Package gov.nih.mipav.model.algorithms

Class AlgorithmSM2

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmSM2

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmSM2
extends AlgorithmBase

Based on the document provided by Daniel Reich: Notes on DCE with SM2 (standard model, aka Tofts model, 2-compartment) 3 model parameters are fit for each voxel in 3D: 1) K_trans in [1.0E-5, 5.0] in /min On input ktrans is converted from /min to /sec and on output ktrans is converted from /sec to /min. 2) ve in [1.0E-5, 0.99] 3) f_vp in [0, 0.99] srcImage is a dynamic "4D volume" of MRI signal (3D over time). The equation used here is virtually identical to equation 10.3 in T1-w DCE-MRI. Ct(t) = vpCp(t) + ktrans*integral from 0 to t of Cp(t') * exp[-ktrans*(t - t')/ve]dt' (10.3) Cp is the concentration of agent in the vascular plasma space, vp. ve is the volume of the extravascular extracellular space per unit volume of tissue. ktrans is the volume transfer constant between vp and ve. Ct is the tracer concentration in the tissue as a whole. Our equation is: R1(t) - R10 = (vp * [R1,p(t) - R10,p] + ktrans*integral from 0 to t of [R1,p(tau) - R10,p]*exp[-ktrans*(t - tau)/ve]d(tau))/(1 - h) where R10 is the tissue R1 map in the absence of contrast material, a 3D volume R1(tj) is the tissue R1 map during contrast infusion, a 4D data set. h = hematocrit with a default value of 0.4. With the sagittal sinus VOI: Average over this VOI to extract the constant R10,p from the R10 map. Average over this VOI to extract the time series R1,p(tj) from the R1(tj) 4D data set. tj is a vector of the center times for each volume, where j = 1,...,n and n is the number of post-contrast volumes. Solve the equation numerically assuming piecewise linearity and using the trapezoid rule. The pre-injection volumes are actually averaged together to generate the R10 map. So you're right, they wouldn't provide any additional information, and we don't need to fit them. After injection (t=t1), the first volume usually has no contrast in it. That's because the contrast has to circulate to the brain. So R1,p(t1) should be the same as R10,p, but in our scheme R1,p(t1) wasn't used to generate the R10 map. Any differences should be due to noise. Does that help explain things? For monomeric gadolinium chelates, Ktrans for the normal blood brain barrier is approximately 10^-4 min^-1 (from the legend to Fig 5 of Li, Rooney, and Springer (MRM, 2005)). So a lower bound of 10^-5 should be ok. If R1,p(t1) = R10,p except for noise, then R1,p(t1) - R10,p is purely noise and contains no useful information 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, pp. 341-364. 4.) Larsson HBW, Courivaud F, Rostrup E, Hansen AE. Measurement of brain perfusion, blood volume, and blood-brain barrier permeability, using dynamic contrast-enhanced T1-weighted MRI at 3 tesla. Magnetic Resonance in Medicine 2009; 62(5):1270-1281. 5.) Li X, Rooney WD, Springer CS. A unified magnetic resonance imaging pharmacokinetic theory: intravascular and extracellular contrast reagents. Magnetic Resonance in Medicine 2005 Dec; 54(6): 1351-1359. 6.) Tofts PS, Modeling tracer kinetics in dynamic Gd-DPTA MR imaging. Journal of Magnetic Resonance Imaging, 1997, 7(1), pp. 91-101. 7.) Tofts PS, Brix G, Buckley DL, Evelhoch JL, Henderson E, Knopp MV, Larsson HB, Mayr NA, Parker GJ, Port RE, Taylor J, Weisskoff RM. Estimating kinetic parameters from dynamic contrast-enhanced T(1)-weighted MRI of a diffusable tracer: standardized quantitites and symbols. J. Magn. Reson Imaging 1999 Sep; 10(3), pp. 223-232.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	AlgorithmSM2.FitAll
(package private) class	AlgorithmSM2.FitAllEP
(package private) class	AlgorithmSM2.FitAllNL2
(package private) class	AlgorithmSM2.FitSM2ConstrainedModel
(package private) class	AlgorithmSM2.FitSM2ConstrainedModelC
(package private) class	AlgorithmSM2.FitSM2nl2solModel
(package private) class	AlgorithmSM2.Integration2All
(package private) class	AlgorithmSM2.Integration2EPAll
(package private) class	AlgorithmSM2.IntModel
class	AlgorithmSM2.sm2Task

