OBJECTIVE: To develop ImageVU, a scalable research imaging infrastructure that integrates clinical imaging data with metadata-driven cohort discovery, enabling secure, efficient, and regulatory-compliant access to imaging for secondary and opportunistic research use. This manuscript presents a detailed description of ImageVU's key components and lessons learned to assist other institutions in developing similar research imaging services and infrastructure. METHODS: ImageVU was designed to support the secondary use of radiological imaging data through a dedicated research imaging store. The system comprises four interconnected components: a Research PACS, an Ad Hoc Backfill Host, Cloud Storage System, and a De-Identification System. Imaging metadata are extracted and stored in the Research Derivative (RD), an identified clinical data repository, and the Synthetic Derivative (SD), a de-identified research data repository, with access facilitated through the RD Discover web portal. Researchers interact with the system via structured metadata queries and multiple data delivery options, including web-based viewing, bulk downloads, and dataset preparation for high-performance computing environments. RESULTS: The integration of metadata-driven search capabilities has streamlined cohort discovery and improved imaging data accessibility. As of December 2024, ImageVU has processed 12.9 million MRI and CT series from 1.36 million studies across 453,403 patients. The system has supported 75 project requests, delivering over 50 TB of imaging data to 55 investigators, leading to 66 published research papers. CONCLUSION: ImageVU demonstrates a scalable and efficient approach for integrating clinical imaging into research workflows. By combining institutional data infrastructure with cloud-based storage and metadata-driven cohort identification, the platform enables secure and compliant access to imaging for translational research.

The analysis of connectivity between parcellated regions of cortex provides insights into the functional architecture of the brain at a systems level. However, the derivation of functional structures from voxel-wise analyses at finer scales remains a challenge. We propose a novel method, called localized topo-connectivity mapping with singular-value-decomposition-informed filtering (or filtered LTM), to identify and characterize voxel-wise functional structures in the human brain from resting-state fMRI data. Here we describe its mathematical formulation and provide a proof-of-concept using simulated data that allow an intuitive interpretation of the results of filtered LTM. The algorithm has also been applied to 7T fMRI data acquired as part of the Human Connectome Project to generate group-average LTM images. Generally, most of the functional structures revealed by LTM images agree in the boundaries with anatomical structures identified by T1-weighted images and fractional anisotropy maps derived from diffusion MRI. In addition, the LTM images also reveal subtle functional variations that are not apparent in the anatomical structures. To assess the performance of LTM images, the subcortical region and occipital white matter were separately parcellated. Statistical tests were performed to demonstrate that the synchronies of fMRI signals in LTM-derived functional parcels are significantly larger than those with geometric perturbations. Overall, the filtered LTM approach can serve as a tool to investigate the functional organization of the brain at the scale of individual voxels as measured in fMRI.

Balun or trap circuits are critical components for suppressing common-mode currents flowing on the outer conductors of coaxial cables in RF coil systems for Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spectroscopy (MRS). Common-mode currents affect coils’ tuning and matching, induce losses, pick up extra noise from the surrounding environment, lead to undesired cross-talk, and cause safety concerns in animal and human imaging. First proposed for microwave antenna applications, the Lattice balun has been widely used in MRI coils. It has a small footprint and can be easily integrated with coil tuning/matching circuits. However, the Lattice balun is typically a single-tuned circuit and cannot be used for multi-nuclear MRI and MRS with two RF frequencies. This work describes a dual-tuned Lattice balun design that is suitable for multi-nuclear MRI/MRS. It was first analyzed theoretically to derive component values. RF circuit simulations were then performed to validate the theoretical analysis and provide guidance for practical construction. Based on the simulation results, a dual-tuned balun circuit was built for 7T1H/23Na MRI and bench tested. The fabricated dual-tuned balun exhibits superior performance at the Larmor frequencies of both1H and23Na, with less than 0.15 dB insertion loss and better than 17 dB common-mode rejection ratio at both frequencies.

This paper presents a novel Riemannian framework for shape analysis of parameterized surfaces. In particular, it provides efficient algorithms for computing geodesic paths which, in turn, are important for comparing, matching, and deforming surfaces. The novelty of this framework is that geodesics are invariant to the parameterizations of surfaces and other shape-preserving transformations of surfaces. The basic idea is to formulate a space of embedded surfaces (surfaces seen as embeddings of a unit sphere in IR3) and impose a Riemannian metric on it in such a way that the reparameterization group acts on this space by isometries. Under this framework, we solve two optimization problems. One, given any two surfaces at arbitrary rotations and parameterizations, we use a path-straightening approach to find a geodesic path between them under the chosen metric. Second, by modifying a technique presented in [25], we solve for the optimal rotation and parameterization (registration) between surfaces. Their combined solution provides an efficient mechanism for computing geodesic paths in shape spaces of parameterized surfaces. We illustrate these ideas using examples from shape analysis of anatomical structures and other general surfaces.

