Publications by Year: 2008

RATIONALE AND OBJECTIVES: This article presents an initiative for the translation of advances in neuroimage analysis techniques to clinical research scientists. Our objective is to bridge the gap between scientific advances made by the biomedical imaging community and their widespread use in the clinical research community. Through national collaborative effort supported by the National Institutes of Health Roadmap, the integration of the most sophisticated algorithms into usable working open-source systems enables clinical researchers to have access to a broad spectrum of cutting edge analysis techniques. A critical step to maximize the long-term positive impact of this collaborative effort is to translate these techniques into new skills of clinical researchers. To address this challenge, we developed a methodology based on three criteria: a multidisciplinary approach, a balance between theory and common practice, and an immersive collaborative environment. The article illustrates our initiative through the exemplar case of diffusion tensor imaging tractography, and reports on our experience over the past two years of designing and delivering training workshops to more than 300 clinicians and scientists using the developed methodology.

Diffusion tensor imaging (DTI) has become one of the most popular MRI techniques in brain research, as well as in clinical practice. The number of brain studies with DTI is growing steadily and, over the last decade, has produced more than 700 publications. Diffusion tensor imaging enables visualization and characterization of white matter fascicli in two and three dimensions. Since the introduction of this methodology in 1994, it has been used to study the white matter architecture and integrity of the normal and diseased brains (multiple sclerosis, stroke, aging, dementia, schizophrenia, etc.). Although it provided image contrast that was not available with routine MR techniques, unique information on white matter and 3D visualization of neuronal pathways, many questions were raised regarding the origin of the DTI signal. Diffusion tensor imaging is constantly validated, challenged, and developed in terms of acquisition scheme, image processing, analysis, and interpretation. While DTI offers a powerful tool to study and visualize white matter, it suffers from inherent artifacts and limitations. The partial volume effect and the inability of the model to cope with non-Gaussian diffusion are its two main drawbacks. Nevertheless, when combined with functional brain mapping, DTI provides an efficient tool for comprehensive, noninvasive, functional anatomy mapping of the human brain. This review summarizes the development of DTI in the last decade with respect to the specificity and utility of the technique in radiology and anatomy studies.

MR-guided focused ultrasound (MRgFUS) is a non-invasive method by which tissue is ablated using ultrasound energy focused on a point. The procedure has proven effective for stationary targets (e.g. uterine fibroids) but has not yet been used for liver lesion treatment due to organ motion. We describe a method to compensate for organ motion to enable continuous application of ultrasound energy in the presence of target movement in the liver. The method involves tracking several salient features (typically blood vessels) in the vicinity of the target location. The location of the target point(s) themselves are updated using a thin plate spline (TPS) interpolation scheme. We demonstrate sub-pixel tracking accuracy on synthetic sequences and additionally show results on MRI sequences acquired on human subjects. Per-feature tracking times were measured to be 5.7ms with a standard deviation of 1.6ms, sufficient for real-time use.

The level set method is a popular technique used in medical image segmentation; however, the numerics involved make its use cumbersome. This paper proposes an approximate level set scheme that removes much of the computational burden while maintaining accuracy. Abandoning a floating point representation for the signed distance function, we use integral values to represent the signed distance function. For the cases of 2D and 3D, we detail rules governing the evolution and maintenance of these three regions. Arbitrary energies can be implemented in the framework. This scheme has several desirable properties: computations are only performed along the zero level set; the approximate distance function requires only a few simple integer comparisons for maintenance; smoothness regularization involves only a few integer calculations and may be handled apart from the energy itself; the zero level set is represented exactly removing the need for interpolation off the interface; and evolutions proceed on the order of milliseconds per iteration on conventional uniprocessor workstations. To highlight its accuracy, flexibility and speed, we demonstrate the technique on intensity-based segmentations under various statistical metrics. Results for 3D imagery show the technique is fast even for image volumes.

