java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmDEMRI3

All Implemented Interfaces:

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

All Methods Instance Methods Concrete Methods
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, 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
- 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 Detail

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 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

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

Class AlgorithmDEMRI3

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

FIRST_VOLUME_TISSUE

SEPARATE_VOLUME_TISSUE

r1

userSpecifiedBlood

rib

tissueSource

rit

r1i

theta

tr

tf

perMinute

mp

nFirst

useVe

epsilon

min_constr

max_constr

comp

elist

ymodel

i

xDim

yDim

zDim

tDim

cos0

initial

tissueImage

Constructor Detail

AlgorithmDEMRI3

Method Detail

finalize

runAlgorithm