Towards robust and effective shape modeling: sparse shape composition.

Organ shape plays an important role in various clinical practices, e.g., diagnosis, surgical planning and treatment evaluation. It is usually derived from low level appearance cues in medical images. However, due to diseases and imaging artifacts, low level appearance cues might be weak or misleading. In this situation, shape priors become critical to infer and refine the shape derived by image appearances. Effective modeling of shape priors is challenging because: (1) shape variation is complex and cannot always be modeled by a parametric probability distribution; (2) a shape instance derived from image appearance cues (input shape) may have gross errors; and (3) local details of the input shape are difficult to preserve if they are not statistically significant in the training data. In this paper we propose a novel Sparse Shape Composition model (SSC) to deal with these three challenges in a unified framework. In our method, a sparse set of shapes in the shape repository is selected and composed together to infer/refine an input shape. The a priori information is thus implicitly incorporated on-the-fly. Our model leverages two sparsity observations of the input shape instance: (1) the input shape can be approximately represented by a sparse linear combination of shapes in the shape repository; (2) parts of the input shape may contain gross errors but such errors are sparse. Our model is formulated as a sparse learning problem. Using L1 norm relaxation, it can be solved by an efficient expectation-maximization (EM) type of framework. Our method is extensively validated on two medical applications, 2D lung localization in X-ray images and 3D liver segmentation in low-dose CT scans. Compared to state-of-the-art methods, our model exhibits better performance in both studies.

Deformable segmentation via sparse shape representation.

Appearance and shape are two key elements exploited in medical image segmentation. However, in some medical image analysis tasks, appearance cues are weak/misleading due to disease/artifacts and often lead to erroneous segmentation. In this paper, a novel deformable model is proposed for robust segmentation in the presence of weak/misleading appearance cues. Owing to the less trustable appearance information, this method focuses on the effective shape modeling with two contributions. First, a shape composition method is designed to incorporate shape prior on-the-fly. Based on two sparsity observations, this method is robust to false appearance information and adaptive to statistically insignificant shape modes. Second, shape priors are modeled and used in a hierarchical fashion. More specifically, by using affinity propagation method, our deformable surface is divided into multiple partitions, on which local shape models are built independently. This scheme facilitates a more compact shape prior modeling and hence a more robust and efficient segmentation. Our deformable model is applied on two very diverse segmentation problems, liver segmentation in PET-CT images and rodent brain segmentation in MR images. Compared to state-of-art methods, our method achieves better performance in both studies.

Automatic alignment of brain MR scout scans using data-adaptive multi-structural model.

Accurate slice positioning of diagnostic MR brain images is clinically important due to their inherent anisotropic resolution. Recently, a low-res fast 3D "scout" scan has become popular as a prerequisite localizer for the positioning of these diagnostic high-res images on relevant anatomies. Automation of this "scout" scan alignment needs to be highly robust, accurate and reproducible, which can not be achieved by existing methods such as voxel-based registration. Although recently proposed "Learning Ensembles of Anatomical Patterns (LEAP)" framework [4] paves the way to high robustness through redundant anatomy feature detections, the "somewhat conflicting" accuracy and reproducibility goals can not be satisfied simultaneously from the single model-based alignment perspective. Hence, we present a data adaptive multi-structural model based registration algorithm to achieve these joint goals. We validate our system on a large number of clinical data sets (731 adult and 100 pediatric brain MRI scans). Our algorithm demonstrates > 99.5% robustness with high accuracy. The reproducibility is < 0.32 degrees for rotation and < 0.27mm for translation on average within multiple follow-up scans for the same patient.

Auto-alignment of knee MR scout scans through redundant, adaptive and hierarchical anatomy detection.

3D knee magnetic resonance (MR) scout scan is an emerging imaging sequence that facilitates technicians in aligning the imaging planes of diagnostic high resolution MR scans. In this paper, we propose a method to automate this process with the goal of improving the accuracy, robustness and speed of the workflow. To tackle the various challenges coming from MR knee scout scans, our auto-alignment method is built upon a redundant, adaptive and hierarchical anatomy detection system. More specifically, we learn 1) a hierarchical redudant set of anatomy detectors, and 2) ensemble of group-wise spatial configurations across different anatomies, from training data. These learned statistics are integrated into a comprehensive objective function optimized using an expectation-maximization (EM) framework. The optimization provides a new framework for hierarchical detection and adaptive selection of anatomy primitives to derive optimal alignment. Being extensively validated on 744 clinical datasets, our method achieves high accuracy (sub-voxel alignment error), robustness (to severe diseases or imaging artifacts) and fast speed ( 5 sees for 10 alignments).

Robust automatic knee MR slice positioning through redundant and hierarchical anatomy detection.

Diagnostic magnetic resonance (MR) image quality is highly dependent on the position and orientation of the slice groups, due to the intrinsic high in-slice and low through-slice resolutions of MR imaging. Hence, the higher speed, accuracy, and reproducibility of automatic slice positioning, make it highly desirable over manual slice positioning. However, imaging artifacts, diseases, joint articulation, variations across ages and demographics as well as the extremely high performance requirements prevent state-of-the-art methods, such as volumetric registration, to be an off-the-shelf solution. In this paper, we address all these issues through an automatic slice positioning framework based on redundant and hierarchical learning. Our method has two hallmarks that are specifically designed to achieve high robustness and accuracy. 1) A redundant set of anatomy detectors are learned to provide local appearance cues. These detections are pruned and assembled according to a distributed anatomy model, which captures group-wise spatial configurations among anatomy primitives. This strategy brings about a high level of robustness and works even if a large portion of the target is distorted, missing, or occluded. 2) The detectors are learned and invoked in a hierarchical fashion, with each local detection scheduled and iterated according to its intrinsic invariance property. This iterative alignment process is shown to dramatically improve alignment accuracy. The proposed system is extensively validated on a large dataset including 744 clinical MR scans. Compared to state-of-the-art methods, our method exhibits superior performance in terms of robustness, accuracy, and reproducibility. The methodology is general and can be applied to other anatomies and other imaging modalities.

