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Perspectives on Image-Guided Transapical Beating Heart Aortic Valve Intervention
Published in The MIDAS Journal
Published in The MIDAS Journal
Image-guided interventional systems become an essential part of the modern minimally invasive surgical procedures, especially for the cardiac surgery. Transapical aortic valve implantation (TAVI) is a recently developed surgical technique to treat severe [...]
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 [...]
This document describes a contribution to the Insight Toolkit intended to perform landmark-based registration on two meshes. The method implemented here is restricted to meshes with a spherical geometry and topology. Please refer Wahba's paper for the [...]
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 [...]
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 [...]
Although the KappaStatisticImageToImageMetric can be used to obtain the Dice metric (or mean overlap), there are other related measurements that are useful for evaluating results derived from various image analysis tasks. These measures include the target [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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, [...]
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 [...]
A Novel Information-Theoretic Point-Set Measure Based on the Jensen-Havrda-Charvat-Tsallis Divergence
Published in The Insight Journal
Published in The Insight Journal
A novel point-set registration algorithm was proposed in [6] based on minimization of the Jensen-Shannon divergence. In this contribution, we generalize this Jensen-Shannon divergence point-set measure framework to the Jensen-Havrda-Charvat-Tsallis [...]
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 [...]
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 [...]
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 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. [...]
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, [...]
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 [...]
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 [...]
This document describes an ITK class implementing an Adaptive Moment Estimator (Adam) optimizer algorithm within the Insight Toolkit ITK www.itk.org. Adam is an adaptive gradient descent optimizer, which independently adaptively estimates the gradient descent [...]
This paper describes the implementation of the LDFFD and TDFFD algorithms. Both quantify motion and deformation from an input image sequence by taking profit of the temporal dimension of velocity fields in the diffeomorphic registration framework to process [...]
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 [...]
This document describes the workflow for unwarping echo planar MR images (EPI), in particular diffusion-weighted images, using an acquisition method with reversed phase encoding and the tools of the Computational Morphometry Toolkit (CMTK). This technique [...]
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 [...]
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’ [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
Personalized simulations can help assess and predict the clinical status of patients and are a key tenet of the Virtual Physiological Human (VPH) framework. This paper shows how the turnkey access of GIMIAS, an open source software platform built on open [...]
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. [...]
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 [...]
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 [...]
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. [...]
Auto-kNN: Brain Tissue Segmentation using Automatically Trained k-Nearest-Neighbor Classification
Published in The MIDAS Journal
Published in The MIDAS Journal
In this paper we applied one of our regularly used processing pipelines for fully automated brain tissue segmentation. Brain tissue was segmented in cerebrospinal fluid (CSF), gray matter (GM) and white matter (WM). Our algorithms for skull stripping, tissue [...]
Nonlinear optimization is a key component of many image registration algorithms. Improving registration speed is almost always desirable. One way to do this is to accelerate the optimization cost function using a parallel implementation. The purpose of this [...]
We have implemented filters for computing phase symmetry (PS) in ITK using steerable filters computed and applied in the Fourier domain. In some recent publications, phase symmetry has been shown to be a useful pre-processing measure for performing image [...]
This document describes the workflow for unwarping structural MR images, in particular T1-weighted SPGR and MP-RAGE scans, using reference scans of the Magphan(R) EMR051 Quantitative Imaging Phantom (a.k.a. ADNI Phantom) and the tools of the Computational [...]
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 [...]
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 [...]
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 [...]
