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In this article, we present an implementation of a flexible framework for non-parametric variational image registration, realized as part of ITK's finite difference solver hierarchy.
In a variational registration setting, the transformation is found by [...]
Kernel-based transforms such as the thin plate spline are frequently used to model deformations in medical
imaging. The existing implementation in ITK is capable of being used to warp images, but does not
work in the registration framework. The existing [...]
Model-Image Registration of Parametric Shape Models: Fitting a Shell to the Cochlea
Published in The Insight Journal
Published in The Insight Journal
Mathematical models are often used to describe natural phenomena, organisms and anatomy. This paper presents a Model-Image Registration framework that can be used to evaluate models of anatomical shape. An optimisation process is applied to the model [...]
Homogeneous transformations are widely used in computer vision and graphics. They commonly arise
when considering the transformation of an image of a planar object under arbitrary camera motion, or the
transformation of two images of the same scene due to [...]
The recent ITKv4 refactoring includes several enhancements to the existing registration framework. These additional transform classes provide access to mappings described by dense displacement fields and their corresponding optimization which complement the [...]
Affine Transformation for Landmark Based Registration Initializer in ITK
Published in The MIDAS Journal
Published in The MIDAS Journal
This document describes an affine transformation algorithm as an additional feature for landmark based registration in ITK www.itk.org. The algorithm is based on the paper by Spath, H [1]. The author derives a set of linear equations from paired landmarks and [...]
A Framework for Comparison and Evaluation of Nonlinear Intra-Subject Image Registration Algorithms
Published in The Insight Journal
Published in The Insight Journal
Performance validation of nonlinear registration algorithms is a difficult problem due to the lack of a suitable ground truth in most applications. However, the ill-posed nature of the nonlinear registration problem and the large space of possible solutions [...]
In this paper, a software application is introduced for image registration. BrainDemonsWarp is a com-
mand line program using Thirion and diffeomorphic demons algorithms. The program takes in a template
image and a target image along with other optional [...]
An ITK implementation of the Normalized Gradient Field Image to Image Metric
Published in The Insight Journal
Published in The Insight Journal
This article describes the ITK implementation of a Normalized Gradient Fields
based image-to-image metric. Some properties of the metric are discussed and example registrations are presented.
Information-Theoretic Directly Manipulated Free-Form Deformation Labeled Point-Set Registration
Published in The Insight Journal
Published in The Insight Journal
Our previous contributions to the ITK community include a generalized B-spline approximation scheme as well as a generalized information-theoretic measure for assessing point-set correspondence known as the Jensen-Havrda-Charvat-Tsallis (JHCT) divergence. In [...]
Diffeomorphic demons registration was widely used for medical image registration. This document describes the addition of mask processing mode with spatial objects for itkDiffeomorphicemonsRegistrationFilter when just considering the deformation field at the [...]
This document presents a GUI application to manually select corresponding points in two data sets. The data sets can each be either an image or a point cloud. If both data sets are images, the functionality is equivalent to Matlab's 'cpselect' function. There [...]
BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit
Published in The Insight Journal
Published in The Insight Journal
The University of Iowa’s Psychiatric Iowa Neuroimaging Consortium (PINC) has developed a program for mutual information registration of 3D brain imaging data using ITK classes, called BRAINSFit. We have written a helper class, [...]
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy
Published in The Insight Journal
Published in The Insight Journal
This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion's demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver [...]
Rotational Registration of Spherical Surfaces Represented as QuadEdge Meshes
Published in The Insight Journal
Published in The Insight Journal
This document describes a contribution to the Insight Toolkit intended to support the process of registering two Meshes. The methods included here are restricted to Meshes with a Spherical geometry and topology, and with scalar values associated to their [...]
In this work,
we extend a previously demonstrated entropy based groupwise registration method
to include a non-rigid deformation model based on B-splines.
We describe an open source implementation of the groupwise registration algorithm
using the [...]
An ITK Implementation of the Symmetric Log-Domain Diffeomorphic Demons Algorithm
Published in The Insight Journal
Published in The Insight Journal
This article provides an implementation of the symmetric log-domain diffeomorphic image registration algorithm, or symmetric demons algorithm for short. It generalizes Thirion's demons and the diffeomorphic demons algorithm. The main practical advantages of [...]
Robot assisted prostate surgery using augmented reality with deformable models
Published in The MIDAS Journal
Published in The MIDAS Journal
We present preliminary results of our work to develop an augmented display for improved visualization
of the prostate and surrounding critical anatomy for robot-assisted prostate surgery. Prostate
cancer is the second leading cause of cancer-related deaths in [...]
