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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmBrainExtractor
extends AlgorithmBase
```
A class for segmenting the brain from a 3D MRI. The algorithm is partially based on the paper:
```
  BET: Brain Extraction Tool
 

  Stephen M. Smith
 

  FMRIB Technical Report TR00SMS2
 

  Oxford Centre for Functional Magnetic Resonance Imaging of the Brain
 

 
```
See the document BrainExtraction.pdf for a detailed description of the algorithm as implemented in this class. A few modifications to the original algorithm were made.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`protected class`	`AlgorithmBrainExtractor.Edge`	A representation of an edge for the vertex-edge-triangle table.
`private class`	`AlgorithmBrainExtractor.UnorderedSetInt`	An unordered set of 'int' stored in an array.

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 boolean`	`abort`	If true stop processing.
`private float`	`aboveMedian`	factor above median at which edge values are taken to zero.
`private float[]`	`box`	DOCUMENT ME!
`private int[]`	`direction`	DOCUMENT ME!
`private boolean`	`extractPaint`	If true, do not phyically segment the image but generate a paint mask.
`private float`	`fUpdate1`	Factor used in controlling the input of the tangetial component of the surface evolution.
`protected float`	`imageFactor`	Controls how much the image influences the surface evolution.
`private WildMagic.LibGraphics.SceneGraph.TriMesh`	`initialMesh`
`protected float[]`	`m_afCurvature`	Stores curvature information of the surface.
`protected float[]`	`m_afLength`	Triangle edge length.
`protected int[]`	`m_aiConnect`	Surface triangle connection.
`protected int[]`	`m_aiImage`	The 3D MRI image stored as a 1D array.
`protected byte[]`	`m_aiMask`	Brain segmenation mask.
`protected AlgorithmBrainExtractor.UnorderedSetInt[]`	`m_akAdjacent`	Surface adjacentcy list.
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akSNormal`	Surface normals.
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akSTangent`	Surface tangents.
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akVertex`	Surface vertex list.
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akVMean`	Average vector.
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akVNormal`	Vertex normal.
`private float`	`m_fBrainSelection`	Factored used to adjust image influence - this is a fixed value.
`protected float`	`m_fEParam`	DOCUMENT ME!
`protected float`	`m_fFParam`	DOCUMENT ME!
`protected float`	`m_fMeanEdgeLength`	Mean length of the vector.
`protected float`	`m_fRayDelta`	DOCUMENT ME!
`protected float`	`m_fReductionX`	Reduce the size of the 1st axis of the ellipsoid so that it fits entirely into brain.
`protected float`	`m_fReductionY`	Reduce the size of the 2st axis of the ellipsoid so that it fits entirely into brain.
`protected float`	`m_fReductionZ`	Reduce the size of the 3st axis of the ellipsoid so that it fits entirely into brain.
`protected float`	`m_fStiffness`	Stiffness of the surface.
`protected float`	`m_fXDelta`	The size of a voxel, in voxel units.
`protected float`	`m_fYDelta`	The size of a voxel, in voxel units.
`protected float`	`m_fZDelta`	The size of a voxel, in voxel units.
`protected int`	`m_iBackThreshold`	Backgroung threshold.
`protected int`	`m_iBrightThreshold`	High threshold.
`protected int`	`m_iDMax`	Dilation size used in generating boundary from the surface.
`protected int`	`m_iMaxDepth`	The length of the vector _normal_ to the surface to sample along.
`protected int`	`m_iMaxThreshold`	Histogram maximum intensity parameter.
`protected int`	`m_iMedianIntensity`	Histogram median intensity parameter.
`protected int`	`m_iMinThreshold`	Histogram minimum intensity parameter.
`protected int`	`m_iQuantity`	The MRI image bounds and quantity of voxels.
`protected int`	`m_iTQuantity`	The number of triangle in the ellipsoid.
`protected int`	`m_iVQuantity`	The number of vertices in the ellipsoid.
`protected int`	`m_iXBound`	The MRI image bounds and quantity of voxels.
`protected int`	`m_iYBound`	The MRI image bounds and quantity of voxels.
`protected int`	`m_iZBound`	The MRI image bounds and quantity of voxels.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`m_kCenter`	initial ellipsoid parameters.
`protected java.util.HashMap<AlgorithmBrainExtractor.Edge,java.lang.Integer>`	`m_kEMap`	Edge map.
