https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf

Cortical surface-based analysis. I. Segmentation and surface reconstruction

Stereo matching is one of the most active research areas in computer vision. While a large number of algorithms for stereo correspondence have been developed, relatively little work has been done on characterizing their performance. In this paper, we present a taxonomy of dense, two-frame stereo methods designed to assess the different components and design decisions made in individual stereo algorithms. Using this taxonomy, we compare existing stereo methods and present experiments evaluating the performance of many different variants. In order to establish a common software platform and a collection of data sets for easy evaluation, we have designed a stand-alone, flexible C++ implementation that enables the evaluation of individual components and that can be easily extended to include new algorithms. We have also produced several new multiframe stereo data sets with ground truth, and are making both the code and data sets available on the Web.

/pdf/a-taxonomy-and-evaluation-of-dense-two-frame-stereo-4c20etkubp.pdf

A taxonomy and evaluation of dense two-frame stereo correspondence algorithms

A novel scheme for the detection of object boundaries is presented. The technique is based on active contours deforming according to intrinsic geometric measures of the image. The evolving contours naturally split and merge, allowing the simultaneous detection of several objects and both interior and exterior boundaries. The proposed approach is based on the relation between active contours and the computation of geodesics or minimal distance curves. The minimal distance curve lays in a Riemannian space whose metric as defined by the image content. This geodesic approach for object segmentation allows to connect classical "snakes" based on energy minimization and geometric active contours based on the theory of curve evolution. Previous models of geometric active contours are improved as showed by a number of examples. Formal results concerning existence, uniqueness, stability, and correctness of the evolution are presented as well. >

/pdf/geodesic-active-contours-4wqlqxa13k.pdf

Geodesic active contours

Accurate and automated methods for measuring the thickness of human cerebral cortex could provide powerful tools for diagnosing and studying a variety of neurodegenerative and psychiatric disorders. Manual methods for estimating cortical thickness from neuroimaging data are labor intensive, requiring several days of effort by a trained anatomist. Furthermore, the highly folded nature of the cortex is problematic for manual techniques, frequently resulting in measurement errors in regions in which the cortical surface is not perpendicular to any of the cardinal axes. As a consequence, it has been impractical to obtain accurate thickness estimates for the entire cortex in individual subjects, or group statistics for patient or control populations. Here, we present an automated method for accurately measuring the thickness of the cerebral cortex across the entire brain and for generating cross-subject statistics in a coordinate system based on cortical anatomy. The intersubject standard deviation of the thickness measures is shown to be less than 0.5 mm, implying the ability to detect focal atrophy in small populations or even individual subjects. The reliability and accuracy of this new method are assessed by within-subject test-retest studies, as well as by comparison of cross-subject regional thickness measures with published values.

/pdf/measuring-the-thickness-of-the-human-cerebral-cortex-from-2nsexa0rmk.pdf

Measuring the thickness of the human cerebral cortex from magnetic resonance images

A novel scheme for the detection of object boundaries is presented. The technique is based on active contours evolving in time according to intrinsic geometric measures of the image. The evolving contours naturally split and merge, allowing the simultaneous detection of several objects and both interior and exterior boundaries. The proposed approach is based on the relation between active contours and the computation of geodesics or minimal distance curves. The minimal distance curve lays in a Riemannian space whose metric is defined by the image content. This geodesic approach for object segmentation allows to connect classical “snakes” based on energy minimization and geometric active contours based on the theory of curve evolution. Previous models of geometric active contours are improved, allowing stable boundary detection when their gradients suffer from large variations, including gaps. Formal results concerning existence, uniqueness, stability, and correctness of the evolution are presented as well. The scheme was implemented using an efficient algorithm for curve evolution. Experimental results of applying the scheme to real images including objects with holes and medical data imagery demonstrate its power. The results may be extended to 3D object segmentation as well.

Geodesic Active Contours

https://www.cs.ucla.edu/~dt/papers/mia96/mia96.pdf

Deformable models in medical image analysis: a survey

We develop physically-based models of deformable curves, surfaces, and solids for use in computer graphics. Our deformable models are governed by the mechanical laws of continuous bodies whose shapes can change over time. These laws, expressed in the form of dynamic differential equations, unify the description of shape and motion. By solving the equations numerically we are able to create realistic animations involving the interaction of deformable models with various applied forces, ambient media, and impenetrable obstacles in a simulated physical world. We develop deformable models capable of perfectly elastic behavior and more general inelastic behavior, including viscoelasticity, plasticity, and fracture.

Deformable models

https://www.cs.ucla.edu/~dt/papers/mia00/mia00.pdf

T-snakes: Topology adaptive snakes

A dynamic finite element surface model for segmentation and tracking in multidimensional medical images with application to cardiac 4D image analysis.

The paper presents a typologically adaptable snakes model for image segmentation and object representation. The model is embedded in the framework of domain subdivision using simplicial decomposition. This framework extends the geometric and topological adaptability of snakes while retaining all of the features of traditional snakes, such as user interaction, and overcoming many of the limitations of traditional snakes. By superposing a simplicial grid over the image domain and using this grid to iteratively reparameterize the deforming snakes model, the model is able to flow into complex shapes, even shapes with significant protrusions or branches, and to dynamically change topology as necessitated by the data. Snakes can be created and can split into multiple parts or seamlessly merge into other snakes. The model can also be easily converted to and from the traditional parametric snakes model representation. We apply a 2D model to various synthetic and real images in order to segment objects with complicated shapes and topologies. >

/pdf/topologically-adaptable-snakes-2mbeimserv.pdf

Tim McInerney

Papers

Deformable models in medical image analysis: a survey

Deformable models

T-snakes: Topology adaptive snakes

A dynamic finite element surface model for segmentation and tracking in multidimensional medical images with application to cardiac 4D image analysis.

Topologically adaptable snakes