Medical Imaging Interaction Toolkit
2016.11.0
Medical Imaging Interaction Toolkit
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Performes deterministic streamline tracking on the input tensor image. More...
#include <itkStreamlineTrackingFilter.h>
Public Types | |
typedef StreamlineTrackingFilter | Self |
typedef SmartPointer< Self > | Pointer |
typedef SmartPointer< const Self > | ConstPointer |
typedef ImageToImageFilter< Image< DiffusionTensor3D< TTensorPixelType >, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > > | Superclass |
typedef TTensorPixelType | TensorComponentType |
typedef TPDPixelType | DirectionPixelType |
typedef Superclass::InputImageType | InputImageType |
typedef Superclass::OutputImageType | OutputImageType |
typedef Superclass::OutputImageRegionType | OutputImageRegionType |
typedef itk::Image< unsigned char, 3 > | ItkUcharImgType |
typedef itk::Image< double, 3 > | ItkDoubleImgType |
typedef itk::Image< float, 3 > | ItkFloatImgType |
typedef itk::Image< vnl_vector_fixed< double, 3 >, 3 > | ItkPDImgType |
typedef vtkSmartPointer< vtkPolyData > | FiberPolyDataType |
Public Member Functions | |
Pointer | Clone () const |
virtual const char * | GetClassName () const |
virtual FiberPolyDataType | GetFiberPolyData () |
Output fibers. More... | |
virtual void | SetSeedImage (ItkUcharImgType::Pointer _arg) |
Seeds are only placed inside of this mask. More... | |
virtual void | SetMaskImage (ItkUcharImgType::Pointer _arg) |
Tracking is only performed inside of this mask image. More... | |
virtual void | SetFaImage (ItkFloatImgType::Pointer _arg) |
Use this FA image instead of the automatically calculated one. Necessary for multi tensor tracking. More... | |
virtual void | SetSeedsPerVoxel (int _arg) |
One seed placed in the center of each voxel or multiple seeds randomly placed inside each voxel. More... | |
virtual void | SetFaThreshold (double _arg) |
FA termination criterion. More... | |
virtual void | SetStepSize (double _arg) |
Integration step size in mm. More... | |
virtual void | SetF (double _arg) |
Tensor deflection parameter f. More... | |
virtual void | SetG (double _arg) |
Tensor deflection parameter g. More... | |
virtual void | SetInterpolate (bool _arg) |
Toggle between nearest neighbour (false) and trilinear interpolation (true) More... | |
virtual void | SetMinTractLength (double _arg) |
Shorter tracts are discarded. More... | |
virtual double | GetMinTractLength () |
virtual void | SetMinCurvatureRadius (double _arg) |
Tracking is stopped if curvature radius (in mm) is too small. More... | |
virtual double | GetMinCurvatureRadius () |
virtual void | SetResampleFibers (bool _arg) |
If enabled, the resulting fibers are resampled to feature point distances of 0.5*MinSpacing. This is recommendable for very short integration steps and many seeds. If disabled, the resulting fiber bundle might become very large. More... | |
Static Public Member Functions | |
static Pointer | New () |
Protected Member Functions | |
StreamlineTrackingFilter () | |
~StreamlineTrackingFilter () | |
void | PrintSelf (std::ostream &os, Indent indent) const |
void | CalculateNewPosition (itk::ContinuousIndex< double, 3 > &pos, vnl_vector_fixed< double, 3 > &dir, typename InputImageType::IndexType &index) |
Calculate next integration step. More... | |
double | FollowStreamline (itk::ContinuousIndex< double, 3 > pos, int dirSign, vtkPoints *points, std::vector< vtkIdType > &ids, int imageIdx) |
Start streamline in one direction. More... | |
bool | IsValidPosition (itk::ContinuousIndex< double, 3 > &pos, typename InputImageType::IndexType &index, vnl_vector_fixed< double, 8 > &interpWeights, int imageIdx) |
Are we outside of the mask image? Is the FA too low? More... | |
double | RoundToNearest (double num) |
void | BeforeThreadedGenerateData () |
void | ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) |
void | AfterThreadedGenerateData () |
FiberPolyDataType | AddPolyData (FiberPolyDataType poly1, FiberPolyDataType poly2) |
