Feasibility of automated 3-dimensional magnetic resonance imaging pancreas segmentation.

PurposeWith the advent of MR guided radiotherapy, internal organ motion can be imaged simultaneously during treatment. In this study, we evaluate the feasibility of pancreas MRI segmentation using state-of-the-art segmentation methods.Methods and materialT2 weighted HASTE and T1 weighted VIBE images were acquired on 3 patients and 2 healthy volunteers for a total of 12 imaging volumes. A novel dictionary learning (DL) method was used to segment the pancreas and compared to t mean-shift merging (MSM), distance regularized level set (DRLS), graph cuts (GC) and the segmentation results were compared to manual contours using Dice's index (DI), Hausdorff distance and shift of the-center-of-the-organ (SHIFT).ResultsAll VIBE images were successfully segmented by at least one of the auto-segmentation method with DI >0.83 and SHIFT ≤2 mm using the best automated segmentation method. The automated segmentation error of HASTE images was significantly greater. DL is statistically superior to the other methods in Dice's overlapping index. For the Hausdorff distance and SHIFT measurement, DRLS and DL performed slightly superior to the GC method, and substantially superior to MSM. DL required least human supervision and was faster to compute.ConclusionOur study demonstrated potential feasibility of automated segmentation of the pancreas on MRI images with minimal human supervision at the beginning of imaging acquisition. The achieved accuracy is promising for organ localization

Finsler Active Contours

©2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.DOI: 10.1109/TPAMI.2007.70713In this paper, we propose an image segmentation technique based on augmenting the conformal (or geodesic) active contour framework with directional information. In the isotropic case, the euclidean metric is locally multiplied by a scalar conformal factor based on image information such that the weighted length of curves lying on points of interest (typically edges) is small. The conformal factor that is chosen depends only upon position and is in this sense isotropic. Although directional information has been studied previously for other segmentation frameworks, here, we show that if one desires to add directionality in the conformal active contour framework, then one gets a well-defined minimization problem in the case that the factor defines a Finsler metric. Optimal curves may be obtained using the calculus of variations or dynamic programming-based schemes. Finally, we demonstrate the technique by extracting roads from aerial imagery, blood vessels from medical angiograms, and neural tracts from diffusion-weighted magnetic resonance imagery

Spectral Clustering en IRM de diffusion pour Retrouver les Faisceaux de la Matière Blanche

White matter fiber clustering allows to get insight about anatomical structures in order to generate atlases, perform clear visualizations and compute statistics across subjects, all important and current neuroimaging problems. In this work, we present a Diffusion Maps clustering method applied to diffusion MRI in order to cluster and segment complex white matter fiber bundles. It is well-known that Diffusion Tensor Imaging (DTI) is restricted in complex fiber regions with crossings and this is why recent High Angular Resolution Diffusion Imaging (HARDI) such has Q-Ball Imaging (QBI) have been introduced to overcome these limitations. QBI reconstructs the diffusion orientation distribution function (ODF), a spherical function that has its maxima agreeing with the underlying fiber populations. In this paper, we introduce the usage of the Diffusion Maps technique and show how it can be used to directly cluster set of fiber tracts, that could be obtained through a streamline tractography for instance, and how it can also help in segmenting fields of ODF images, obtained through a linear and regularized ODF estimation algorithm based on a spherical harmonics representation of the Q-Ball data. We first show the advantage of using Diffusion Maps clustering over classical methods such as N-Cuts and Laplacian Eigenmaps in both cases. In particular, our Diffusion Maps requires a smaller number of hypothesis from the input data, reduces the number of artifacts in fiber tract clustering and ODF image segmentation and automatically exhibits the number of clusters in both cases by using an adaptive scale-space parameter. We also show that our ODF Diffusion Maps clustering can reproduce published results using the diffusion tensor (DT) clustering with N-Cuts on simple synthetic images without crossings. On more complex data with crossings, we show that our ODF-based method succeeds to separate fiber bundles and crossing regions whereas the DT-based methods generate artifacts and exhibit wrong number of clusters. Finally, we illustrate the potential of our approach on a real brain dataset where we successfully segment well-known fiber bundles

Diffusion Maps Clustering for Magnetic Resonance Q-Ball Imaging Segmentation

International audienceWhite matter fiber clustering aims to get insight about anatomical structures in order to generate atlases, perform clear visualizations, and compute statistics across subjects, all important and current neuroimaging problems. In this work, we present a diffusion maps clustering method applied to diffusion MRI in order to segment complex white matter fiber bundles. It is well known that diffusion tensor imaging (DTI) is restricted in complex fiber regions with crossings and this is why recent high-angular resolution diffusion imaging (HARDI) such as Q-Ball imaging (QBI) has been introduced to overcome these limitations. QBI reconstructs the diffusion orientation distribution function (ODF), a spherical function that has its maxima agreeing with the underlying fiber populations. In this paper, we use a spherical harmonic ODF representation as input to the diffusion maps clustering method.We first show the advantage of using diffusion maps clustering over classical methods such as N-Cuts and Laplacian eigenmaps. In particular, our ODF diffusion maps requires a smaller number of hypothesis from the input data, reduces the number of artifacts in the segmentation, and automatically exhibits the number of clusters segmenting the Q-Ball image by using an adaptive scalespace parameter.We also show that our ODF diffusion maps clustering can reproduce published results using the diffusion tensor (DT) clustering with N-Cuts on simple synthetic images without crossings. On more complex data with crossings, we show that our ODF-based method succeeds to separate fiber bundles and crossing regions whereas the DT-based methods generate artifacts and exhibit wrong number of clusters. Finally, we show results on a real-brain dataset where we segment well-known fiber bundles