Very preterm birth coincides with a period of major development in the brain, with striking changes in volume, cortex folding and significant change at the microstructural level. Diffusion MRI is sensitive to motion of water on the scale of microns, allowing [...]
Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems
Published in The Insight Journal
Published in The Insight Journal
This document describes work-in-progress for refactoring ITK’s registration methods to exploit the parallel, computation power of multi-processor, shared-memory systems. Refactoring includes making the methods multi-threaded as well as optimizing the [...]
This paper describes the implementation of a multidimensional block-matching nonrigid registration
algorithm. The main features of the algorithm are its simplicity, its free form nature, the modularity of
the similarity measure, which makes it possible [...]
We provide examples and highlights of Advanced Normalization Tools (ANTS) that address practical problems in real data. A variety of image and point similarity metrics and elastic, diffeomorphic, affine and other variations of transformation models are [...]
Voxel Value Ratio Variance Image Registration Metric for the Insight Toolkit
Published in The Insight Journal
Published in The Insight Journal
This document describes a cost function, or metric, for use in image registration using the Insight Toolkit. The RatioVarianceImageToImageMetric class implements a metric which is calculated from the variance of the ratios of voxel values of the moving and [...]
This document describes a new simple gradient descent optimizer which is a potential
replacement or supplement for RegularStepGradientDescentOptimizer. The optimizer requires only the gradient of the parameters and uses a simple linear model internally. [...]
This document describes the implementation of image samplers using the Insight Toolkit ITK url{www.itk.org}. Image samplers take a set of `picks' from an image and store them in an array. A sample consists of the location of the pick (a point) and the [...]
Robot Assisted Needle Placement: Application developed using an open source image guided surgery toolkit (IGSTK)
Published in The Insight Journal
Published in The Insight Journal
Using a robot system to position needles or needle shaped tools during clinical procedures such as biopsy, radio frequency ablation, and target drug delivery has a great potentials in increasing accuracy and speed of the process, and minimizing trauma to [...]
Transitively Consistent and Unbiased Multi-Image Registration using Numerically Stable Transformation Synchronisation
Published in The MIDAS Journal
Published in The MIDAS Journal
Transitive consistency of pairwise transformations is a desirable property of groupwise image registration procedures. The transformation synchronisation method (Bernard et al., 2015) is able to retrieve transitively consistent pairwise transformations from [...]
An ITK-Based Framework for 2D-3D Registration with Multiple Fixed Images
Published in The Insight Journal
Published in The Insight Journal
This document describes an extension of the Insight Toolkit (ITK, www.itk.org) for 2D-3D registration with multiple fixed images, that is, registration of a three-dimensional dataset to a group of fixed planar projections. 2D-3D registration is possible with [...]
Atlas to Image-with-Tumor Registration Based on Demons and Deformation Inpainting
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper presents a method for nonlinear registration of images, where there exists no one-to-one correspondence in parts of the image. Such a situation occurs for instance in the case where an atlas of normal anatomy shall be matched to pathological data, [...]
Cardiac Interventional Guidance using Multimodal Data Processing and Visualisation: medInria as an Interoperability Platform
Published in The MIDAS Journal
Published in The MIDAS Journal
medInria is a free medical imaging software developed at Inria, which aims at
providing clinicians with state-of-the-art algorithms dedicated to medical image
processing and visualization. Efforts have been made to simplify the user
interface, while keeping [...]
Improving The Oriented Image Class For Use In The Registration Framework
Published in The Insight Journal
Published in The Insight Journal
The original design of the ITK registration framework was based around the itk::Image class, which
assumed that the pixel axes were aligned with the coordinate system axes. The itk::OrientedImage
was added later as a subclass, but problems remain with its [...]
Image registration using the Morphon algorithm: an ITK implementation
Published in The Insight Journal
Published in The Insight Journal
Medical image registration is becoming a more and more useful component of a large number of applications. The presented method aims to enrich the ITK library. This method, called Morphon registration algorithm, computes a dense deformation field accepting [...]
This document describes a module that extends the Insight Toolkit, ITK, which reads DICOM Spatial Rogistration Object files in itk::Transform's. Currently, DICOM files are read by applying the DCMTK library as a backend. An itk::DCMTKTransformIO class can be [...]