Transcutaneous ultrasound imaging may be used to detect abdominal hemorrhage in the field setting. The Focused Assessment with Sonography for Trauma (FAST) examination was developed to characterize blunt abdominal trauma and has been shown to be effective for assessing penetrating trauma as well. However, it is unlikely that a minimally trained operator could perform a diagnostic examination. In our system, the operator is be supported by real-time 3D volume displays. The operator will be directed through the examination by prompts from a computer system or outside expert, potentially with knowledge of the anatomy of the injured patient. The key elements of the tele-operated FAST exam capability have been demonstrated; the exam is performed with real-time guidance from anatomic images registered to the body. It appears likely that Image Registration will assist hemorrhage detection at the point of injury or in the initial evaluation by a trauma response team.

Advances in high-resolution computed tomography (CT) imaging are making a full three-dimensional analysis of the lungs feasible. In particular, airway morphology can be studied in vivo and quantitative metrics of airway size and shape can be extracted. The thickening process associated with the inflammatory response in the diseased lung can be quantified by means of image processing techniques that extract the airway lumen and airway wall. In this article, we give an overview of these imaging techniques and their diverse nature. We also offer a comprehensive view of the analysis pipeline for three-dimensional airway trees and a validation framework that is needed to compare different techniques.

This paper presents a tract-oriented analysis of diffusion tensor (DT) images of the human brain. We demonstrate that unlike the commonly used ROI-based methods for population studies, our technique is sensitive to the local variation of diffusivity parameters along the fiber tracts. We show the strength of the proposed approach in identifying the differences in schizophrenic data compared to controls. Statistically significant drops in fractional anisotropy are observed along the genu and bilaterally in the splenium, as well as an increase in principal eigenvalue in uncinate fasciculus. This is the first tract-oriented clinical study in which an anatomical atlas is used to guide the algorithm.

We introduce a versatile framework for characterizing and extracting salient structures in three-dimensional symmetric second-order tensor fields. The key insight is that degenerate lines in tensor fields, as defined by the standard topological approach, are exactly crease (ridge and valley) lines of a particular tensor invariant called mode. This reformulation allows us to apply well-studied approaches from scientific visualization or computer vision to the extraction of topological lines in tensor fields. More generally, this main result suggests that other tensor invariants, such as anisotropy measures like fractional anisotropy (FA), can be used in the same framework in lieu of mode to identify important structural properties in tensor fields. Our implementation addresses the specific challenge posed by the non-linearity of the considered scalar measures and by the smoothness requirement of the crease manifold computation. We use a combination of smooth reconstruction kernels and adaptive refinement strategy that automatically adjust the resolution of the analysis to the spatial variation of the considered quantities. Together, these improvements allow for the robust application of existing ridge line extraction algorithms in the tensor context of our problem. Results are proposed for a diffusion tensor MRI dataset, and for a benchmark stress tensor field used in engineering research.

Several recent studies explored the use of unsupervised segmentation methods for segmenting thalamic nuclei from diffusion tensor images. These methods provide a plausible segmentation on individual subjects; however, they do not address the problem of consistently identifying the same functional areas in a population. The lack of correspondence between the segmented nuclei make it more difficult to use the results from the unsupervised segmentation tools for morphometry. In this paper we present a novel segmentation algorithm to automatically segment the gray matter nuclei while ensuring consistency between subjects in a population. This new algorithm, referred to as Consistency Clustering, finds correspondence between the nuclei as the segmentation is achieved through a single model for the whole population, similar to the brain atlases experts use to identify thalamic nuclei.

We propose a Bayesian approach to incorporate anatomical information in the clustering of fiber trajectories. An expectation-maximization (EM) algorithm is used to cluster the trajectories, in which an atlas serves as the prior on the labels. The atlas guides the clustering algorithm and makes the resulting bundles anatomically meaningful. In addition, it provides the seed points for the tractography and initial settings of the EM algorithm. The proposed approach provides a robust and automated tool for tract-oriented analysis both in a single subject and over a population.