java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmSM2

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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 & 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
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`barMarker`
`private java.util.BitSet`	`bitMask`
`private float[][]`	`destArray`
`private int[]`	`destExitStatusArray`
`private ModelImage[]`	`destImage`
`private int`	`elsuncEngine`
`private int[]`	`exitStatus`
`private double[][]`	`exparray`
`private int`	`fittingEngine`
`private double`	`h`
`private int`	`i`
`private double[]`	`initial`
`private double`	`ktransDivVe`
`private double`	`ktransTotal`
`private double[]`	`max_constr`
`private double[]`	`min_constr`
`private int`	`nl2solEngine`
`private int`	`oldBarMarker`
`private int[]`	`paramInf`
`private double[]`	`paramMax`
`private double[]`	`paramMin`
`private int[]`	`paramNaN`
`private int`	`processors`
`private int`	`processRegionIndex`
`private double`	`r1pt0`
`private double[]`	`r1ptj`
`private double[]`	`r1t0`
`private double[]`	`r1tj`
`private 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

All Methods Instance Methods Concrete Methods
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, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

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 java.util.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 Detail

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 Detail

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)

Class AlgorithmSM2

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

destImage

timeVals

r1t0

r1tj

r1pt0

r1ptj

min_constr

max_constr

h

sagittalSinusIndex

processRegionIndex

ymodel

i

xDim

yDim

zDim

tDim

volSize

initial

trapezoidMidpoint

trapezoidConstant

trapezoidSlope

ktransDivVe

exparray

exitStatus

paramNaN

paramInf

paramMin

paramMax

processors

destArray

destExitStatusArray

voxelsProcessed

barMarker

oldBarMarker

tissueImage

bitMask

validVoxels

ktransTotal

veTotal

vpTotal

wholeImage

elsuncEngine

nl2solEngine

fittingEngine

Constructor Detail

AlgorithmSM2

Method Detail

finalize

runAlgorithm

statusMessage

statusMessageNL2sol

input

output