Segmentation of pulmonary nodules of various densities with morphological approaches and convexity models.

Accurate segmentation of a pulmonary nodule is an important and active area of research in medical image processing. Although many algorithms have been reported in literature for this problem, those that are applicable to various density types have not been available until recently. In this paper, we propose a new algorithm that is applicable to solid, non-solid and part-solid types and solitary, vascularized, and juxtapleural types. First, the algorithm separates lung parenchyma and radiographically denser anatomical structures with coupled competition and diffusion processes. The technique tends to derive a spatially more homogeneous foreground map than an adaptive thresholding based method. Second, it locates the core of a nodule in a manner that is applicable to juxtapleural types using a transformation applied on the Euclidean distance transform of the foreground. Third, it detaches the nodule from attached structures by a region growing on the Euclidean distance map followed by a procedure to delineate the surface of the nodule based on the patterns of the region growing and distance maps. Finally, convex hull of the nodule surface intersected with the foreground constitutes the final segmentation. The performance of the technique is evaluated with two Lung Imaging Database Consortium (LIDC) data sets with 23 and 82 nodules each, and another data set with 820 nodules with manual diameter measurements. The experiments show that the algorithm is highly reliable in segmenting nodules of various types in a computationally efficient manner.

Multi-level ground glass nodule detection and segmentation in CT lung images.

Early detection of Ground Glass Nodule (GGN) in lung Computed Tomography (CT) images is important for lung cancer prognosis. Due to its indistinct boundaries, manual detection and segmentation of GGN is labor-intensive and problematic. In this paper, we propose a novel multi-level learning-based framework for automatic detection and segmentation of GGN in lung CT images. Our main contributions are: firstly, a multi-level statistical learning-based approach that seamlessly integrates segmentation and detection to improve the overall accuracy for GGN detection (in a subvolume). The classification is done at two levels, both voxel-level and object-level. The algorithm starts with a three-phase voxel-level classification step, using volumetric features computed per voxel to generate a GGN class-conditional probability map. GGN candidates are then extracted from this probability map by integrating prior knowledge of shape and location, and the GGN object-level classifier is used to determine the occurrence of the GGN. Secondly, an extensive set of volumetric features are used to capture the GGN appearance. Finally, to our best knowledge, the GGN dataset used for experiments is an order of magnitude larger than previous work. The effectiveness of our method is demonstrated on a dataset of 1100 subvolumes (100 containing GGNs) extracted from about 200 subjects.

Cross modality deformable segmentation using hierarchical clustering and learning.

Segmentation of anatomical objects is always a fundamental task for various clinical applications. Although many automatic segmentation methods have been designed to segment specific anatomical objects in a given imaging modality, a more generic solution that is directly applicable to different imaging modalities and different deformable surfaces is desired, if attainable. In this paper, we propose such a framework, which learns from examples the spatially adaptive appearance and shape of a 3D surface (either open or closed). The application to a new object/surface in a new modality requires only the annotation of training examples. Key contributions of our method include: (1) an automatic clustering and learning algorithm to capture the spatial distribution of appearance similarities/variations on the 3D surface. More specifically, the model vertices are hierarchically clustered into a set of anatomical primitives (sub-surfaces) using both geometric and appearance features. The appearance characteristics of each learned anatomical primitive are then captured through a cascaded boosting learning method. (2) To effectively incorporate non-Gaussian shape priors, we cluster the training shapes in order to build multiple statistical shape models. (3) To our best knowledge, this is the first time the same segmentation algorithm has been directly employed in two very diverse applications: (a) Liver segmentation (closed surface) in PET-CT, in which CT has very low-resolution and low-contrast; (b) Distal femur (condyle) surface (open surface) segmentation in MRI.

Image-based coronary tracking and beat-to-beat motion compensation: feasibility for improving coronary MR angiography.

A method to reduce the effect of motion variability in MRI of the coronary arteries is proposed. It involves acquiring real-time low-resolution images in specific orthogonal orientations, extracting coronary motion from these images, and then using this motion information to guide high-resolution MR image acquisition on a beat-to-beat basis. The present study establishes the feasibility and efficacy of the proposed approach using human motion data in an offline implementation, prior to future online implementation on an MRI scanner. To track the coronary arteries in low-resolution real-time MR images in an accurate manner, a tracking approach is presented and validated. The tracking algorithm was run on real-time images acquired at 15-20 frames per second in four-chamber, short-axis, and coronal views in five volunteers. The systolic and diastolic periods in the cardiac cycles, computed from the extracted motion information, had significant variability during the short time periods typical of cardiac MRI. It is also demonstrated through simulation analysis using human tracked coronary motion data that accounting for this cardiac variability by adaptively changing the trigger delay for acquisition on a beat-to-beat basis improves overall motion compensation and hence MR image quality evaluated in terms of SNR and CNR values.