public class DT_TractographyImage extends PD_TractographyImage
Constructor and Description |
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DT_TractographyImage(DT[][][][] dts,
double[][][][] mps,
int[][][] npds,
int[] dataDims,
double[] voxelDims)
Constructs an image directly from an array of DTs and an array
of mixing parameters.
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DT_TractographyImage(VoxelOrderDataSource tensorSource,
int maxPDs,
int[] dataDims,
double[] voxelDims)
Constructs an image from the data sources.
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Modifier and Type | Method and Description |
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void |
computeIsotropicMask(double faThreshold)
Computes boolean mask, a voxel is true if the voxel contains one DT, and the DT's
FA is below the threshold.
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static DT_TractographyImage |
getDT_TractographyImage(java.lang.String inputFile,
java.lang.String dataType,
int maxPDs,
double[][][] anisMap,
double anisThresh,
int[] dataDims,
double[] voxelDims)
Gets an image from the data file.
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DT[] |
getDTs(int i,
int j,
int k) |
double[] |
getMix(int i,
int j,
int k) |
Vector3D[] |
getPDs(int i,
int j,
int k) |
getPD_TractographyImage
computeIsotropicMask, computeIsotropicMask, getDataDims, getIsotropicMask, getPDs, getVoxelDims, numberOfPDs, xDataDim, xVoxelDim, yDataDim, yVoxelDim, zDataDim, zVoxelDim
public DT_TractographyImage(DT[][][][] dts, double[][][][] mps, int[][][] npds, int[] dataDims, double[] voxelDims)
dts
- The array of tensors.mps
- The array of mixing parametersnpds
- The array of numbers of directionsdataDims
- array of data dimensions {xDataDim,
yDataDim, zDataDim}.voxelDims
- array of voxel dimensions (in mm) {xVoxelDim,
yVoxelDim, zVoxelDim}.public DT_TractographyImage(VoxelOrderDataSource tensorSource, int maxPDs, int[] dataDims, double[] voxelDims)
tensorSource
- sources for the diffusion tensor volumes.maxPDs
- the maximum number of PDs in a voxel.dataDims
- array of data dimensions {xDataDim, yDataDim, zDataDim}.voxelDims
- array of voxel dimensions (in mm) {xVoxelDim, yVoxelDim, zVoxelDim}.public void computeIsotropicMask(double faThreshold)
public Vector3D[] getPDs(int i, int j, int k)
getPDs
in class TractographyImage
public DT[] getDTs(int i, int j, int k)
public double[] getMix(int i, int j, int k)
public static final DT_TractographyImage getDT_TractographyImage(java.lang.String inputFile, java.lang.String dataType, int maxPDs, double[][][] anisMap, double anisThresh, int[] dataDims, double[] voxelDims)
anisMapFile
is not null
, it is read and used
for isotropic masking.inputFile
- the data file.dataType
- the data type of the data file and anisMapFile
.maxPDs
- the maximum number of PDs in a voxel.anisMap
- the anisotropy map, which is used to create the tract mask.
May be null
if not required, in which case fractional anisotropy will be used.anisThresh
- threshold for the anisotropy in the computation of the tract mask.dataDims
- array of data dimensions {xDataDim, yDataDim, zDataDim}.voxelDims
- array of voxel dimensions (in mm) {xVoxelDim, yVoxelDim, zVoxelDim}.