`protected WildMagic.LibFoundation.Mathematics.Matrix3f`	`m_kRotate`	Used to rotate the initial mesh into the same orientation as the data.
`private int`	`nBrainVoxels`	The number of voxels that define the brain.
`protected int`	`nIterations`	Number of surface evolutions.
`protected int`	`orientationFlag`	Indicated the orientation of the dataset.
`private boolean`	`runOneIter`	If true run one iteration so that one can observe initial surface location.
`static int`	`SAT_COR`	Indicates that the image is in Sagittal or Coronal orientation.
`private boolean`	`saveBrainMesh`	If true, the surface representing the brain (mesh) is saved.
`private boolean`	`secondStageErosion`	Tells whether second stage which erodes edge values exceeding median by a factor >= aboveMedian occurs.
`private float[]`	`startLocation`	Origin of the image.
`private boolean`	`useSphere`	If true initialize surface as a sphere.

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
`AlgorithmBrainExtractor(ModelImage srcImg, int orientation, boolean runOneIteration, boolean estimateSphere, WildMagic.LibFoundation.Mathematics.Vector3f centerPoint)`	Create an extractor for segmenting the brain from a 3D magnetic resonance image.
`AlgorithmBrainExtractor(ModelImage srcImg, int orientation, WildMagic.LibGraphics.SceneGraph.TriMesh initialMesh, int medianIntensity, WildMagic.LibFoundation.Mathematics.Vector3f centerPoint)`	Create an extractor for segmenting the brain from a 3D magnetic resonance image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`computeMeanEdgeLength()`	Compute the average length of all the edges in the triangle mesh.
`protected void`	`computeMedianIntensity()`	Compute the median intensity of those voxels inside the initial ellipsoid.
`protected void`	`computeMedianIntensityInitial()`	Compute the median intensity of those voxels inside the initial ellipsoid.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`computeNewCenter()`
`protected void`	`computeVertexInformation()`	Let V[i] be a vertex in the triangle mesh.
`protected void`	`computeVertexNormals()`	Compute the vertex normals of the triangle mesh.
`protected boolean`	`estimateEllipsoid()`	Approximate the brain surface by an ellipsoid.
`protected void`	`estimateSphere()`	Approximate the intial brain surface by an sphere.
`void`	`extractBrain()`	The segmentation function.
`void`	`finalize()`	Prepares this class for destruction.
`protected void`	`floodFill(int iX, int iY, int iZ)`	Identify voxels enclosed by the brain surface by using a flood fill.
`protected void`	`generateEllipsoidMesh(int iSubdivisions)`	Tessellate a unit sphere centered at the origin.
`byte[]`	`getBrainMask()`	Get the 3D image that represents the extracted brain.
`float`	`getBrainSelection()`	Get the current brain selection term, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`float`	`getBrainVolume()`	Get the 3D image that represents the extracted brain.
`int`	`getDilationSize()`	Get the dilation size for dilating the voxelized brain surface obtained by rasterizing the triangle mesh.
`protected int`	`getIndex(int iX, int iY, int iZ)`	A convenience function for mapping the 3D voxel position (iX,iY,iZ) to a 1D array index.
`protected void`	`getInsideVoxels(boolean doErode)`	Identify all voxels that are inside or on the mesh that represents the brain surface.
`protected int`	`getIntersectX(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f kV2, int iY, int iZ)`	Compute the point of intersection between a line (0,iY,iZ)+t(1,0,0) and the triangle defined by the three input points.
`protected int`	`getIntersectY(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f kV2, int iX, int iZ)`	Compute the point of intersection between a line (iX,0,iZ)+t(0,1,0) and the triangle defined by the three input points.
`protected int`	`getIntersectZ(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f kV2, int iX, int iY)`	Compute the point of intersection between a line (iX,iY,0)+t(0,0,1) and the triangle defined by the three input points.
`int`	`getMaxDepth()`	Get the maximum depth, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`float`	`getRayDelta()`	Get the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`float`	`getReductionX()`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`float`	`getReductionY()`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`float`	`getReductionZ()`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`float`	`getStiffness()`	Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution.
