SimpleITK
1.0.1
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Deformably register two images using a diffeomorphic demons algorithm. More...
#include <sitkDiffeomorphicDemonsRegistrationFilter.h>
Public Types | |
typedef BasicPixelIDTypeList | PixelIDTypeList |
typedef DiffeomorphicDemonsRegistrationFilter | Self |
enum | UseGradientTypeType { Symmetric, Fixed, WarpedMoving, MappedMoving } |
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typedef ImageFilter | Self |
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typedef ProcessObject | Self |
Public Member Functions | |
DiffeomorphicDemonsRegistrationFilter () | |
Image | Execute (const Image &fixedImage, const Image &movingImage, const Image &initialDisplacementField) |
Image | Execute (const Image &fixedImage, const Image &movingImage) |
Image | Execute (const Image &fixedImage, const Image &movingImage, const Image &initialDisplacementField, const std::vector< double > &standardDeviations, uint32_t numberOfIterations, double maximumRMSError, DiffeomorphicDemonsRegistrationFilter::UseGradientTypeType useGradientType, bool useFirstOrderExp, double maximumUpdateStepLength, bool smoothDisplacementField, bool smoothUpdateField, const std::vector< double > &updateFieldStandardDeviations, unsigned int maximumKernelWidth, double maximumError, double intensityDifferenceThreshold, bool useImageSpacing) |
Image | Execute (const Image &fixedImage, const Image &movingImage, const std::vector< double > &standardDeviations, uint32_t numberOfIterations, double maximumRMSError, DiffeomorphicDemonsRegistrationFilter::UseGradientTypeType useGradientType, bool useFirstOrderExp, double maximumUpdateStepLength, bool smoothDisplacementField, bool smoothUpdateField, const std::vector< double > &updateFieldStandardDeviations, unsigned int maximumKernelWidth, double maximumError, double intensityDifferenceThreshold, bool useImageSpacing) |
uint32_t | GetElapsedIterations () const |
Number of iterations run. More... | |
double | GetIntensityDifferenceThreshold () const |
double | GetMaximumError () const |
unsigned int | GetMaximumKernelWidth () const |
double | GetMaximumRMSError () const |
double | GetMaximumUpdateStepLength () const |
double | GetMetric () const |
std::string | GetName () const |
uint32_t | GetNumberOfIterations () const |
double | GetRMSChange () const |
bool | GetSmoothDisplacementField () const |
bool | GetSmoothUpdateField () const |
std::vector< double > | GetStandardDeviations () const |
std::vector< double > | GetUpdateFieldStandardDeviations () const |
bool | GetUseFirstOrderExp () const |
UseGradientTypeType | GetUseGradientType () const |
bool | GetUseImageSpacing () const |
Self & | SetIntensityDifferenceThreshold (double IntensityDifferenceThreshold) |
Self & | SetMaximumError (double MaximumError) |
Self & | SetMaximumKernelWidth (unsigned int MaximumKernelWidth) |
Self & | SetMaximumRMSError (double MaximumRMSError) |
Self & | SetMaximumUpdateStepLength (double MaximumUpdateStepLength) |
Self & | SetNumberOfIterations (uint32_t NumberOfIterations) |
Self & | SetSmoothDisplacementField (bool SmoothDisplacementField) |
Self & | SetSmoothUpdateField (bool SmoothUpdateField) |
Self & | SetStandardDeviations (const std::vector< double > &StandardDeviations) |
Self & | SetStandardDeviations (double value) |
Self & | SetUpdateFieldStandardDeviations (const std::vector< double > &UpdateFieldStandardDeviations) |
Self & | SetUpdateFieldStandardDeviations (double value) |
Self & | SetUseFirstOrderExp (bool UseFirstOrderExp) |
Self & | SetUseGradientType (UseGradientTypeType UseGradientType) |
Self & | SetUseImageSpacing (bool UseImageSpacing) |
Self & | SmoothDisplacementFieldOff () |
Self & | SmoothDisplacementFieldOn () |
Self & | SmoothUpdateFieldOff () |
Self & | SmoothUpdateFieldOn () |
std::string | ToString () const |
Self & | UseFirstOrderExpOff () |
Self & | UseFirstOrderExpOn () |
Self & | UseImageSpacingOff () |
Self & | UseImageSpacingOn () |
~DiffeomorphicDemonsRegistrationFilter () | |
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ImageFilter () | |
virtual | ~ImageFilter ()=0 |
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virtual void | Abort () |
virtual int | AddCommand (itk::simple::EventEnum event, itk::simple::Command &cmd) |
Add a Command Object to observer the event. More... | |
