Nikos Paragios

Slice-to-volume medical image registration: A survey

During the last decades, the research community of medical imaging has witnessed continuous advances in image registration methods, which pushed the limits of the state-of-the-art and enabled the development of novel medical procedures. A particular type of image registration problem, known as slice-to-volume registration, played a fundamental role in areas like image guided surgeries and volumetric image reconstruction. However, to date, and despite the extensive literature available on this topic, no survey has been written to discuss this challenging problem. This paper introduces the first comprehensive survey of the literature about slice-to-volume registration, presenting a categorical study of the algorithms according to an ad-hoc taxonomy and analyzing advantages and disadvantages of every category. We draw some general conclusions from this analysis and present our perspectives on the future of the field.

Sub-cortical brain structure segmentation using F-CNN'S

In this paper we propose a deep learning approach for segmenting sub-cortical structures of the human brain in Magnetic Resonance (MR) image data. We draw inspiration from a state-of-the-art Fully-Convolutional Neural Network (F-CNN) architecture for semantic segmentation of objects in natural images, and adapt it to our task. Unlike previous CNN-based methods that operate on image patches, our model is applied on a full blown 2D image, without any alignment or registration steps at testing time. We further improve segmentation results by interpreting the CNN output as potentials of a Markov Random Field (MRF), whose topology corresponds to a volumetric grid. Alpha-expansion is used to perform approximate inference imposing spatial volumetric homogeneity to the CNN priors. We compare the performance of the proposed pipeline with a similar system using Random Forest-based priors, as well as state-of-art segmentation algorithms, and show promising results on two different brain MRI datasets.

(Hyper)-graphical models in biomedical image analysis.

Computational vision, visual computing and biomedical image analysis have made tremendous progress over the past two decades. This is mostly due the development of efficient learning and inference algorithms which allow better and richer modeling of image and visual understanding tasks. Hyper-graph representations are among the most prominent tools to address such perception through the casting of perception as a graph optimization problem. In this paper, we briefly introduce the importance of such representations, discuss their strength and limitations, provide appropriate strategies for their inference and present their application to address a variety of problems in biomedical image analysis.

Deformable Registration Through Learning of Context-Specific Metric Aggregation

We propose a novel weakly supervised discriminative algorithm for learning context specific registration metrics as a linear combination of conventional similarity measures. Conventional metrics have been extensively used over the past two decades and therefore both their strengths and limitations are known. The challenge is to find the optimal relative weighting (or parameters) of different metrics forming the similarity measure of the registration algorithm. Hand-tuning these parameters would result in sub optimal solutions and quickly become infeasible as the number of metrics increases. Furthermore, such hand-crafted combination can only happen at global scale (entire volume) and therefore will not be able to account for the different tissue properties. We propose a learning algorithm for estimating these parameters locally, conditioned to the data semantic classes. The objective function of our formulation is a special case of non-convex function, difference of convex function, which we optimize using the concave convex procedure. As a proof of concept, we show the impact of our approach on three challenging datasets for different anatomical structures and modalities.

Hyper-Graphs Inference through Convex Relaxations and Move Making Algorithms: Contributions and Applications in Artificial Vision

Computational visual perception seeks to reproduce human visionthrough the combination of visual sensors, artificial intelligence andcomputing. To this end, computer vision tasks are often reformulatedas mathematical inference problems where the objective is to determinethe set of parameters corresponding to the lowest potential of a taskspecificobjective function. Graphical models have been the most popularformulation in the field over the past two decades where the problemis viewed as a discrete assignment labeling one. Modularity, scalabilityand portability are the main strengths of these methods which oncecombined with efficient inference algorithms they could lead to state ofthe art results. In this tutorial we focus on the inference component ofthe problem and in particular we discuss in a systematic manner themost commonly used optimization principles in the context of graphicalmodels. Our study concerns inference over low rank models interactionsbetween variables are constrained to pairs as well as higher orderones arbitrary set of variables determine hyper-cliques on which constraintsare introduced and seeks a concise, self-contained presentationof prior art as well as the presentation of the current state of the artmethods in the field.