Combine tracking results generated by the individual threads. More... | |
Protected Attributes | |
FiberPolyDataType | m_FiberPolyData |
vtkSmartPointer< vtkPoints > | m_Points |
vtkSmartPointer< vtkCellArray > | m_Cells |
std::vector< ItkDoubleImgType::Pointer > | m_EmaxImage |
Stores largest eigenvalues per voxel (one for each tensor) More... | |
ItkFloatImgType::Pointer | m_FaImage |
FA image used to determine streamline termination. More... | |
std::vector< ItkPDImgType::Pointer > | m_PdImage |
Stores principal direction of each tensor in each voxel. More... | |
std::vector< typename InputImageType::Pointer > | m_InputImage |
Input tensor images. For multi tensor tracking provide multiple tensor images. More... | |
int | m_NumberOfInputs |
double | m_FaThreshold |
double | m_MinCurvatureRadius |
double | m_StepSize |
int | m_MaxLength |
double | m_MinTractLength |
int | m_SeedsPerVoxel |
double | m_F |
double | m_G |
bool | m_Interpolate |
double | m_PointPistance |
bool | m_ResampleFibers |
std::vector< int > | m_ImageSize |
std::vector< double > | m_ImageSpacing |
ItkUcharImgType::Pointer | m_SeedImage |
ItkUcharImgType::Pointer | m_MaskImage |
itk::VectorContainer< int, FiberPolyDataType >::Pointer | m_PolyDataContainer |
Performes deterministic streamline tracking on the input tensor image.
Definition at line 42 of file itkStreamlineTrackingFilter.h.
typedef SmartPointer<const Self> itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::ConstPointer |
Definition at line 51 of file itkStreamlineTrackingFilter.h.
typedef TPDPixelType itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::DirectionPixelType |
Definition at line 62 of file itkStreamlineTrackingFilter.h.
typedef vtkSmartPointer< vtkPolyData > itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::FiberPolyDataType |
Definition at line 70 of file itkStreamlineTrackingFilter.h.
typedef Superclass::InputImageType itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::InputImageType |
Definition at line 63 of file itkStreamlineTrackingFilter.h.
typedef itk::Image<double, 3> itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::ItkDoubleImgType |
Definition at line 67 of file itkStreamlineTrackingFilter.h.
typedef itk::Image<float, 3> itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::ItkFloatImgType |
Definition at line 68 of file itkStreamlineTrackingFilter.h.
typedef itk::Image< vnl_vector_fixed<double,3>, 3> itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::ItkPDImgType |
Definition at line 69 of file itkStreamlineTrackingFilter.h.
typedef itk::Image<unsigned char, 3> itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::ItkUcharImgType |
Definition at line 66 of file itkStreamlineTrackingFilter.h.
typedef Superclass::OutputImageRegionType itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::OutputImageRegionType |
Definition at line 65 of file itkStreamlineTrackingFilter.h.
typedef Superclass::OutputImageType itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::OutputImageType |
Definition at line 64 of file itkStreamlineTrackingFilter.h.
typedef SmartPointer<Self> itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::Pointer |
Definition at line 50 of file itkStreamlineTrackingFilter.h.
typedef StreamlineTrackingFilter itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::Self |
Definition at line 49 of file itkStreamlineTrackingFilter.h.
typedef ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >, Image< Vector< TPDPixelType, 3 >, 3 > > itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::Superclass |
Definition at line 52 of file itkStreamlineTrackingFilter.h.
typedef TTensorPixelType itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::TensorComponentType |
Definition at line 61 of file itkStreamlineTrackingFilter.h.
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Definition at line 37 of file itkStreamlineTrackingFilter.cpp.
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Definition at line 90 of file itkStreamlineTrackingFilter.h.