virtual float | GetProgress () const |
An Active Measurement of the progress of execution. More... | |
virtual bool | HasCommand (itk::simple::EventEnum event) const |
Query of this object has any registered commands for event. More... | |
ProcessObject () | |
virtual void | RemoveAllCommands () |
Remove all registered commands. More... | |
virtual | ~ProcessObject () |
virtual void | DebugOn () |
virtual void | DebugOff () |
virtual bool | GetDebug () const |
virtual void | SetDebug (bool debugFlag) |
virtual void | SetNumberOfThreads (unsigned int n) |
virtual unsigned int | GetNumberOfThreads () const |
Private Types | |
typedef Image(Self::* | MemberFunctionType) (const Image *fixedImage, const Image *movingImage, const Image *initialDisplacementField) |
Private Member Functions | |
template<class TImageType > | |
Image | ExecuteInternal (const Image *fixedImage, const Image *movingImage, const Image *initialDisplacementField) |
Private Attributes | |
itk::ProcessObject * | m_Filter |
double | m_IntensityDifferenceThreshold |
double | m_MaximumError |
unsigned int | m_MaximumKernelWidth |
double | m_MaximumRMSError |
double | m_MaximumUpdateStepLength |
nsstd::auto_ptr< detail::MemberFunctionFactory< MemberFunctionType > > | m_MemberFactory |
uint32_t | m_NumberOfIterations |
nsstd::function< uint32_t()> | m_pfGetElapsedIterations |
nsstd::function< double()> | m_pfGetMetric |
double | m_RMSChange |
bool | m_SmoothDisplacementField |
bool | m_SmoothUpdateField |
std::vector< double > | m_StandardDeviations |
std::vector< double > | m_UpdateFieldStandardDeviations |
bool | m_UseFirstOrderExp |
UseGradientTypeType | m_UseGradientType |
bool | m_UseImageSpacing |
Friends | |
struct | detail::MemberFunctionAddressor< MemberFunctionType > |
Additional Inherited Members | |
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static bool | GetGlobalDefaultDebug () |
static void | GlobalDefaultDebugOff () |
static void | GlobalDefaultDebugOn () |
static void | SetGlobalDefaultDebug (bool debugFlag) |
static void | GlobalWarningDisplayOn () |
static void | GlobalWarningDisplayOff () |
static void | SetGlobalWarningDisplay (bool flag) |
static bool | GetGlobalWarningDisplay () |
static void | SetGlobalDefaultNumberOfThreads (unsigned int n) |
static unsigned int | GetGlobalDefaultNumberOfThreads () |
static double | GetGlobalDefaultCoordinateTolerance () |
Access the global tolerance to determine congruent spaces. More... | |
static void | SetGlobalDefaultCoordinateTolerance (double) |
Access the global tolerance to determine congruent spaces. More... | |
static double | GetGlobalDefaultDirectionTolerance () |
Access the global tolerance to determine congruent spaces. More... | |
static void | SetGlobalDefaultDirectionTolerance (double) |
Access the global tolerance to determine congruent spaces. More... | |
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virtual unsigned long | AddITKObserver (const itk::EventObject &, itk::Command *) |
virtual itk::ProcessObject * | GetActiveProcess () |
virtual void | OnActiveProcessDelete () |
virtual void | onCommandDelete (const itk::simple::Command *cmd) throw () |
virtual void | PreUpdate (itk::ProcessObject *p) |
virtual void | RemoveITKObserver (EventCommand &e) |
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NonCopyable () | |
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static void | FixNonZeroIndex (TImageType *img) |
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template<class TImageType > | |
static TImageType::ConstPointer | CastImageToITK (const Image &img) |
template<class TImageType > | |
static Image | CastITKToImage (TImageType *img) |
template<class TPixelType , unsigned int VImageDimension, unsigned int VLength, template< typename, unsigned int > class TVector> | |
static Image | CastITKToImage (itk::Image< TVector< TPixelType, VLength >, VImageDimension > *img) |
static const itk::EventObject & | GetITKEventObject (EventEnum e) |
template<typename T > | |
static std::ostream & | ToStringHelper (std::ostream &os, const T &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const char &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const signed char &v) |
static std::ostream & | ToStringHelper (std::ostream &os, const unsigned char &v) |
Deformably register two images using a diffeomorphic demons algorithm.