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	barMarker
private BitSet	bitMask
private float[][]	destArray
private int[]	destExitStatusArray
private ModelImage[]	destImage
private final int	elsuncEngine
private int[]	exitStatus
private double[][]	exparray
private final int	fittingEngine
private final double	h
private int	i
private double[]	initial
private double	ktransDivVe
private double	ktransTotal
private double[]	max_constr
private double[]	min_constr
private final int	nl2solEngine
private int	oldBarMarker
private final int[]	paramInf
private final double[]	paramMax
private final double[]	paramMin
private final int[]	paramNaN
private int	processors
private int	processRegionIndex
private double	r1pt0
private double[]	r1ptj
private double[]	r1t0
private double[]	r1tj
private final int	sagittalSinusIndex
private int	tDim
private double[]	timeVals	A vector of center times for each volume
private ModelImage	tissueImage
private double[]	trapezoidConstant
private double[]	trapezoidMidpoint
private double[]	trapezoidSlope
private int	validVoxels
private double	veTotal
private int	volSize
private long	voxelsProcessed
private double	vpTotal
private boolean	wholeImage
private int	xDim
private int	yDim
private double[]	ymodel
private int	zDim

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

destFlag, 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
AlgorithmSM2(ModelImage[] destImage, ModelImage srcImage, double[] min_constr, double[] max_constr, double[] initial, ModelImage tissueImage, double[] timeVals, double h, int sagittalSinusIndex, int processRegionIndex)	Creates a new AlgorithmDEMRI3 object.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for destruction.
void	input(double[] y_array, int i)
void	output(double[] params, double paramSecs0, int i, int exitBits, float chi_squared)
void	runAlgorithm()	starts the algorithm.
private void	statusMessage(int status)
private void	statusMessageNL2sol(int status, int numParam)

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

destImage

private ModelImage[] destImage

timeVals

private double[] timeVals

A vector of center times for each volume

r1t0

private double[] r1t0

r1tj

private double[] r1tj

r1pt0

private double r1pt0

r1ptj

private double[] r1ptj

min_constr

private double[] min_constr

max_constr

private double[] max_constr

h

private final double h

sagittalSinusIndex

private final int sagittalSinusIndex

processRegionIndex

private int processRegionIndex

ymodel

private double[] ymodel

i

private int i

xDim

private int xDim

yDim

private int yDim

zDim

private int zDim

tDim

private int tDim

volSize

private int volSize

initial

private double[] initial

trapezoidMidpoint

private double[] trapezoidMidpoint

trapezoidConstant

private double[] trapezoidConstant

trapezoidSlope

private double[] trapezoidSlope

ktransDivVe

private double ktransDivVe

exparray

private double[][] exparray

exitStatus

private int[] exitStatus

paramNaN

private final int[] paramNaN

paramInf

private final int[] paramInf

paramMin

private final double[] paramMin

paramMax

private final double[] paramMax

processors

private int processors

destArray

private float[][] destArray

destExitStatusArray

private int[] destExitStatusArray

voxelsProcessed

private long voxelsProcessed

barMarker

private int barMarker

oldBarMarker

private int oldBarMarker

tissueImage

private ModelImage tissueImage

bitMask

private BitSet bitMask

validVoxels

private int validVoxels

ktransTotal

private double ktransTotal

veTotal

private double veTotal

vpTotal

private double vpTotal

wholeImage

private boolean wholeImage

elsuncEngine

private final int elsuncEngine

See Also:

• Constant Field Values

nl2solEngine

private final int nl2solEngine

See Also:

• Constant Field Values

fittingEngine

private final int fittingEngine

See Also:

• Constant Field Values

Constructor Details

AlgorithmSM2

public AlgorithmSM2(ModelImage[] destImage,
 ModelImage srcImage,
 double[] min_constr,
 double[] max_constr,
 double[] initial,
 ModelImage tissueImage,
 double[] timeVals,
 double h,
 int sagittalSinusIndex,
 int processRegionIndex)

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

statusMessage

private void statusMessage(int status)

statusMessageNL2sol

private void statusMessageNL2sol(int status,
 int numParam)

input

public void input(double[] y_array,
 int i)

output

public void output(double[] params,
 double paramSecs0,
 int i,
 int exitBits,
 float chi_squared)