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Combine tracking results generated by the individual threads.
Definition at line 836 of file itkStreamlineTrackingFilter.cpp.
References mitk::New().
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Definition at line 870 of file itkStreamlineTrackingFilter.cpp.
References MITK_INFO.
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Definition at line 75 of file itkStreamlineTrackingFilter.cpp.
References MITK_INFO, and mitk::New().
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Calculate next integration step.
Definition at line 234 of file itkStreamlineTrackingFilter.cpp.
References mitk::eps.
Pointer itk::StreamlineTrackingFilter< TTensorPixelType, TPDPixelType >::Clone | ( | ) | const |
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Start streamline in one direction.
Definition at line 467 of file itkStreamlineTrackingFilter.cpp.
References mitk::eps.
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Runtime information support.
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Output fibers.
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Are we outside of the mask image? Is the FA too low?
Definition at line 391 of file itkStreamlineTrackingFilter.cpp.
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Method for creation through the object factory.
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Definition at line 885 of file itkStreamlineTrackingFilter.cpp.
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Definition at line 67 of file itkStreamlineTrackingFilter.cpp.
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Tensor deflection parameter f.
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Use this FA image instead of the automatically calculated one. Necessary for multi tensor tracking.
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FA termination criterion.
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Tensor deflection parameter g.
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Toggle between nearest neighbour (false) and trilinear interpolation (true)
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Tracking is only performed inside of this mask image.
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Tracking is stopped if curvature radius (in mm) is too small.
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Shorter tracts are discarded.
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If enabled, the resulting fibers are resampled to feature point distances of 0.5*MinSpacing. This is recommendable for very short integration steps and many seeds. If disabled, the resulting fiber bundle might become very large.
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Seeds are only placed inside of this mask.
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One seed placed in the center of each voxel or multiple seeds randomly placed inside each voxel.
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Integration step size in mm.
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Definition at line 736 of file itkStreamlineTrackingFilter.cpp.
References line, and mitk::New().
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Definition at line 106 of file itkStreamlineTrackingFilter.h.
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Stores largest eigenvalues per voxel (one for each tensor)
Definition at line 108 of file itkStreamlineTrackingFilter.h.
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Definition at line 120 of file itkStreamlineTrackingFilter.h.
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FA image used to determine streamline termination.
Definition at line 109 of file itkStreamlineTrackingFilter.h.
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Definition at line 114 of file itkStreamlineTrackingFilter.h.
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Definition at line 104 of file itkStreamlineTrackingFilter.h.
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Definition at line 121 of file itkStreamlineTrackingFilter.h.
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Definition at line 125 of file itkStreamlineTrackingFilter.h.
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Definition at line 126 of file itkStreamlineTrackingFilter.h.
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Input tensor images. For multi tensor tracking provide multiple tensor images.
Definition at line 111 of file itkStreamlineTrackingFilter.h.
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Definition at line 122 of file itkStreamlineTrackingFilter.h.
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Definition at line 128 of file itkStreamlineTrackingFilter.h.
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Definition at line 117 of file itkStreamlineTrackingFilter.h.
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Definition at line 115 of file itkStreamlineTrackingFilter.h.
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Definition at line 118 of file itkStreamlineTrackingFilter.h.
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Definition at line 113 of file itkStreamlineTrackingFilter.h.
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Stores principal direction of each tensor in each voxel.
Definition at line 110 of file itkStreamlineTrackingFilter.h.
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Definition at line 123 of file itkStreamlineTrackingFilter.h.
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Definition at line 105 of file itkStreamlineTrackingFilter.h.
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Definition at line 130 of file itkStreamlineTrackingFilter.h.
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Definition at line 124 of file itkStreamlineTrackingFilter.h.
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Definition at line 127 of file itkStreamlineTrackingFilter.h.
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Definition at line 119 of file itkStreamlineTrackingFilter.h.
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Definition at line 116 of file itkStreamlineTrackingFilter.h.