`void`	`histogramAnalysis()`	Analyze the histogram of the 10-bit binned 3D MRI.
`void`	`reIntialize()`	Reinitialize when secondStageErosion has been performed so that the mask will match the eroded image.
`void`	`runAlgorithm()`	Starts the program.
`protected void`	`saveMesh(boolean flip)`	Internal support to write vertices, normals, and connectivity indices to the file.
`void`	`setAboveMedian(float aboveMedian)`	sets the aboveMedian ratio for second stage erosion Edge values >= median * aboveMedian are taken to zero.
`void`	`setBrainSelection(float fBrainSelection)`	Set the brain selection term, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`void`	`setDilationSize(int iDMax)`	Set the dilation size for dilating the voxelized brain surface obtained by rasterizing the triangle mesh.
`void`	`setExtractPaint(boolean extractPaint)`	Sets whether to extract the brain to a paint mask instead of removing non-brain image data.
`void`	`setImageRatio(float ratio)`	Sets the number of iterations.
`void`	`setIterations(int nIter)`	Sets the number of iterations.
`void`	`setJustIntialEllipsoid(boolean flag)`	Indicates if surface evolution should be skipped.
`void`	`setMaxDepth(int iMaxDepth)`	Set the maximum depth, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`void`	`setOrientation(int orientation)`	Indicates the orientation of the image for use in the ellipsoid estimation.
`void`	`setRayDelta(float fRayDelta)`	Set the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution.
`void`	`setReductionX(float fReduction)`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`void`	`setReductionY(float fReduction)`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`void`	`setReductionZ(float fReduction)`	Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf.
`void`	`setSaveBrainMesh(boolean saveMesh)`	Sets whether to save a surface mesh of the extracted brain.
`void`	`setSecondStageErosion(boolean secondStageErosion)`	Sets whether or not second stage erosion occurs taking edge values exceeding median by a factor >= aboveMedian to zero.
`void`	`setStiffness(float fStiffness)`	Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution.
`void`	`setUseSphere(boolean flag)`	Don't try estimating ellipse as initial surface use sphere estimate.
`protected float`	`update2(int i)`	Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction.
`protected float`	`update3(int i)`	Compute the coefficient of the vertex normal for the update of the mesh vertex V[i] in the VNormal[i] direction.
`protected boolean`	`updateCenter(WildMagic.LibFoundation.Mathematics.Vector3f Center)`
`void`	`updateMesh()`	The heart of the segmentation.

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
  - SAT_COR
```
public static final int SAT_COR
```
    Indicates that the image is in Sagittal or Coronal orientation.
    
    See Also:
    
    Constant Field Values
  - imageFactor
```
protected float imageFactor
```
    Controls how much the image influences the surface evolution.
  - m_afCurvature
```
protected float[] m_afCurvature
```
    Stores curvature information of the surface.
  - m_afLength
```
protected float[] m_afLength
```
    Triangle edge length.
  - m_aiConnect
```
protected int[] m_aiConnect
```
    Surface triangle connection.
  - m_aiImage
```
protected int[] m_aiImage
```
    The 3D MRI image stored as a 1D array. The mapping from (x,y,z) to 1D is: index = x + xbound*(y + ybound*z).
  - m_aiMask
```
protected byte[] m_aiMask
```
    Brain segmenation mask.
  - m_akAdjacent
```
protected AlgorithmBrainExtractor.UnorderedSetInt[] m_akAdjacent
```
    Surface adjacentcy list.
  - m_akSNormal
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akSNormal
```
    Surface normals.
  - m_akSTangent
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akSTangent
```
    Surface tangents.
  - m_akVertex
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akVertex
```
    Surface vertex list.
  - m_akVMean
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akVMean
```
    Average vector.
  - m_akVNormal
```
protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akVNormal