Graph-Based Slice-to-Volume Deformable Registration

Deformable image registration is a fundamental problem in computer vision and medical image computing. In this paper we investigate the use of graphical models in the context of a particular type of image registration problem, known as slice-to-volume registration. We introduce a scalable, modular and flexible formulation that can accommodate low-rank and high order terms, that simultaneously selects the plane and estimates the in-plane deformation through a single shot optimization approach. The proposed framework is instantiated into different variants seeking either a compromise between computational efficiency (soft plane selection constraints and approximate definition of the data similarity terms through pair-wise components) or exact definition of the data terms and the constraints on the plane selection. Simulated and real-data in the context of ultrasound and magnetic resonance registration (where both framework instantiations as well as different optimization strategies are considered) demonstrate the potentials of our method.

Prior-Based Coregistration and Cosegmentation

We propose a modular and scalable framework for dense coregistration and cosegmentation with two key characteristics: first, we substitute ground truth data with the semantic map output of a classifier; second, we combine this output with population deformable registration to improve both alignment and segmentation. Our approach deforms all volumes towards consensus, taking into account image similarities and label consistency. Our pipeline can incorporate any classifier and similarity metric. Results on two datasets, containing annotations of challenging brain structures, demonstrate the potential of our method.

Rigid Slice-To-Volume Medical Image Registration Through Markov Random Fields

Rigid slice-to-volume registration is a challenging task, which finds application in medical imaging problems like image fusion for image guided surgeries and motion correction for volume reconstruction. It is usually formulated as an optimization problem and solved using standard continuous methods. In this paper, we discuss how this task be formulated as a discrete labeling problem on a graph. Inspired by previous works on discrete estimation of linear transformations using Markov Random Fields (MRFs), we model it using a pairwise MRF, where the nodes are associated to the rigid parameters, and the edges encode the relation between the variables. We compare the performance of the proposed method to a continuous formulation optimized using simplex, and we discuss how it can be used to further improve the accuracy of our approach. Promising results are obtained using a monomodal dataset composed of magnetic resonance images (MRI) of a beating heart.

Comparison of Multi-resolution Analysis Patterns for Texture Classification of Breast Tumors Based On DCE-MRI

Although Fourier and Wavelet Transform have been widely used for texture classification methods in medical images, the discrimination performance of FDCT has not been investigated so far in respect to breast cancer detection. Ιn this paper, three multi-resolution transforms, namely the Discrete Wavelet Transform (DWT), the Stationary Wavelet Transform (SWT) and the Fast Discrete Curvelet Transform (FDCT) were comparatively assessed with respect to their ability to discriminate between malignant and benign breast tumors in Dynamic Contrast-Enhanced Magnetic Resonance Images (DCE-MRI). The mean and entropy of the detail sub-images for each decomposition scheme were used as texture features, which were subsequently fed as input into several classifiers. FDCT features fed to a Linear Discriminant Analysis (LDA) classifier produced the highest overall classification performance (93.18 % Accuracy).

Deformable group-wise registration using a physiological model: Application to diffusion-weighted MRI

Intensity variations can often be described by a physiological or temporal model applied on a voxel-wise basis across a group of images. However the voxel correspondence might be unknown, imposing the need for a group-wise deformable registration coupled with the computation of the model parameters. In this paper we propose a group-wise registration method of medical images that incorporates the temporal dimension (reflecting the change of signal amplitude) of the acquisition process. Consistency on the spatiotemporal physiological model, as well as deformation smoothness, is imposed in order to produce anatomically meaningful representations of the 3D images. The performance of the proposed method is compared to two different group-wise registration approaches; one that penalizes the absolute differences in the intensities and one that penalizes the intensity range among the images on corresponding regions. We chose as an application paradigm the registration of diffusion-weighted magnetic resonance (DW-MR) images for the evaluation of patients with lymphomas. A dataset consisting of 25 patients, each scanned with 3 “b values”, was used to evaluate the methods accuracy. The proposed registration method outperfomed the other two registration approaches, making it a very promising method for highlighting the importance of DWI as an imaging biomarker.