Intensity inhomogeneity often occurs in real-world images, which presents a considerable challenge in image segmentation. The most widely used image segmentation algorithms are region-based and typically rely on the homogeneity of the image intensities in the regions of interest, which often fail to provide accurate segmentation results due to the intensity inhomogeneity. This paper proposes a novel region-based method for image segmentation, which is able to deal with intensity inhomogeneities in the segmentation. First, based on the model of images with intensity inhomogeneities, we derive a local intensity clustering property of the image intensities, and define a local clustering criterion function for the image intensities in a neighborhood of each point. This local clustering criterion function is then integrated with respect to the neighborhood center to give a global criterion of image segmentation. In a level set formulation, this criterion defines an energy in terms of the level set functions that represent a partition of the image domain and a bias field that accounts for the intensity inhomogeneity of the image. Therefore, by minimizing this energy, our method is able to simultaneously segment the image and estimate the bias field, and the estimated bias field can be used for intensity inhomogeneity correction (or bias correction). Our method has been validated on synthetic images and real images of various modalities, with desirable performance in the presence of intensity inhomogeneities. Experiments show that our method is more robust to initialization, faster and more accurate than the well-known piecewise smooth model. As an application, our method has been used for segmentation and bias correction of magnetic resonance (MR) images with promising results.

This paper proposes a new energy minimization framework for simultaneous estimation of the bias field and segmentation of tissues for magnetic resonance images. The bias field is modeled as a linear combination of a set of basis functions, and thereby parameterized by the coefficients of the basis functions. We define an energy that depends on the coefficients of the basis functions, the membership functions of the tissues in the image, and the constants approximating the true signal from the corresponding tissues. This energy is convex in each of its variables. Bias field estimation and image segmentation are simultaneously achieved as the result of minimizing this energy. We provide an efficient iterative algorithm for energy minimization, which converges to the optimal solution at a fast rate. A salient advantage of our method is that its result is independent of initialization, which allows robust and fully automated application. The proposed method has been successfully applied to 3-Tesla MR images with desirable results. Comparisons with other approaches demonstrate the superior performance of this algorithm.

Magnetic resonance diffusion tensor imaging is being widely used to reconstruct brain white matter fiber tracts. To characterize structural properties of the tracts, reconstructed fibers are often grouped into bundles that correspond to coherent anatomic structures. For further group analysis of fiber bundles, it is desirable that corresponding bundles from different studies are coregistered. To address these needs simultaneously, a unified fiber bundling and registration (UFIBRE) framework is proposed in this work. The framework is based on maximizing a posteriori Bayesian probabilities using an expectation maximization algorithm. Given a set of segmented template bundles and a whole-brain target fiber set, the UFIBRE algorithm optimally bundles the target fibers and registers them with the template. The bundling component in the UFIBRE algorithm simplifies fiber-based registration into bundle-to-bundle registration, and the registration component in turn guides the bundling process to find bundles consistent with the template. Experiments with in vivo data demonstrate that the estimated bundles have an approximately 80% consistency with ground truth and the root mean square error between their bundle medial axes is less than one voxel. The proposed algorithm is highly efficient, offering potential routine use for group analysis of white matter fibers.

Intensity inhomogeneities often occur in real-world images and may cause considerable difficulties in image segmentation. In order to overcome the difficulties caused by intensity inhomogeneities, we propose a region-based active contour model that draws upon intensity information in local regions at a controllable scale. A data fitting energy is defined in terms of a contour and two fitting functions that locally approximate the image intensities on the two sides of the contour. This energy is then incorporated into a variational level set formulation with a level set regularization term, from which a curve evolution equation is derived for energy minimization. Due to a kernel function in the data fitting term, intensity information in local regions is extracted to guide the motion of the contour, which thereby enables our model to cope with intensity inhomogeneity. In addition, the regularity of the level set function is intrinsically preserved by the level set regularization term to ensure accurate computation and avoids expensive reinitialization of the evolving level set function. Experimental results for synthetic and real images show desirable performances of our method.

Local image information is crucial for accurate segmentation of images with intensity inhomogeneity. However, image information in local region is not embedded in popular region-based active contour models, such as the piecewise constant models. In this paper, we propose a region-based active contour model that is able to utilize image information in local regions. The major contribution of this paper is the introduction of a local binary fitting energy with a kernel function, which enables the extraction of accurate local image information. Therefore, our model can be used to segment images with intensity inhomogeneity, which overcomes the limitation of piecewise constant models. Comparisons with other major region-based models, such as the piece-wise smooth model, show the advantages of our method in terms of computational efficiency and accuracy. In addition, the proposed method has promising application to image denoising.

To improve the accuracy of tissue structural and architectural characterization with diffusion tensor imaging, an anisotropic smoothing algorithm is presented for reducing noise in diffusion tensor images efficiently and effectively. The presented algorithm is based on previous anisotropic diffusion filtering, which is implemented with a straightforward but inefficient explicit numerical scheme. The main contribution of this paper is to improve the performance of the previous method considerably by using unconditionally stable and second order time accurate semi-implicit scheme. Our new method needs only few or even one iteration to achieve better smoothed images than what is generated by tens of iterations of the previous method, which makes it more attractive to practical use. Experiments with simulated and in vivo data have demonstrated the advantage of our new algorithm for denoising diffusion tensor images in terms of efficiency and effectiveness.

It is of significant interest for neurological studies to determine and visualize neuronal fiber pathways in the human brain. By exploiting the capability of diffusion tensor magnetic resonance imaging to detect local orientations of neuronal fibers, we have developed a system of algorithms to reconstruct, visualize and quantify neuronal fiber pathways in vivo. Illustrative results show that the system is a promising tool for visual analysis of fiber connectivity and quantitative studies of neuronal fibers.