```
    Vertex normal.
  - m_fEParam
```
protected float m_fEParam
```
    DOCUMENT ME!
  - m_fFParam
```
protected float m_fFParam
```
    DOCUMENT ME!
  - m_fMeanEdgeLength
```
protected float m_fMeanEdgeLength
```
    Mean length of the vector.
  - m_fRayDelta
```
protected float m_fRayDelta
```
    DOCUMENT ME!
  - m_fReductionX
```
protected float m_fReductionX
```
    Reduce the size of the 1st axis of the ellipsoid so that it fits entirely into brain.
  - m_fReductionY
```
protected float m_fReductionY
```
    Reduce the size of the 2st axis of the ellipsoid so that it fits entirely into brain.
  - m_fReductionZ
```
protected float m_fReductionZ
```
    Reduce the size of the 3st axis of the ellipsoid so that it fits entirely into brain.
  - m_fStiffness
```
protected float m_fStiffness
```
    Stiffness of the surface.
  - m_fXDelta
```
protected float m_fXDelta
```
    The size of a voxel, in voxel units.
  - m_fYDelta
```
protected float m_fYDelta
```
    The size of a voxel, in voxel units.
  - m_fZDelta
```
protected float m_fZDelta
```
    The size of a voxel, in voxel units.
  - m_iBackThreshold
```
protected int m_iBackThreshold
```
    Backgroung threshold.
  - m_iBrightThreshold
```
protected int m_iBrightThreshold
```
    High threshold.
  - m_iDMax
```
protected int m_iDMax
```
    Dilation size used in generating boundary from the surface.
  - m_iMaxDepth
```
protected int m_iMaxDepth
```
    The length of the vector _normal_ to the surface to sample along.
  - m_iMaxThreshold
```
protected int m_iMaxThreshold
```
    Histogram maximum intensity parameter.
  - m_iMedianIntensity
```
protected int m_iMedianIntensity
```
    Histogram median intensity parameter.
  - m_iMinThreshold
```
protected int m_iMinThreshold
```
    Histogram minimum intensity parameter.
  - m_iTQuantity
```
protected int m_iTQuantity
```
    The number of triangle in the ellipsoid.
  - m_iVQuantity
```
protected int m_iVQuantity
```
    The number of vertices in the ellipsoid.
  - m_iXBound
```
protected int m_iXBound
```
    The MRI image bounds and quantity of voxels.
  - m_iYBound
```
protected int m_iYBound
```
    The MRI image bounds and quantity of voxels.
  - m_iZBound
```
protected int m_iZBound
```
    The MRI image bounds and quantity of voxels.
  - m_iQuantity
```
protected int m_iQuantity
```
    The MRI image bounds and quantity of voxels.
  - m_kCenter
```
protected WildMagic.LibFoundation.Mathematics.Vector3f m_kCenter
```
    initial ellipsoid parameters.
  - m_kEMap
```
protected java.util.HashMap<AlgorithmBrainExtractor.Edge,java.lang.Integer> m_kEMap
```
    Edge map.
  - m_kRotate
```
protected WildMagic.LibFoundation.Mathematics.Matrix3f m_kRotate
```
    Used to rotate the initial mesh into the same orientation as the data.
  - nIterations
```
protected int nIterations
```
    Number of surface evolutions.
  - orientationFlag
```
protected int orientationFlag
```
    Indicated the orientation of the dataset. Default sagittal/cornal
  - abort
```
private final boolean abort
```
    If true stop processing.
    
    See Also:
    
    Constant Field Values
  - aboveMedian
```
private float aboveMedian
```
    factor above median at which edge values are taken to zero.
  - box
```
private float[] box
```
    DOCUMENT ME!
  - direction
```
private int[] direction
```
    DOCUMENT ME!
  - extractPaint
```
private boolean extractPaint
```
    If true, do not phyically segment the image but generate a paint mask.
  - fUpdate1
```
private float fUpdate1
```
    Factor used in controlling the input of the tangetial component of the surface evolution.
  - m_fBrainSelection
```
private float m_fBrainSelection
```
    Factored used to adjust image influence - this is a fixed value.
  - nBrainVoxels
```
private int nBrainVoxels
```
    The number of voxels that define the brain.
  - runOneIter
```
private boolean runOneIter
```
    If true run one iteration so that one can observe initial surface location.
  - saveBrainMesh
```
private boolean saveBrainMesh
```
    If true, the surface representing the brain (mesh) is saved.
  - secondStageErosion
```
private boolean secondStageErosion
```
    Tells whether second stage which erodes edge values exceeding median by a factor >= aboveMedian occurs.
  - startLocation
```
private float[] startLocation
