diff --git a/SoftwareGuide/Art/DeformableRegistration1CheckerboardAfter.jpg b/SoftwareGuide/Art/DeformableRegistration1CheckerboardAfter.jpg deleted file mode 100644 index 26cc8961..00000000 Binary files a/SoftwareGuide/Art/DeformableRegistration1CheckerboardAfter.jpg and /dev/null differ diff --git a/SoftwareGuide/Art/DeformableRegistration1CheckerboardBefore.jpg b/SoftwareGuide/Art/DeformableRegistration1CheckerboardBefore.jpg deleted file mode 100644 index ef26c258..00000000 Binary files a/SoftwareGuide/Art/DeformableRegistration1CheckerboardBefore.jpg and /dev/null differ diff --git a/SoftwareGuide/Art/DeformableRegistration1Output.jpg b/SoftwareGuide/Art/DeformableRegistration1Output.jpg deleted file mode 100644 index 97d7624a..00000000 Binary files a/SoftwareGuide/Art/DeformableRegistration1Output.jpg and /dev/null differ diff --git a/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex b/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex index 205ec079..53f8ad56 100644 --- a/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex +++ b/SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex @@ -1403,12 +1403,12 @@ \section{Namespaces}% \begin{minted}[baselinestretch=1,fontsize=\footnotesize,linenos=false,bgcolor=ltgray]{cpp} namespace itk { -namespace fem +namespace Statistics { ... -} // end namespace fem +} // end namespace Statistics } // end namespace itk \end{minted} \normalsize diff --git a/SoftwareGuide/Latex/Architecture/SpatialObjects.tex b/SoftwareGuide/Latex/Architecture/SpatialObjects.tex index 61334911..473074ec 100644 --- a/SoftwareGuide/Latex/Architecture/SpatialObjects.tex +++ b/SoftwareGuide/Latex/Architecture/SpatialObjects.tex @@ -27,7 +27,7 @@ \section{Introduction}% \item[Model-to-model registration.] Iterative closest point, landmark, and surface distance minimization methods can be used with any ITK transform, - to rigidly and non-rigidly register image, FEM, and Fourier + to rigidly and non-rigidly register image and Fourier descriptor-based representations of objects as SpatialObjects. \item[Atlas formation.] Collections of images or SpatialObjects can be diff --git a/SoftwareGuide/Latex/Architecture/SystemOverview.tex b/SoftwareGuide/Latex/Architecture/SystemOverview.tex index 63918541..5ca51707 100644 --- a/SoftwareGuide/Latex/Architecture/SystemOverview.tex +++ b/SoftwareGuide/Latex/Architecture/SystemOverview.tex @@ -58,14 +58,8 @@ \section{System Organization}% anatomical priors in both segmentation and registration methods. \item[Registration Framework.] A flexible framework for registration - supports four different types of registration: image registration, - multiresolution registration, PDE-based registration, and FEM (finite - element method) registration. - - \item[FEM Framework.] ITK includes a subsystem for solving general - FEM problems, in particular non-rigid registration. The FEM package - includes mesh definition (nodes and elements), loads, and boundary - conditions. + supports several different types of registration: image registration, + multiresolution registration, and PDE-based registration. \item[Level Set Framework.] The level set framework is a set of classes for creating filters to solve partial differential equations @@ -549,8 +543,7 @@ \section{Numerics}% use VNL under the hood and integrate with the registration framework are available. A large collection of statistics functions---not available from VNL---are also provided in the \code{Insight/Numerics/Statistics} -directory. In addition, a complete finite element (FEM) package is available, -primarily to support the deformable registration in ITK. +directory. \section{Data Representation}% diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/DeformableRegistration.tex b/SoftwareGuide/Latex/DesignAndFunctionality/DeformableRegistration.tex index 08a7593d..cc000b88 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/DeformableRegistration.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/DeformableRegistration.tex @@ -10,42 +10,6 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\subsection{FEM-Based Image Registration}% -\label{sec:FEMBasedImageRegistration} - -\begin{figure} -\centering -\includegraphics[width=0.44\textwidth]{DeformableRegistration1CheckerboardBefore.eps} -\includegraphics[width=0.44\textwidth]{DeformableRegistration1CheckerboardAfter.eps} -\itkcaption[FEM-based deformable registration results]{Checkerboard comparisons -before and after FEM-based deformable registration.