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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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
