public class StreamlineROI_Filter
extends java.lang.Object
FibreTracker
. Transforms streamlines
into the seed space and processes waypoints and exclusion ROIs. Also resamples points along the
streamline to a specified minimum resolution. By default, the filtered streamline has a minimum
resolution of one tenth of the smallest voxel dimension passed to the filter.Constructor and Description |
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StreamlineROI_Filter(int[] dataDims,
double[] voxelDims)
Initializes the filter with the dimensions of the seed space.
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StreamlineROI_Filter(int xDataDim,
int yDataDim,
int zDataDim,
double xVoxelDim,
double yVoxelDim,
double zVoxelDim)
Initializes the filter with the dimensions of the seed space.
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Modifier and Type | Method and Description |
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TractCollection |
processTract(Tract t) |
TractCollection |
processTracts(TractCollection tc) |
void |
setDiscardLoops(boolean disc) |
void |
setDiscardOnExclusionEntry(boolean discard) |
void |
setEndZones(short[][][] endZones)
Set the end zones volume.
|
void |
setExclusionROIs(short[][][] exclusionROI)
Set the exclusion volume.
|
void |
setMaxTractLength(double length)
Truncates tracts if their length is more than
length mm
before any exclusion ROIs are applied. |
void |
setMaxTractPoints(int p)
Truncates tracts if they have more than
p points
before resampling and before any exclusion ROIs are applied. |
void |
setMinTractLength(double length)
Automatically remove tracts if their length is less than
length mm
before any exclusion ROIs are applied. |
void |
setMinTractPoints(int p)
Automatically remove tracts if they have less than
p points
before resampling and before any exclusion ROIs are applied. |
void |
setResampleStepSize(double size)
Filtered streamlines will be resampled to the specified step size.
|
void |
setResampleTracts(boolean resampleTracts)
Determines whether tracts will be resampled.
|
void |
setTransIntoSeedSpace(RealMatrix matrix)
Sets the transformation that warps the streamlines from diffusion space into seed space.
|
void |
setTruncateLoops(boolean trunc) |
void |
setWaypoints(short[][][] waypoints)
Set the waypoint volume.
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public StreamlineROI_Filter(int[] dataDims, double[] voxelDims)
public StreamlineROI_Filter(int xDataDim, int yDataDim, int zDataDim, double xVoxelDim, double yVoxelDim, double zVoxelDim)
public void setWaypoints(short[][][] waypoints)
waypoints
- a volume in the same voxel space as the streamlines, after transformation (if any).public void setEndZones(short[][][] endZones)
endZones
- a volume in the same voxel space as the streamlines, after transformation (if any).public void setExclusionROIs(short[][][] exclusionROI)
exclusionROI
- a volume in the same voxel space as the streamlines, after transformation (if any).public void setTransIntoSeedSpace(RealMatrix matrix)
matrix
- a 4 x 4 affine
transformation matrix.public TractCollection processTract(Tract t)
t
(truncated if necessary) or
is empty.public TractCollection processTracts(TractCollection tc)
Tract
's that pass through all waypoints, with excluded tracts
trimmed or discarded.public void setDiscardOnExclusionEntry(boolean discard)
public void setResampleTracts(boolean resampleTracts)
public void setResampleStepSize(double size)
public void setMinTractPoints(int p)
p
points
before resampling and before any exclusion ROIs are applied.public void setMinTractLength(double length)
length
mm
before any exclusion ROIs are applied.public void setMaxTractPoints(int p)
p
points
before resampling and before any exclusion ROIs are applied.public void setMaxTractLength(double length)
length
mm
before any exclusion ROIs are applied.public void setTruncateLoops(boolean trunc)
trunc
- if true, truncate loops that enter waypoint regions more than once.public void setDiscardLoops(boolean disc)
disc
- if true, discard streamlines with loops that enter waypoint regions more than once.