This class was contributed by Tom Vercauteren, INRIA & Mauna Kea Technologies, based on a variation of the DemonsRegistrationFilter . The basic modification is to use diffeomorphism exponentials.
See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache, "Non-parametric Diffeomorphic Image Registration with the Demons Algorithm", Proc. of MICCAI 2007.
DiffeomorphicDemonsRegistrationFilter implements the demons deformable algorithm that register two images by computing the deformation field which will map a moving image onto a fixed image.
A deformation field is represented as a image whose pixel type is some vector type with at least N elements, where N is the dimension of the fixed image. The vector type must support element access via operator []. It is assumed that the vector elements behave like floating point scalars.
This class is templated over the fixed image type, moving image type and the deformation field type.
The input fixed and moving images are set via methods SetFixedImage and SetMovingImage respectively. An initial deformation field maybe set via SetInitialDisplacementField or SetInput. If no initial field is set, a zero field is used as the initial condition.
The output deformation field can be obtained via methods GetOutput or GetDisplacementField.
This class make use of the finite difference solver hierarchy. Update for each iteration is computed in DemonsRegistrationFunction .
This implementation was taken from the Insight Journal paper: https://hdl.handle.net/1926/510
Definition at line 66 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Setup for member function dispatching
Definition at line 274 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
Define the pixels types supported by this filter
Definition at line 78 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
typedef DiffeomorphicDemonsRegistrationFilter itk::simple::DiffeomorphicDemonsRegistrationFilter::Self |
Definition at line 68 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
Enumerator | |
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Symmetric | |
Fixed | |
WarpedMoving | |
MappedMoving |
Definition at line 112 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
itk::simple::DiffeomorphicDemonsRegistrationFilter::DiffeomorphicDemonsRegistrationFilter | ( | ) |
Default Constructor that takes no arguments and initializes default parameters
itk::simple::DiffeomorphicDemonsRegistrationFilter::~DiffeomorphicDemonsRegistrationFilter | ( | ) |
Destructor
Image itk::simple::DiffeomorphicDemonsRegistrationFilter::Execute | ( | const Image & | fixedImage, |
const Image & | movingImage, | ||
const Image & | initialDisplacementField | ||
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Execute the filter on the input image
Image itk::simple::DiffeomorphicDemonsRegistrationFilter::Execute | ( | const Image & | fixedImage, |
const Image & | movingImage | ||
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Image itk::simple::DiffeomorphicDemonsRegistrationFilter::Execute | ( | const Image & | fixedImage, |
const Image & | movingImage, | ||
const Image & | initialDisplacementField, | ||
const std::vector< double > & | standardDeviations, | ||
uint32_t | numberOfIterations, | ||
double | maximumRMSError, | ||
DiffeomorphicDemonsRegistrationFilter::UseGradientTypeType | useGradientType, | ||
bool | useFirstOrderExp, | ||
double | maximumUpdateStepLength, | ||
bool | smoothDisplacementField, | ||
bool | smoothUpdateField, | ||
const std::vector< double > & | updateFieldStandardDeviations, | ||
unsigned int | maximumKernelWidth, | ||
double | maximumError, | ||
double | intensityDifferenceThreshold, | ||
bool | useImageSpacing | ||
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Execute the filter on the input image with the given parameters
Image itk::simple::DiffeomorphicDemonsRegistrationFilter::Execute | ( | const Image & | fixedImage, |
const Image & | movingImage, | ||
const std::vector< double > & | standardDeviations, | ||
uint32_t | numberOfIterations, | ||
double | maximumRMSError, | ||
DiffeomorphicDemonsRegistrationFilter::UseGradientTypeType | useGradientType, | ||
bool | useFirstOrderExp, | ||
double | maximumUpdateStepLength, | ||
bool | smoothDisplacementField, | ||
bool | smoothUpdateField, | ||
const std::vector< double > & | updateFieldStandardDeviations, | ||
unsigned int | maximumKernelWidth, | ||
double | maximumError, | ||
double | intensityDifferenceThreshold, | ||
bool | useImageSpacing | ||
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Number of iterations run.