Doctor of Philosophy

dissertationImage segmentation entails the partitioning of an image domain, usually two or three dimensions, so that each partition or segment has some meaning that is relevant to the application at hand. Accurate image segmentation is a crucial challenge in many disciplines, including medicine, computer vision, and geology. In some applications, heterogeneous pixel intensities; noisy, ill-defined, or diffusive boundaries; and irregular shapes with high variability can make it challenging to meet accuracy requirements. Various segmentation approaches tackle such challenges by casting the segmentation problem as an energy-minimization problem, and solving it using efficient optimization algorithms. These approaches are broadly classified as either region-based or edge (surface)-based depending on the features on which they operate. The focus of this dissertation is on the development of a surface-based energy model, the design of efficient formulations of optimization frameworks to incorporate such energy, and the solution of the energy-minimization problem using graph cuts. This dissertation utilizes a set of four papers whose motivation is the efficient extraction of the left atrium wall from the late gadolinium enhancement magnetic resonance imaging (LGE-MRI) image volume. This dissertation utilizes these energy formulations for other applications, including contact lens segmentation in the optical coherence tomography (OCT) data and the extraction of geologic features in seismic data. Chapters 2 through 5 (papers 1 through 4) explore building a surface-based image segmentation model by progressively adding components to improve its accuracy and robustness. The first paper defines a parametric search space and its discrete formulation in the form of a multilayer three-dimensional mesh model within which the segmentation takes place. It includes a generative intensity model, and we optimize using a graph formulation of the surface net problem. The second paper proposes a Bayesian framework with a Markov random field (MRF) prior that gives rise to another class of surface nets, which provides better segmentation with smooth boundaries. The third paper presents a maximum a posteriori (MAP)-based surface estimation framework that relies on a generative image model by incorporating global shape priors, in addition to the MRF, within the Bayesian formulation. Thus, the resulting surface not only depends on the learned model of shapes,but also accommodates the test data irregularities through smooth deviations from these priors. Further, the paper proposes a new shape parameter estimation scheme, in closed form, for segmentation as a part of the optimization process. Finally, the fourth paper (under review at the time of this document) presents an extensive analysis of the MAP framework and presents improved mesh generation and generative intensity models. It also performs a thorough analysis of the segmentation results that demonstrates the effectiveness of the proposed method qualitatively, quantitatively, and clinically. Chapter 6, consisting of unpublished work, demonstrates the application of an MRF-based Bayesian framework to segment coupled surfaces of contact lenses in optical coherence tomography images. This chapter also shows an application related to the extraction of geological structures in seismic volumes. Due to the large sizes of seismic volume datasets, we also present fast, approximate surface-based energy minimization strategies that achieve better speed-ups and memory consumption

Active Contour Models for Manifold Valued Image Segmentation

Image segmentation is the process of partitioning a image into different regions or groups based on some characteristics like color, texture, motion or shape etc. Active contours is a popular variational method for object segmentation in images, in which the user initializes a contour which evolves in order to optimize an objective function designed such that the desired object boundary is the optimal solution. Recently, imaging modalities that produce Manifold valued images have come up, for example, DT-MRI images, vector fields. The traditional active contour model does not work on such images. In this paper, we generalize the active contour model to work on Manifold valued images. As expected, our algorithm detects regions with similar Manifold values in the image. Our algorithm also produces expected results on usual gray-scale images, since these are nothing but trivial examples of Manifold valued images. As another application of our general active contour model, we perform texture segmentation on gray-scale images by first creating an appropriate Manifold valued image. We demonstrate segmentation results for manifold valued images and texture images

Interactive Segmentation and Visualization of DTI Data Using a Hierarchical Watershed Representation

Magnetic resonance diffusion tensor imaging (DTI) measures diffusion of water molecules and is used to characterize orientation of white matter fibers and connectivity of neurological structures. Segmentation and visualization of DT images is challenging, because of low data quality and complexity of anatomical structures. In this paper, we propose an interactive segmentation approach, based on a hierarchical representation of the input DT image through a tree structure. The tree is obtained by successively merging watershed regions, based on the morphological waterfall approach, hence the name watershed tree. Region merging is done according to a combined similarity and homogeneity criterion. We introduce filters that work on the proposed tree representation, and that enable region-based attribute filtering of DTI data. Linked views between the visualizations of the simplified DT image and the tree enable a user to visually explore both data and tree at interactive rates. The coupling of filtering, semiautomatic segmentation by labeling nodes in the tree, and various interaction mechanisms support the segmentation task. Our method is robust against noise, which we demonstrate on synthetic and real DTI data