```
    Origin of the image. Upper left hand corner of the first image.
  - useSphere
```
private boolean useSphere
```
    If true initialize surface as a sphere.
  - initialMesh
```
private WildMagic.LibGraphics.SceneGraph.TriMesh initialMesh
```
- Constructor Detail
  - AlgorithmBrainExtractor
```
public AlgorithmBrainExtractor(ModelImage srcImg,
                               int orientation,
                               boolean runOneIteration,
                               boolean estimateSphere,
                               WildMagic.LibFoundation.Mathematics.Vector3f centerPoint)
```
    Create an extractor for segmenting the brain from a 3D magnetic resonance image.
    
    Parameters:
    
    srcImg - The source image. Should be MR image of the brain
    
    orientation - Image orienation
    
    runOneIteration - Run one iteration so that one can observe initial surface location.
    
    estimateSphere - Use sphere as the initial surface to be evolved.
    
    centerPoint - The center of the initial ellipsoid or sphere.
  - AlgorithmBrainExtractor
```
public AlgorithmBrainExtractor(ModelImage srcImg,
                               int orientation,
                               WildMagic.LibGraphics.SceneGraph.TriMesh initialMesh,
                               int medianIntensity,
                               WildMagic.LibFoundation.Mathematics.Vector3f centerPoint)
```
    Create an extractor for segmenting the brain from a 3D magnetic resonance image.
    
    Parameters:
    
    srcImg - The source image. Should be MR image of the brain
    
    orientation - Image orienation
    
    runOneIteration - Run one iteration so that one can observe initial surface location.
    
    estimateSphere - Use sphere as the initial surface to be evolved.
    
    centerPoint - The center of the initial ellipsoid or sphere.
- Method Detail
  - extractBrain
```
public void extractBrain()
```
    The segmentation function. Ideally, the only work an application needs to do is create an MjBrainExtractor object and call the method extractBrain(). Various parameters managed by MjBrainExtractor may be modified, if necessary, before the call.
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getBrainMask
```
public final byte[] getBrainMask()
```
    Get the 3D image that represents the extracted brain. The image is ternary and has the same dimensions as the input MRI. A voxel value of 0 indicates background. A voxel value of 1 indicates brain surface. A voxel value of 2 indicates a voxel inside the brain surface.
    
    Returns:
    
    the image that represents the extracted brain
  - getBrainSelection
```
public final float getBrainSelection()
```
    Get the current brain selection term, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 0.5.
    
    Returns:
    
    the current brain selection term
  - getBrainVolume
```
public final float getBrainVolume()
```
    Get the 3D image that represents the extracted brain. The image is ternary and has the same dimensions as the input MRI. A voxel value of 0 indicates background. A voxel value of 1 indicates brain surface. A voxel value of 2 indicates a voxel inside the brain surface.
    
    Returns:
    
    the image that represents the extracted brain
  - getDilationSize
```
public final int getDilationSize()
```
    Get the dilation size for dilating the voxelized brain surface obtained by rasterizing the triangle mesh. The rasterization is designed so that the voxel surface has no holes, thereby allowing it to be flood-filled. But just in case numerical round-off errors cause a few holes, this parameter is exposed for public use. The default value is 0 (no dilation). If the value is D > 0, the dilation mask is a cube of size (2*D+1)x(2*D+1)x(2*D+1).
    
    Returns:
    
    the current dilation size
  - getMaxDepth
```
public final int getMaxDepth()
```
    Get the maximum depth, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 7.
    
    Returns:
    
    the current maximum depth
  - getRayDelta
```
public final float getRayDelta()
```
    Get the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 1.0.
    
    Returns:
    
    the current spacing
  - getReductionX
```
public final float getReductionX()
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.6.
    