N-Dimensional Computation of Strain Tensor Images in the Insight Toolkit
Published in The Insight Journal
Published in The Insight Journal
Strain quantifies local deformation of a solid body. In medical imaging, strain reflects how tissue deforms
under load. Or, it can quantify growth or atrophy of tissue, such as the growth of a tumor. Additionally,
strain from the transformation that results [...]
Being able to quickly compute the inverse of a deformation field is often useful in the context of medical image analysis. While ITK supports this functionality, the current algorithms are slow and do not always yield accurate results. In this paper we [...]
Helper class for initializing the grid parameters of a BSpline deformable transform by using an image as reference
Published in The Insight Journal
Published in The Insight Journal
This document describes a simple helper class intended for making easy to initialize the grid parameters of a BSplineDeformableTranform. This paper is accompanied with the source code, input data, parameters and output data that we used for validating the [...]
Gauss-Newton Method for Segmentation assisted Deformable Registration
Published in The MIDAS Journal
Published in The MIDAS Journal
In this work, we try to develop a fast converging method for
segmentation assisted deformable registration. The segmentation step
consists of a piece-wise constant Mumford-Shah energy model while reg-
istration is driven by the sum of squared distances of [...]
Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
Published in The MIDAS Journal
Published in The MIDAS Journal
Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]
Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
Published in The MIDAS Journal
Published in The MIDAS Journal
Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]
BioImage Suite is an integrated image analysis software suite
developed at Yale. It uses a combination of C++ and Tcl in the same
fashion as that pioneered by the Visualization Toolkit (VTK) and it
leverages both VTK and the Insight Toolkit. It has [...]
Impact of motion correction on the quantitative analysis of DCE-MR Images
Published in The Insight Journal
Published in The Insight Journal
Dynamic magnetic resonance imaging (DCE-MRI) carried out with
contrast media such as Gd-chelate complex (Gd-DTPA) allows the
non-invasive assessment of microcirculatory characteristics of
malignant lesions. Quantitative estimation of lesion [...]
This paper focuses on the important role of open-source software in the development of a fully-automatic and accurate registration system for images of Quadrature Tomographic Microscopy. The system is correspondence-based, using the framework provided by [...]
Optimal mass transport for deformable registration and warping of 2D images
Published in The Insight Journal
Published in The Insight Journal
We implement a warping method which is using the properties of elastic materials to compute the deformation between two images. The proposed elastic registration method incorporates the L2 Kantorovich-Wasserstein distance, also known as the Earth Mover’s [...]
This paper describes the implementation of a multidimensional block-matching nonrigid registration algorithm. The main features of the algorithm are its simplicity, its free form nature, the modularity of the similarity measure, which makes it possible using [...]
We propose an open source and cross platform medical image viewer, named VV, designed for qualita tive evaluation of images registration, in particular for deformable registration of 4D CT images. VV can display multiple spatio-temporal image sequences (2D+t [...]
Many image registration algorithms are formulated as optimization
problems with a gradient descent based solver, One difficulty with
designing and implementing such methods is in the implementation of
the [...]
This guide is intended as a very brief introduction of the main tools in the Computational Morphometry Toolkit (CMTK), which is available in source code and as precompiled binaries from http://www.nitrc.org/projects/cmtk/. The target audience of this document [...]
As demonstrated by the example videos accompanying this submission of the
multiresolution implementation of Spherical Demons, the registration appears
reasonable. However, we are still unable to replicate the warps from the
stable and well verified [...]
Fully Automatic Left Ventricle Segmentation in Cardiac Cine MR Images Using Registration and Minimum Surfaces
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper describes a fully automatic system to segment the left ventricle in all slices and all phases of a magnetic resonance cardiac cine study. After localizing the left ventricle blood pool using motion, thresholding and clustering, slices are [...]
Mattes’ Mutual Information Metric for Multimodality Registration of DESS and T2 Mapped Knee Articular MR Sequences
Published in The Insight Journal
Published in The Insight Journal
Registration of multiple MR sequences remains a challenging problem. The Insight Toolkit (ITK) implements the Mattes’ mutual information metric for multimodality registration. Here, example source code, data, and executable files to implement the Mattes’ [...]
Non-destructive evaluation(NDE) is a group of analysis techniques used in industry to evaluate the property of a material, component or product without causing damage. Among all the techniques, radiology and thermography are two most common methods that are [...]
This document describes the use and implementation of first and second order spatial derivatives of coordinate transformations in the Insight Toolkit url{www.itk.org}). Spatial derivatives are useful for many types of regularising or penalty terms frequently [...]
Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
Published in The MIDAS Journal
Published in The MIDAS Journal
Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]
This paper describes the Statismo framework, which is a framework for PCA based statistical models.Statistical models are used to describe the variability of an object within a population, learned from a set of training samples. Originally developed to model [...]
Nonrigid image registration is an important, but resource demanding and time-consuming task in medical image analysis. This limits its application in time-critical clinical routines. In this report we explore acceleration of two time-consuming parts of a [...]
A Multi-atlas Approach for the Automatic Segmentation of Multiple Structures in Head and Neck CT Images
Published in The MIDAS Journal
Published in The MIDAS Journal
A multi-atlas approach is proposed for the automatic segmentation of nine different structures in a set of head and neck CT images for radiotherapy. The approach takes advantage of a training dataset of 25 images to build average head and neck atlases of [...]
To facilitate the analysis of medical image data in research environment, MATITK is developed to allow ITK algorithms to be called in MATLAB. ITK is a powerful open-source image analysis toolkit, but it requires the knowledge of C++ to use it. With the help [...]
Validation of real-time intensity based 2D/3D registration for image guided radiotherapy
Published in The MIDAS Journal
Published in The MIDAS Journal
Patient motion during radiotherapy or intra-fractional motion, is one of the major sources of uncertainty in dose application. 2D/3D registration is an intensity based method used successfully to track tumor motion with the potential to reduce uncertainty. [...]
Incorporating Metric Flows and Sparse Jacobian Transformations in ITK
Published in The Insight Journal
Published in The Insight Journal
Various metrics have been proposed in the literature for performing intrinsic automatic image to image registration. Among these measures, mutual information is a very popular one because of its robustness and accuracy for a wide variety of applications. In [...]
ITK-based Registration of Large Images from Light Microscopy: A Biomedical Application
Published in The Insight Journal
Published in The Insight Journal
Inactivation of the retinoblastoma gene in mouse embryos results
in morphological changes in the placenta, which has been shown to
affect fetal survivability. The construction of a 3D virtual
placenta aids in accurately quantifying structural changes [...]
Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK
Published in The Insight Journal
Published in The Insight Journal
The Allen Brain Atlas (ABA) project aims to create a
cellular-resolution, genome-wide map of gene expression in the adult
mouse brain. The resulting in situ hybridization (ISH) image data
will be available free-of-charge to the public. Additionally, we [...]
Realistic And Efficient Brain-Skull Interaction Model For Brain Shift Computation
Published in The MIDAS Journal
Published in The MIDAS Journal
In this paper we propose the usage of a very efficient contact implementation for modeling the brain-skull interaction. This contact algorithm is specially design for our Dynamic Relaxation solution method for solving soft-tissue registration problems. It [...]
Extending MITK by a real-time online video overlay navigation system for minimally invasive surgery
Published in The MIDAS Journal
Published in The MIDAS Journal
The purpose of this paper is to present our extension of the MITK toolkit by a real-time navigation system for computer assisted surgery. The system was developed with laparoscopic partial nephrectomies as a first application scenario. The main goal of the [...]
This paper describes an integrated system for dental implantation including both preoperative planning utilizing computer-aided technology and automatic robot operation during the intra-operative stage. A novel two-step registration procedure was applied for [...]
Robust Scattered Data Points Approximation Using Finite Element Biomechanical Model
Published in The Insight Journal
Published in The Insight Journal
Many enabling technologies like non-rigid registration in medical image computing rely on the construction of a function by interpolating scattered points; however, the outliers contained in the data and the approximation error make the robust and accurate [...]
A GPU-based Implementation of Multimodal Deformable Image Registration Based on Mutual Information or Bhattacharyya Distance
Published in The Insight Journal
Published in The Insight Journal
This paper describes a multimodal deformable image registration method on the GPU. It is a CUDA-based implementation of a paper by E. D'Agostino et. al, ''A viscous fluid model for multimodal non-rigid image registration using mutual information''. In [...]
Phase Correlation Method (PCM or SPOMF - Symmetric Phase-Only Matched Filter) is a well known image registration method, that exploits Fourier Shift Theorem property of Fourier Transform. Even though it is limited to estimate only shifts between two images, [...]
Automatic accuracy measurement for multi-modal rigid registration using feature descriptors
Published in The MIDAS Journal
Published in The MIDAS Journal
In radiotherapy (RT) for tumor delineation and diagnostics, complementary information of multi-modal images is used. Using high ionizing radiation, the accuracy of registered volume data is crucial; therefore a reliable and robust evaluation method for [...]
