRI: T1-weighted Dynamic Contrast-enhanced MRI by Geoff J. M. Parker and Anwar R. Padhani.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	AlgorithmDEMRI3.Fit24DModel	DOCUMENT ME!
(package private) class	AlgorithmDEMRI3.Fit25HModel	DOCUMENT ME!
(package private) class	AlgorithmDEMRI3.FitDEMRI3ConstrainedModel

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private double[]	comp
private double	cos0
private double[]	elist
private double	epsilon
private int	FIRST_VOLUME_TISSUE
private int	i
(package private) double[]	initial
private double[]	max_constr
private double[]	min_constr
private double[]	mp	1D Mp(t) data from sagittal sinus VOI
private int	nFirst	nfirst injection TR index of input dataset (0 - 1000) Number of TRs before Gd injection
private boolean	perMinute	If perMinute == false, K_trans and k_ep are per second If perMinute == true, K_trans and k_ep are per minute
private double	r1	Contrast relaxivity rate in 1/(mMol*sec) (0.0 - 1000.0)
private double[]	r1i	non-uniform tissue intrinsic relaxivity map from input 3d + t = 4D image
private double	rib	blood intrinsic relaxivity rate in 1/(mMol * sec) input as reciprocal, in seconds (0.001 - 10000.0)
private double	rit	tissue intrinsic relaxivity rate in 1/(mMol * sec) specified as reciprocal, in seconds (0.001 - 10000.0)
private int	SEPARATE_VOLUME_TISSUE
private int	tDim
private double	tf	Time between frames (volumes) in seconds (0.1 - 30.0)
private double	theta	Flip angle in degrees (0.0 - 90.0)
private ModelImage	tissueImage
private int	tissueSource
private double	tr	Time between shots in seconds (0.0 - 10000.0)
private boolean	userSpecifiedBlood	If true, user specifed rib, otherwise, voi specified rib
private boolean	useVe	If false, second parameter is back-transfer rate (k_ep) If true, Second parameter is external celluar volume fraction (ve)
private int	xDim
private int	yDim
private double[]	ymodel
private int	zDim

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
AlgorithmDEMRI3(ModelImage destImage, ModelImage srcImage, double[] min_constr, double[] max_constr, double r1, boolean userSpecifiedBlood, double rib, int tissueSource, double rit, ModelImage tissueImage, double theta, double tr, boolean perMinute, int nFirst, boolean useVe)	Creates a new AlgorithmDEMRI3 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

FIRST_VOLUME_TISSUE

private int FIRST_VOLUME_TISSUE

SEPARATE_VOLUME_TISSUE

private int SEPARATE_VOLUME_TISSUE

r1

private double r1

Contrast relaxivity rate in 1/(mMol*sec) (0.0 - 1000.0)

userSpecifiedBlood

private boolean userSpecifiedBlood

If true, user specifed rib, otherwise, voi specified rib

rib

private double rib

blood intrinsic relaxivity rate in 1/(mMol * sec) input as reciprocal, in seconds (0.001 - 10000.0)

tissueSource

private int tissueSource

rit

private double rit

tissue intrinsic relaxivity rate in 1/(mMol * sec) specified as reciprocal, in seconds (0.001 - 10000.0)

r1i

private double[] r1i

non-uniform tissue intrinsic relaxivity map from input 3d + t = 4D image

theta

private double theta

Flip angle in degrees (0.0 - 90.0)

tr

private double tr

Time between shots in seconds (0.0 - 10000.0)

tf

private double tf

Time between frames (volumes) in seconds (0.1 - 30.0)

perMinute

private boolean perMinute

If perMinute == false, K_trans and k_ep are per second If perMinute == true, K_trans and k_ep are per minute

mp

private double[] mp

1D Mp(t) data from sagittal sinus VOI

nFirst

private int nFirst

nfirst injection TR index of input dataset (0 - 1000) Number of TRs before Gd injection

useVe

private boolean useVe

If false, second parameter is back-transfer rate (k_ep) If true, Second parameter is external celluar volume fraction (ve)

epsilon

private double epsilon

min_constr

private double[] min_constr

max_constr

private double[] max_constr

comp

private double[] comp

elist

private double[] elist

ymodel

private double[] ymodel

i

private int i

xDim

private int xDim

yDim

private int yDim

zDim

private int zDim

tDim

private int tDim

cos0

private double cos0

initial

double[] initial

tissueImage

private ModelImage tissueImage

Constructor Details

AlgorithmDEMRI3

public AlgorithmDEMRI3(ModelImage destImage,
 ModelImage srcImage,
 double[] min_constr,
 double[] max_constr,
 double r1,
 boolean userSpecifiedBlood,
 double rib,
 int tissueSource,
 double rit,
 ModelImage tissueImage,
 double theta,
 double tr,
 boolean perMinute,
 int nFirst,
 boolean useVe)

Creates a new AlgorithmDEMRI3 object.

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