    Returns:
    
    the current reduction factor
  - getReductionY
```
public final float getReductionY()
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.4.
    
    Returns:
    
    the current reduction factor
  - getReductionZ
```
public final float getReductionZ()
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.6.
    
    Returns:
    
    the current reduction factor
  - getStiffness
```
public final float getStiffness()
```
    Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution. The default value is 0.1.
    
    Returns:
    
    the current stiffness
  - histogramAnalysis
```
public void histogramAnalysis()
```
    Analyze the histogram of the 10-bit binned 3D MRI. The function computes a minimum threshold, a maximum threshold, and a background threshold that are used in the image term of the surface evolution. A brightness threshold is also computed that is used for determining the initial ellipsoid that approximates the brain surface.
  - reIntialize
```
public void reIntialize()
```
    Reinitialize when secondStageErosion has been performed so that the mask will match the eroded image.
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setAboveMedian
```
public final void setAboveMedian(float aboveMedian)
```
    sets the aboveMedian ratio for second stage erosion Edge values >= median * aboveMedian are taken to zero.
    
    Parameters:
    
    aboveMedian - DOCUMENT ME!
  - setBrainSelection
```
public final void setBrainSelection(float fBrainSelection)
```
    Set the brain selection term, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 0.5.
    
    Parameters:
    
    fBrainSelection - the new brain selection term
  - setDilationSize
```
public final void setDilationSize(int iDMax)
```
    Set the dilation size for dilating the voxelized brain surface obtained by rasterizing the triangle mesh. The rasterization is designed so that the voxel surface has no holes, thereby allowing it to be flood-filled. But just in case numerical round-off errors cause a few holes, this parameter is exposed for public use. The default value is 0 (no dilation). If the value is D > 0, the dilation mask is a cube of size (2*D+1)x(2*D+1)x(2*D+1).
    
    Parameters:
    
    iDMax - the new dilation size
  - setExtractPaint
```
public void setExtractPaint(boolean extractPaint)
```
    Sets whether to extract the brain to a paint mask instead of removing non-brain image data.
    
    Parameters:
    
    extractPaint - whether to extract the brain to a paint mask
  - setImageRatio
```
public final void setImageRatio(float ratio)
```
    Sets the number of iterations.
    
    Parameters:
    
    ratio - DOCUMENT ME!
  - setIterations
```
public final void setIterations(int nIter)
```
    Sets the number of iterations.
    
    Parameters:
    
    nIter - DOCUMENT ME!
  - setJustIntialEllipsoid
```
public final void setJustIntialEllipsoid(boolean flag)
```
    Indicates if surface evolution should be skipped. This is helpful when determining if the initial ellipsoid is a good estimate.
    
    Parameters:
    
    flag - if true skip evolution of surface
  - setMaxDepth
```
public final void setMaxDepth(int iMaxDepth)
```
    Set the maximum depth, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 7.
    
    Parameters:
    
    iMaxDepth - the new maximum depth
  - setOrientation
```
public final void setOrientation(int orientation)
```
    Indicates the orientation of the image for use in the ellipsoid estimation.
    
    Parameters:
    
    orientation - the new image orientation
  - setRayDelta
```
public final void setRayDelta(float fRayDelta)
```
    Set the spacing along the vertex normal rays, as described in BrainExtraction.pdf, that is part of the image term in the surface evolution. The default value is 1.0.
    
    Parameters:
    
    fRayDelta - the new normal ray spacing
  - setReductionX
```
public final void setReductionX(float fReduction)
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.6.
    
    Parameters:
    
    fReduction - the amount to reduce the axis of the ellipsoid.
  - setReductionY
```
public final void setReductionY(float fReduction)
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.5.
    
    Parameters:
    
    fReduction - the amount to reduce the axis of the ellipsoid.
  - setReductionZ
```
public final void setReductionZ(float fReduction)
```
    Set the reduction factor for estimating the initial ellipsoid, as described in BrainExtraction.pdf. The default value is 0.6.
    
    Parameters:
    
    fReduction - the amount to reduce the axis of the ellipsoid.
  - setSaveBrainMesh
```
public void setSaveBrainMesh(boolean saveMesh)
```
    Sets whether to save a surface mesh of the extracted brain.
    
    Parameters:
    
    saveMesh - whether to save a brain surface mesh
  - setSecondStageErosion
```
public final void setSecondStageErosion(boolean secondStageErosion)
```
    Sets whether or not second stage erosion occurs taking edge values exceeding median by a factor >= aboveMedian to zero.
    
    Parameters:
    
    secondStageErosion - DOCUMENT ME!
  - setStiffness
```
public final void setStiffness(float fStiffness)
```
    Set the stiffness of the mesh, as described in BrainExtraction.pdf, that is part of the surface normal term in the surface evolution. The default value is 0.1.
    
    Parameters:
    
    fStiffness - the new stiffness
  - setUseSphere
```
public final void setUseSphere(boolean flag)
```
    Don't try estimating ellipse as initial surface use sphere estimate.
    