This is an active measurement. It may be accessed while the filter is being executing in command call-backs and can be accessed after execution.
Definition at line 234 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 214 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired maximum error of the Guassian kernel approximate.
Definition at line 205 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired limits of the Gaussian kernel width.
Definition at line 195 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 110 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 143 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Get the metric value. The metric value is the mean square difference in intensity between the fixed image and transforming moving image computed over the the overlapping region between the two images. This value is calculated for the current iteration
This is an active measurement. It may be accessed while the filter is being executing in command call-backs and can be accessed after execution.
Definition at line 251 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Name of this class
Implements itk::simple::ProcessObject.
Definition at line 254 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 102 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the root mean squared change of the previous iteration. May not be used by all solvers.
This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
Definition at line 242 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the displacement field is smoothed (regularized). Smoothing the displacement yields a solution elastic in nature. If SmoothDisplacementField is on, then the displacement field is smoothed with a Gaussian whose standard deviations are specified with SetStandardDeviations()
Definition at line 157 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the update field is smoothed (regularized). Smoothing the update field yields a solution viscous in nature. If SmoothUpdateField is on, then the update field is smoothed with a Gaussian whose standard deviations are specified with SetUpdateFieldStandardDeviations()
Definition at line 171 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
Definition at line 94 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
Definition at line 185 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Use a first-order approximation of the exponential. This amounts to using an update rule of the type s <- s o (Id + u) instead of s <- s o exp(u)
Definition at line 134 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 120 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 226 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the threshold below which the absolute difference of intensity yields a match. When the intensities match between a moving and fixed image pixel, the update vector (for that iteration) will be the zero vector. Default is 0.001.
Definition at line 210 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired maximum error of the Guassian kernel approximate.
Definition at line 200 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the desired limits of the Gaussian kernel width.
Definition at line 190 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 106 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the maximum length in terms of pixels of the vectors in the update buffer.
Definition at line 139 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 98 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the displacement field is smoothed (regularized). Smoothing the displacement yields a solution elastic in nature. If SmoothDisplacementField is on, then the displacement field is smoothed with a Gaussian whose standard deviations are specified with SetStandardDeviations()
Definition at line 148 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get whether the update field is smoothed (regularized). Smoothing the update field yields a solution viscous in nature. If SmoothUpdateField is on, then the update field is smoothed with a Gaussian whose standard deviations are specified with SetUpdateFieldStandardDeviations()
Definition at line 162 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
Definition at line 85 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the values of the StandardDeviations vector all to value
Definition at line 88 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
Definition at line 176 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the values of the UpdateFieldStandardDeviations vector all to value
Definition at line 179 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Use a first-order approximation of the exponential. This amounts to using an update rule of the type s <- s o (Id + u) instead of s <- s o exp(u)
Definition at line 125 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 116 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 218 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 152 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of SmoothDisplacementField to true or false respectfully.
Definition at line 151 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 166 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of SmoothUpdateField to true or false respectfully.
Definition at line 165 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Print ourselves out
Reimplemented from itk::simple::ProcessObject.
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Definition at line 129 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of UseFirstOrderExp to true or false respectfully.
Definition at line 128 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 222 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Set the value of UseImageSpacing to true or false respectfully.
Definition at line 221 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 279 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 307 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 297 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 296 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 295 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 288 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 291 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 281 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 286 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 300 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 304 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 302 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 292 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 293 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 284 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 294 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 290 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 289 of file sitkDiffeomorphicDemonsRegistrationFilter.h.
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Definition at line 298 of file sitkDiffeomorphicDemonsRegistrationFilter.h.