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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 [...]
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 [...]
Adapting the ITK Registration Framework to Fit Parametric Image Models
Published in The Insight Journal
Published in The Insight Journal
The image registration framework in the Insight Tookit offers a powerful body of code for finding the optimal spatial transform that registers one image with another. However, ITK currently lacks a way to fit parametric models of image pixel values to an [...]
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 [...]
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 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 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 [...]
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 [...]
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 [...]
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, [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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. [...]
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.
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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. [...]
For over two decades, the National Library of Medicine (NLM)
has provided support for the collection of biomedical image data for use
throughout the biomedical image, visualization and analysis community.
Data collected during the Visible Human Project has [...]
We have successfully created a software environment in which ultrasound data can be manipulated by, ITK (the Insight Tool-Kit), in real-time. We were able to access each frame generated within the resident computer of a TerasonTM Ultrasound Machine, convert [...]
The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations
Published in The Insight Journal
Published in The Insight Journal
This paper describes the Datatree module of BioImage Suite, that allows for rapid and flexible reslicing
of images based on a user-defined tree structure that organizes image and transformation data as well as
electrode localizations, image landmarks, and [...]
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 [...]
An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open-source software
Published in The Insight Journal
Published in The Insight Journal
This paper describes a new open-source tutorial for image-guided therapy (IGT) and medical robotics that is both accessible and hands-on using the LEGO Mindstorms NXT (a commercially available robotics kit) and 3D Slicer (an open-source application for [...]
Inverse Nonlinear Finite Element Methods for Surgery Simulation and Image Guidance
Published in The MIDAS Journal
Published in The MIDAS Journal
Nonlinear finite element methods are described in which cyclic organ motion is implied from 4D scan data. The equations of motion corresponding to an explicit integration of the total Lagrangian formulation are reversed, such that the sequence of node forces [...]
Characterization of anatomical structure of the brain and effi cient algorithms for automatically analyzing brain MRI have gained an increasing interest in recent years. In this paper, we propose an algorithm that automatically segments the anatomical [...]
FusionViewer: An Open Source Toolkit for Viewing Multimodality Images
Published in The Insight Journal
Published in The Insight Journal
FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) [...]
The Lung Tissue Research Consortium: An extensive open database containing histological, clinical, and radiological data to study chronic lung disease
Published in The Insight Journal
Published in The Insight Journal
The Lung Tissue Research Consortium (LTRC) is an NHLBI sponsored project which is studying histological, radiological, and clinical data on patients with Chronic Obstructive Pulmonary Disease (COPD) and idiopathic pulmonary fibrosis (IPF). At completion, [...]