    Parameters:
    
    flag - if true estimate initial surface with sphere and not ellipse.
  - updateMesh
```
public void updateMesh()
```
    The heart of the segmentation. This function is responsible for the evolution of the triangle mesh that approximates the brain surface. The update has a tangential component, a surface normal component, and a vertex normal component for each vertex in the mesh. The first two components control the geometry of the mesh. The last component is based on the MRI data itself. See BrainExtraction.pdf for a detailed description of the update terms.
  - computeMeanEdgeLength
```
protected void computeMeanEdgeLength()
```
    Compute the average length of all the edges in the triangle mesh.
  - computeMedianIntensityInitial
```
protected void computeMedianIntensityInitial()
```
    Compute the median intensity of those voxels inside the initial ellipsoid. This intensity is used in the image term of the surface evolution.
  - computeMedianIntensity
```
protected void computeMedianIntensity()
```
    Compute the median intensity of those voxels inside the initial ellipsoid. This intensity is used in the image term of the surface evolution.
  - computeVertexInformation
```
protected void computeVertexInformation()
```
    Let V[i] be a vertex in the triangle mesh. This function computes VMean[i], the average of the immediate neighbors of V[i]. Define S[i] = VMean[i] - V[i]. The function also computes a surface normal SNormal[i], the component of S[i] in the vertex normal direction. STangent[i] = S[i] - SNormal[i] is computed as an approximation to a tangent to the surface. Finally, Curvature[i] is an approximation of the surface curvature at V[i].
  - computeVertexNormals
```
protected void computeVertexNormals()
```
    Compute the vertex normals of the triangle mesh. Each vertex normal is the unitized average of the non-unit triangle normals for those triangles sharing the vertex.
  - computeNewCenter
```
protected WildMagic.LibFoundation.Mathematics.Vector3f computeNewCenter()
```
  - estimateEllipsoid
```
protected boolean estimateEllipsoid()
```
    Approximate the brain surface by an ellipsoid. The approximation is based on locating all voxels of intensity larger than a brightness threshold and that are part of the upper-half of the head. The idea is that the scalp voxels in the upper-half form lie approximately on an ellipsoidal surface.
    
    NOTE. The assumption is that the traversal from bottom to top of head is in the y-direction of the 3D image. It does not matter if the top of the head has y-values smaller/larger than those for the bottom of the head. If this assumption is not met, the image should be permuted OR this code must be modified to attempt to recognize the orientation of the head
    
    Returns:
    
    DOCUMENT ME!
  - estimateSphere
```
protected void estimateSphere()
```
    Approximate the intial brain surface by an sphere. Find the center of mass and approimate radius
  - floodFill
```
protected void floodFill(int iX,
                         int iY,
                         int iZ)
```
    Identify voxels enclosed by the brain surface by using a flood fill. The flood fill is nonrecursive to avoid overflowing the program stack.
    
    Parameters:
    
    iX - the x-value of the seed point for the fill
    
    iY - the y-value of the seed point for the fill
    
    iZ - the z-value of the seed point for the fill
  - generateEllipsoidMesh
```
protected void generateEllipsoidMesh(int iSubdivisions)
```
    Tessellate a unit sphere centered at the origin. Start with an octahedron and subdivide. The final mesh is then affinely mapped to the initial ellipsoid produced by estimateEllipsoid(). The subdivision scheme is described in BrainExtraction.pdf.
    
    Parameters:
    
    iSubdivisions - the number of levels to subdivide the ellipsoid
  - getIndex
```
protected final int getIndex(int iX,
                             int iY,
                             int iZ)
```
    A convenience function for mapping the 3D voxel position (iX,iY,iZ) to a 1D array index. The images are stored as 1D arrays, so this function is used frequently.
    
    Parameters:
    
    iX - the x-value of the voxel position
    
    iY - the y-value of the voxel position
    
    iZ - the z-value of the voxel position
    
    Returns:
    
    the 1D array index corresponding to (iX,iY,iZ)
  - getInsideVoxels
```
protected void getInsideVoxels(boolean doErode)
```
    Identify all voxels that are inside or on the mesh that represents the brain surface. The surface voxels are constructed by rasterizing the triangles of the mesh in 3D. The centroid of these voxels is used as a seed point for a flood fill of the region enclosed by the surface.
    
    Parameters:
    
    doErode - DOCUMENT ME!
  - getIntersectX
```
protected int getIntersectX(WildMagic.LibFoundation.Mathematics.Vector3f kV0,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV1,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV2,
                            int iY,
                            int iZ)
```
    Compute the point of intersection between a line (0,iY,iZ)+t(1,0,0) and the triangle defined by the three input points. All calculations are in voxel coordinates and the x-value of the intersection point is truncated to an integer.
    