An ITK-based Implementation of the Stochastic Rank Correlation (SRC) Metric
Published in The Insight Journal
Published in The Insight Journal
Recently, Birkfellner et al. proposed a novel image-to-image merit function (stochastic rank correlation, SRC) for robust intensity-based 2D/3D image registration. In this work, we summarize the basic idea of SRC, and present a generic ITK-based [...]
An ITK Implementation of Physics-based Non-rigid Registration Method
Published in The Insight Journal
Published in The Insight Journal
As part of the ITK v4 project efforts, we have developed ITK filters for physics-based non-rigid registration (PBNRR), which satisfies the following requirements: account for tissue properties in the registration, improve accuracy compared to rigid [...]
A novel atlas-selection approach for multi-atlas based segmentation using the correlation of inter-atlas similarities
Published in The MIDAS Journal
Published in The MIDAS Journal
Automated segmentation is a frequently applied task in the course of medical imaging. Furthermore, it is a substantial component of image-guided radiotherapy. Atlas based segmentation is one of the most frequently used approach for automated segmentation. [...]
BioImage Suite: An integrated medical image analysis suite: An update
Published in The Insight Journal
Published in The Insight Journal
BioImage Suite is an NIH-supported medical image analysis software suite developed at Yale. It
leverages both the Visualization Toolkit (VTK) and the Insight Toolkit (ITK) and it includes many additional
algorithms for image analysis especially in the areas [...]
We describe the open source implementation of an adaptive tetrahedral mesh generator particularly targeted for non-rigid FEM registration of MR images. While many medical imaging applications require robust mesh generation, there are few codes available. [...]
3D Voxel-Based Volumetric Image Registration with Volume-View Guidance
Published in The Insight Journal
Published in The Insight Journal
In this article, we will present a novel interactive image registration technique using the 3D volumetric view as guidance throughout the registration process. The registration criterion used in this technique is the homogeneity of the color distribution on [...]
Nonlinear Elastic Registration with Unbiased Regularization in Three Dimensions
Published in The MIDAS Journal
Published in The MIDAS Journal
We propose a new nonlinear image registration model which is based on nonlinear elastic regularization and unbiased registration. The nonlinear elastic and the unbiased regularization terms are simplified using the change of variables by introducing an [...]
Multimodal Registration of White Matter Brain Data via Optimal Mass Transport
Published in The MIDAS Journal
Published in The MIDAS Journal
The elastic registration of medical scans from different acquisition sequences is becoming an important topic for many research labs that would like to continue the post-processing of medical scans acquired via the new generation of high-field-strength [...]
Segmentation of Head and Neck CT Scans Using Atlas-based Level Set Method
Published in The MIDAS Journal
Published in The MIDAS Journal
In this paper, we present an atlas-based level set automatic method for segmenting anatomical structures in head and neck CT data, such as mandible and brainstem. The proposed method is a hybrid method that combines two aspects. First, we register the atlas [...]
ITK-Based Implementation of Two-Projection 2D/3D Registration Method with an Application in Patient Setup for External Beam Radiotherapy
Published in The Insight Journal
Published in The Insight Journal
This document describes an ITK-based implementation of intensity-based 2D/3D rigid image registration for patient setup assessment in external beam radiotherapy. The registration framework was designed to simultaneously register two projection images to a 3D [...]
Multiple Sclerosis Detection in Multispectral Magnetic Resonance Images with Principal Components Analysis.
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper presents a local feature vector based method for automated Multiple Sclerosis (MS) lesion segmentation of multi spectral MRI data. Twenty datasets from MS patients with FLAIR, T1,T2, MD and FA data with expert annotations are available as training [...]
Automatic Segmentation of Head and Neck CT Images by GPU-Accelerated Multi-atlas Fusion
Published in The MIDAS Journal
Published in The MIDAS Journal
Treatment planning for high precision radiotherapy of head and neck (H&N) cancer patients requires accurate delineation of critical structures. Manual contouring is tedious and often suffers from large inter- and intra-rater variability. In this paper, we [...]
Active Contour-Based Segmentation of Head and Neck with Adaptive Atlas Selection
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper presents automated segmentation of structures in the Head and Neck (H&N) region, using an active contour-based joint registration and segmentation model. A new atlas selection strategy is also used. Segmentation is performed based on the dense [...]