}% -\label{fig:DeformableRegistration1Output} -\end{figure} - -\input{DeformableRegistration1.tex} - -Figure~\ref{fig:DeformableRegistration1Output} presents the results of -the FEM-based deformable registration applied to two time-separated -slices of a living rat dataset. Checkerboard comparisons of the two -images are shown before registration (left) and after registration -(right). Both images were acquired from the same living rat, the -first after inspiration of air into the lungs and the second after -exhalation. Deformation occurs due to the relaxation of the diaphragm -and the intercostal muscles, both of which exert force on the lung tissue -and cause air to be expelled. - -The following is a documented sample parameter file that can be used with this -deformable registration example. This example demonstrates the setup of a -basic registration problem that does not use multi-resolution strategies. As a -result, only one value for the parameters between \texttt{(\# of pixels per -element)} and \texttt{(maximum iterations)} is necessary. In order to use a -multi-resolution strategy, you would have to specify values for those -parameters at each level of the pyramid. - -\small -\verbatiminput{FiniteElementRegistrationParameters1.txt} -\normalsize - \subsection{BSplines Image Registration}% \label{sec:BSplinesImageRegistration} \input{DeformableRegistration4.tex} diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/FiniteElementRegistrationParameters1.txt b/SoftwareGuide/Latex/DesignAndFunctionality/FiniteElementRegistrationParameters1.txt deleted file mode 100644 index c7a1d2ac..00000000 --- a/SoftwareGuide/Latex/DesignAndFunctionality/FiniteElementRegistrationParameters1.txt +++ /dev/null @@ -1,60 +0,0 @@ -% Configuration file #1 for DeformableRegistration1.cxx -% -% This example demonstrates the setup of a basic registration -% problem that does NOT use multi-resolution strategies. As a -% result, only one value for the parameters between -% (# of pixels per element) and (maximum iterations) is necessary. -% If you were using multi-resolution, you would have to specify -% values for those parameters at each level of the pyramid. -% -% Note: the paths in the parameters assume you have the traditional -% ITK file hierarchy as shown below: -% -% ITK/Examples/RegistrationITKv4/DeformableRegistration1.cxx -% ITK/Examples/Data/RatLungSlice* -% ITK_Build_Dir/bin/DeformableRegistration1 -% -% --------------------------------------------------------- -% Parameters for the single- or multi-resolution techniques -% --------------------------------------------------------- -1 % Number of levels in the multi-res pyramid (1 = single-res) -1 % Highest level to use in the pyramid - 1 1 % Scaling at lowest level of pyramid - 4 % Number of pixels per element - 1.e4 % Elasticity (E) - 1.e4 % Density x capacity (RhoC) - 1 % Image energy scaling (gamma) - sets gradient step size - 2 % NumberOfIntegrationPoints - 1 % WidthOfMetricRegion - 20 % MaximumIterations -% ------------------------------- -% Parameters for the registration -% ------------------------------- -0 0.99 % Similarity metric (0=mean sq, 1 = ncc, 2=pattern int, 3=MI, 5=demons) -1.0 % Alpha -0 % DescentDirection (1 = max, 0 = min) -0 % DoLineSearch (0=never, 1=always, 2=if needed) -1.e1 % TimeStep -0.5 % Landmark variance -0 % Employ regridding / enforce diffeomorphism ( >= 1 -> true) -% ---------------------------------- -% Information about the image inputs -% ---------------------------------- -128 % Nx (image x dimension) -128 % Ny (image y dimension) -0 % Nz (image z dimension - not used if 2D) -../../Insight/Examples/Data/RatLungSlice1.mha % ReferenceFileName -../../Insight/Examples/Data/RatLungSlice2.mha % TargetFileName -% ------------------------------------------------------------------- -% The actions below depend on the values of the flags preceding them. -% For example, to write out the displacement fields, you have to set -% the value of WriteDisplacementField to 1. -% ------------------------------------------------------------------- -0 % UseLandmarks? - read the file name below if this is true -- % LandmarkFileName -./RatLung_result % ResultsFileName (prefix only) -1 % WriteDisplacementField? -./RatLung_disp % DisplacementsFileName (prefix only) -0 % ReadMeshFile? -- % MeshFileName -END diff --git a/SoftwareGuide/Latex/Introduction/Installation.tex b/SoftwareGuide/Latex/Introduction/Installation.tex index 4857c736..db1873d2 100644 --- a/SoftwareGuide/Latex/Introduction/Installation.tex +++ b/SoftwareGuide/Latex/Introduction/Installation.tex @@ -399,8 +399,8 @@ \subsection{Advanced Module Configuration}% \end{minted} \normalsize -where \code{Module\_{Module1}} could be, for example, \code{Module\_ITKFEM} for -the non-default, built-in \code{FEM} module, or \code{Module\_Cuberille} for +where \code{Module\_{Module1}} could be, for example, \code{Module\_ITKReview} for +the non-default, built-in \code{Review} module, or \code{Module\_Cuberille} for the \code{Cuberille} remote module. \item \textbf{Example 4}: Enable examples. diff --git a/SoftwareGuide/Latex/Introduction/Introduction.tex b/SoftwareGuide/Latex/Introduction/Introduction.tex index 7479112b..18af5bae 100644 --- a/SoftwareGuide/Latex/Introduction/Introduction.tex +++ b/SoftwareGuide/Latex/Introduction/Introduction.tex @@ -153,7 +153,7 @@ \section{Software Organization}% \item \code{ITK/Modules/IO} --- classes that support the reading and writing of images, transforms, and geometry. \item \code{ITK/Modules/Numerics} --- a collection of numeric modules, including - FEM, Optimization, Statistics, Neural Networks, etc. + Optimization, Statistics, Neural Networks, etc. \item \code{ITK/Modules/Registration} --- classes for registration of images or other data structures to each other. \item \code{ITK/Modules/Remote} --- a group of modules distributed outside