Automatic Segmentation, Localization, and Identification of Vertebrae in 3D CT Images Using Cascaded Convolutional Neural Networks

This paper presents a method for automatic segmentation, localization, and identification of vertebrae in arbitrary 3D CT images. Many previous works do not perform the three tasks simultaneously even though requiring a priori knowledge of which part of the anatomy is visible in the 3D CT images. Our method tackles all these tasks in a single multi-stage framework without any assumptions. In the first stage, we train a 3D Fully Convolutional Networks to find the bounding boxes of the cervical, thoracic, and lumbar vertebrae. In the second stage, we train an iterative 3D Fully Convolutional Networks to segment individual vertebrae in the bounding box. The input to the second networks have an auxiliary channel in addition to the 3D CT images. Given the segmented vertebra regions in the auxiliary channel, the networks output the next vertebra. The proposed method is evaluated in terms of segmentation, localization, and identification accuracy with two public datasets of 15 3D CT images from the MICCAI CSI 2014 workshop challenge and 302 3D CT images with various pathologies introduced in [1]. Our method achieved a mean Dice score of 96%, a mean localization error of 8.3 mm, and a mean identification rate of 84%. In summary, our method achieved better performance than all existing works in all the three metrics

Automatic Localization and Identification of Vertebrae in Arbitrary Field-of-View CT Scans

Abstract. This paper presents a new method for automatic localiza-tion and identification of vertebrae in arbitrary field-of-view CT scans. No assumptions are made about which section of the spine is visible or to which extent. Thus, our approach is more general than previous work while being computationally efficient. Our algorithm is based on re-gression forests and probabilistic graphical models. The discriminative, regression part aims at roughly detecting the visible part of the spine. Ac-curate localization and identification of individual vertebrae is achieved through a generative model capturing spinal shape and appearance. The system is evaluated quantitatively on 200 CT scans, the largest dataset reported for this purpose. We obtain an overall median localization error of less than 6mm, with an identification rate of 81%.

Evaluation of 4D-CT lung registration

Non-rigid registration accuracy assessment is typically performed by evaluating the target registration error at manually placed landmarks. For 4D-CT lung data, we compare two sets of landmark distributions: a smaller set primarily defined on vessel bifurcations as commonly described in the literature and a larger set being well-distributed throughout the lung volume. For six different registration schemes (three in-house schemes and three schemes frequently used by the community) the landmark error is evaluated and found to depend significantly on the distribution of the landmarks. In particular, lung regions near to the pleura show a target registration error three times larger than near-mediastinal regions. While the inter-method variability on the landmark positions is rather small, the methods show discriminating differences with respect to consistency and local volume change. In conclusion, both a well-distributed set of landmarks and a deformation vector field analysis are necessary for reliable non-rigid registration accuracy assessment. © 2009 Springer-Verlag

Spine segmentation using articulated shape models

Abstract. Including prior shape in the form of anatomical models is a well-known approach for improving segmentation results in medical images. Currently, most approaches are focused on the modeling and segmentation of individual objects. In case of object constellations, a simultaneous segmentation of the ensemble that uses not only prior knowledge of individual shapes but also additional information about spatial relations between the objects is often beneficial. In this paper, we present a two-scale framework for the modeling and segmentation of the spine as an example for object constellations. The global spine shape is expressed as a consecution of local vertebra coordinate systems while individual vertebrae are modeled as triangulated surface meshes. Adaptation is performed by attracting the model to image features but restricting the attraction to a former learned shape. With the developed approach, we obtained a segmentation accuracy of 1.0 mm in average for ten thoracic CT images improving former results.

Abdomen segmentation in 3D fetal ultrasound using CNN-powered deformable models

In this paper, voxel probability maps generated by a novel fovea fully convolutional network architecture (FovFCN) are used as additional feature images in the context of a segmentation approach based on deformable shape models. The method is applied to fetal 3D ultrasound image data aiming at a segmentation of the abdominal outline of the fetal torso. This is of interest, e.g., for measuring the fetal abdominal circumference, a standard biometric measure in prenatal screening. The method is trained on 126 3D ultrasound images and tested on 30 additional scans. The results show that the approach can successfully combine the advantages of FovFCNs and deformable shape models in the context of challenging image data, such as given by fetal ultrasound. With a mean error of 2.24 mm, the combination of model-based segmentation and neural networks outperforms the separate approaches

Abdomen segmentation in 3D fetal ultrasound using CNN-powered deformable models

In this paper, voxel probability maps generated by a novel fovea fully convolutional network architecture (FovFCN) are used as additional feature images in the context of a segmentation approach based on deformable shape models. The method is applied to fetal 3D ultrasound image data aiming at a segmentation of the abdominal outline of the fetal torso. This is of interest, e.g., for measuring the fetal abdominal circumference, a standard biometric measure in prenatal screening. The method is trained on 126 3D ultrasound images and tested on 30 additional scans. The results show that the approach can successfully combine the advantages of FovFCNs and deformable shape models in the context of challenging image data, such as given by fetal ultrasound. With a mean error of 2.24 mm, the combination of model-based segmentation and neural networks outperforms the separate approaches

3D active shape model segmentation with nonlinear shape priors

The Active Shape Model (ASM) is a segmentation algorithm which uses a Statistical Shape Model (SSM) to constrain segmentations to 'plausible' shapes. This makes it possible to robustly segment organs with low contrast to adjacent structures. The standard SSM assumes that shapes are Gaussian distributed, which implies that unseen shapes can be expressed by linear combinations of the training shapes. Although this assumption does not always hold true, and several nonlinear SSMs have been proposed in the literature, virtually all applications in medical imaging use the linear SSM. In this work, we investigate 3D ASM segmentation with a nonlinear SSM based on Kernel PCA. We show that a recently published energy minimization approach for constraining shapes with a linear shape model extends to the nonlinear case, and overcomes shortcomings of previously published approaches. Our approach for nonlinear ASM segmentation is applied to vertebra segmentation and evaluated against the linear model