public class TractographyImage
extends java.lang.Object
Constructor and Description |
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TractographyImage(int[] dataDims,
double[] voxelDims,
int vectorsPerPD)
Basic constructor initialises dimensions only.
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TractographyImage(Vector3D[][][][] vectors,
double[] voxelDims,
int vectorsPerPD)
Matlab constructor.
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Modifier and Type | Method and Description |
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void |
computeIsotropicMask()
Computes mask for tracking.
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void |
computeIsotropicMask(double[][][] anisMap,
double threshold)
Computes mask for tracking.
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int[] |
getDataDims()
Array of data dimensions.
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boolean[][][] |
getIsotropicMask()
Gets a boolean mask image for tracking.
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Vector3D[] |
getPDs(int i,
int j,
int k) |
Vector3D[] |
getPDs(int i,
int j,
int k,
Vector3D fibreOrientation) |
double[] |
getVoxelDims()
Array of voxel dimensions in mm.
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int |
numberOfPDs(int i,
int j,
int k) |
int |
xDataDim()
Size of image in x dimension.
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double |
xVoxelDim()
Size (mm) of x voxel length.
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int |
yDataDim()
Size of image in y dimension.
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double |
yVoxelDim()
Size (mm) of y voxel length.
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int |
zDataDim()
Size of image in z dimension.
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double |
zVoxelDim()
Size (mm) of z voxel length.
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public TractographyImage(int[] dataDims, double[] voxelDims, int vectorsPerPD)
dataDims
- array of data dimensions {xDataDim, yDataDim, zDataDim}.voxelDims
- array of voxel dimensions (in mm) {xVoxelDim, yVoxelDim, zVoxelDim}.vectorsPerPD
- the number of vectors the image contains per principal direction.public TractographyImage(Vector3D[][][][] vectors, double[] voxelDims, int vectorsPerPD)
vectors
- vector data. If PDs only, there should be one vector per voxel. If eigen systems,
they should be ordered {e1, e2, e3}.dataDims
- array of data dimensions {xDataDim, yDataDim, zDataDim}.voxelDims
- array of voxel dimensions (in mm) {xVoxelDim, yVoxelDim, zVoxelDim}.vectorsPerPD
- the number of vectors the image contains per principal direction.public Vector3D[] getPDs(int i, int j, int k)
public Vector3D[] getPDs(int i, int j, int k, Vector3D fibreOrientation)
public final int numberOfPDs(int i, int j, int k)
public final int xDataDim()
public final double xVoxelDim()
public final int yDataDim()
public final double yVoxelDim()
public final int zDataDim()
public final double zVoxelDim()
public final double[] getVoxelDims()
public final int[] getDataDims()
public final void computeIsotropicMask()
true
if streamlines should terminate on entry to the voxel. This method creates a brain / background
mask. A voxel is isotropic if the number of PDs in the voxel is zero.public final void computeIsotropicMask(double[][][] anisMap, double threshold)
true
if streamlines should terminate on entry to the voxel. Background voxels are always
true
, voxels with multiple fibres are always false
.anisMap
- an image containing the some quantitative measurement of the
anisotropy of the diffusion in the voxel.threshold
- voxels with one PD and anisotropy below this value will be set
to true
.public final boolean[][][] getIsotropicMask()
true
if streamlines should terminate on entry to the voxel.