    Parameters:
    
    kV0 - a 3D vertex of the triangle
    
    kV1 - a 3D vertex of the triangle
    
    kV2 - a 3D vertex of the triangle
    
    iY - the y-value of the origin of the line
    
    iZ - the z-value of the origin of the line
    
    Returns:
    
    the x-value of the intersection
  - getIntersectY
```
protected int getIntersectY(WildMagic.LibFoundation.Mathematics.Vector3f kV0,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV1,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV2,
                            int iX,
                            int iZ)
```
    Compute the point of intersection between a line (iX,0,iZ)+t(0,1,0) and the triangle defined by the three input points. All calculations are in voxel coordinates and the y-value of the intersection point is truncated to an integer.
    
    Parameters:
    
    kV0 - a 3D vertex of the triangle
    
    kV1 - a 3D vertex of the triangle
    
    kV2 - a 3D vertex of the triangle
    
    iX - the x-value of the origin of the line
    
    iZ - the z-value of the origin of the line
    
    Returns:
    
    the y-value of the intersection
  - getIntersectZ
```
protected int getIntersectZ(WildMagic.LibFoundation.Mathematics.Vector3f kV0,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV1,
                            WildMagic.LibFoundation.Mathematics.Vector3f kV2,
                            int iX,
                            int iY)
```
    Compute the point of intersection between a line (iX,iY,0)+t(0,0,1) and the triangle defined by the three input points. All calculations are in voxel coordinates and the z-value of the intersection point is truncated to an integer.
    
    Parameters:
    
    kV0 - a 3D vertex of the triangle
    
    kV1 - a 3D vertex of the triangle
    
    kV2 - a 3D vertex of the triangle
    
    iX - the x-value of the origin of the line
    
    iY - the y-value of the origin of the line
    
    Returns:
    
    the z-value of the intersection
  - saveMesh
```
protected void saveMesh(boolean flip)
                 throws java.io.IOException
```
    Internal support to write vertices, normals, and connectivity indices to the file.
    
    Parameters:
    
    flip - if the y axis should be flipped - true for extract, false for from another surface
    
    Throws:
    
    java.io.IOException - if there is an error writing to the file
  - update2
```
protected float update2(int i)
```
    Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction. See BrainExtraction.pdf for a description of the update.
    
    Parameters:
    
    i - the index of the vertex to update
    
    Returns:
    
    the coefficient of SNormal[i] for the update
  - update3
```
protected float update3(int i)
```
    Compute the coefficient of the vertex normal for the update of the mesh vertex V[i] in the VNormal[i] direction. See BrainExtraction.pdf for a description of the update.
    
    Parameters:
    
    i - the index of the vertex to update
    
    Returns:
    
    the coefficient of VNormal[i] for the update
  - updateCenter
```
protected boolean updateCenter(WildMagic.LibFoundation.Mathematics.Vector3f Center)
```

Class AlgorithmBrainExtractor

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

SAT_COR

imageFactor

m_afCurvature

m_afLength

m_aiConnect

m_aiImage

m_aiMask

m_akAdjacent

m_akSNormal

m_akSTangent

m_akVertex

m_akVMean

m_akVNormal

m_fEParam

m_fFParam

m_fMeanEdgeLength

m_fRayDelta

m_fReductionX

m_fReductionY

m_fReductionZ

m_fStiffness

m_fXDelta

m_fYDelta

m_fZDelta

m_iBackThreshold

m_iBrightThreshold

m_iDMax

m_iMaxDepth

m_iMaxThreshold

m_iMedianIntensity

m_iMinThreshold

m_iTQuantity

m_iVQuantity

m_iXBound

m_iYBound

m_iZBound

m_iQuantity

m_kCenter

m_kEMap

m_kRotate

nIterations

orientationFlag

abort

aboveMedian

box

direction

extractPaint

fUpdate1

m_fBrainSelection

nBrainVoxels

runOneIter

saveBrainMesh

secondStageErosion

startLocation

useSphere

initialMesh

Constructor Detail

AlgorithmBrainExtractor

AlgorithmBrainExtractor

Method Detail

extractBrain

finalize

getBrainMask

getBrainSelection

getBrainVolume

getDilationSize

getMaxDepth

getRayDelta