Rathi Y, Gagoski B, Setsompop K, Michailovich O, Grant E, Westin CF. Diffusion Propagator Estimation from Sparse Measurements in a Tractography Framework. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):510–7.

Estimation of the diffusion propagator from a sparse set of diffusion MRI (dMRI) measurements is a field of active research. Sparse reconstruction methods propose to reduce scan time and are particularly suitable for scanning un-coperative patients. Recent work on reconstructing the diffusion signal from very few measurements using compressed sensing based techniques has focussed on propagator (or signal) estimation at each voxel independently. However, the goal of many neuroscience studies is to use tractography to study the pathology in white matter fiber tracts. Thus, in this work, we propose a joint framework for robust estimation of the diffusion propagator from sparse measurements while simultaneously tracing the white matter tracts. We propose to use a novel multi-tensor model of diffusion which incorporates the biexponential radial decay of the signal. Our preliminary results on in-vivo data show that the proposed method produces consistent and reliable fiber tracts from very few gradient directions while simultaneously estimating the bi-exponential decay of the diffusion propagator.

Wassermann D, Makris N, Rathi Y, Shenton M, Kikinis R, Kubicki M, Westin CF. On Describing Human White Matter Anatomy: The White Matter Query Language. Med Image Comput Comput Assist Interv. 2013;16(Pt 1):647–54.

The main contribution of this work is the careful syntactical definition of major white matter tracts in the human brain based on a neuroanatomist’s expert knowledge. We present a technique to formally describe white matter tracts and to automatically extract them from diffusion MRI data. The framework is based on a novel query language with a near-to-English textual syntax. This query language allows us to construct a dictionary of anatomical definitions describing white matter tracts. The definitions include adjacent gray and white matter regions, and rules for spatial relations. This enables automated coherent labeling of white matter anatomy across subjects. We use our method to encode anatomical knowledge in human white matter describing 10 association and 8 projection tracts per hemisphere and 7 commissural tracts. The technique is shown to be comparable in accuracy to manual labeling. We present results applying this framework to create a white matter atlas from 77 healthy subjects, and we use this atlas in a proof-of-concept study to detect tract changes specific to schizophrenia.

Sweet A, Venkataraman A, Stufflebeam SM, Liu H, Tanaka N, Madsen J, Golland P. Detecting Epileptic Regions Based on Global Brain Connectivity Patterns. Med Image Comput Comput Assist Interv. 2013;16(Pt 1):98–105.

We present a method to detect epileptic regions based on functional connectivity differences between individual epilepsy patients and a healthy population. Our model assumes that the global functional characteristics of these differences are shared across patients, but it allows for the epileptic regions to vary between individuals. We evaluate the detection performance against intracranial EEG observations and compare our approach with two baseline methods that use standard statistics. The baseline techniques are sensitive to the choice of thresholds, whereas our algorithm automatically estimates the appropriate model parameters and compares favorably with the best baseline results. This suggests the promise of our approach for pre-surgical planning in epilepsy.

Wassermann D, Ross J, Washko G, Westin CF, Estepar RSJ. Diffeomorphic Point Set Registration using Non-Stationary Mixture Models. Proc IEEE Int Symp Biomed Imaging. 2013;.

This paper investigates a diffeomorphic point-set registration based on non-stationary mixture models. The goal is to improve the non-linear registration of anatomical structures by representing each point as a general non-stationary kernel that provides information about the shape of that point. Our framework generalizes work done by others that use stationary models. We achieve this by integrating the shape at each point when calculating the point-set similarity and transforming it according to the calculated deformation. We also restrict the non-rigid transform to the space of symmetric diffeomorphisms. Our algorithm is validated in synthetic and human datasets in two different applications: fiber bundle and lung airways registration. Our results shows that non-stationary mixture models are superior to Gaussian mixture models and methods that do not take into account the shape of each point.

Savadjiev P, Rathi Y, Bouix S, Smith AR, Schultz RT, Verma R, Westin CF. Combining Surface and Fiber Geometry: An Integrated Approach to Brain Morphology. Med Image Comput Comput Assist Interv. 2013;16(Pt 1):50–7.

Despite the fact that several theories link cortical development and function to the development of white matter and its geometrical structure, the relationship between gray and white matter morphology has not been widely researched. In this paper, we propose a novel framework for investigating this relationship. Given a set of fiber tracts which connect to a particular cortical region, the key idea is to compute two scalar fields that represent geometrical characteristics of the white matter and of the surface of the cortical region. The distributions of these scalar values are then linked via Mutual Information, which results in a quantitative marker that can be used in the study of normal and pathological brain structure and development. We apply this framework to a population study on autism spectrum disorder in children.

Vosburgh KG, Golby A, Pieper SD. Surgery, Virtual Reality, and the Future. Stud Health Technol Inform. 2013;184:7–13.

MMVR has provided the leading forum for the multidisciplinary interaction and development of the use of Virtual Reality (VR) techniques in medicine, particularly in surgical practice. Here we look back at the foundations of our field, focusing on the use of VR in Surgery and similar interventional procedures, sum up the current status, and describe the challenges and opportunities going forward.

Donnell LJO, Golby AJ, Westin CF. Fiber Clustering versus the Parcellation-based Connectome. Neuroimage. 2013;80:283–9.

We compare two strategies for modeling the connections of the brain’s white matter: fiber clustering and the parcellation-based connectome. Both methods analyze diffusion magnetic resonance imaging fiber tractography to produce a quantitative description of the brain’s connections. Fiber clustering is designed to reconstruct anatomically-defined white matter tracts, while the parcellation-based white matter segmentation enables the study of the brain as a network. From the perspective of white matter segmentation, we compare and contrast the goals and methods of the parcellation-based and clustering approaches, with special focus on reviewing the field of fiber clustering. We also propose a third category of new hybrid methods that combine the aspects of parcellation and clustering, for joint analysis of connection structure and anatomy or function. We conclude that these different approaches for segmentation and modeling of the white matter can advance the neuroscientific study of the brain’s connectivity in complementary ways.

Zhou B, Konstorum A, Duong T, Tieu KH, Wells WM III, Brown GG, Stern HS, Shahbaba B. A Hierarchical Modeling Approach to Data Analysis and Study Design in a Multi-site Experimental fMRI Study. Psychometrika. 2013;78(2):260–78.

We propose a hierarchical Bayesian model for analyzing multi-site experimental fMRI studies. Our method takes the hierarchical structure of the data (subjects are nested within sites, and there are multiple observations per subject) into account and allows for modeling between-site variation. Using posterior predictive model checking and model selection based on the deviance information criterion (DIC), we show that our model provides a good fit to the observed data by sharing information across the sites. We also propose a simple approach for evaluating the efficacy of the multi-site experiment by comparing the results to those that would be expected in hypothetical single-site experiments with the same sample size.

Egger J, Kapur T, Fedorov A, Pieper S, Miller J V, Veeraraghavan H, Freisleben B, Golby AJ, Nimsky C, Kikinis R. GBM Volumetry using the 3D Slicer Medical Image Computing Platform. Sci Rep. 2013;3:1364.

Volumetric change in glioblastoma multiforme (GBM) over time is a critical factor in treatment decisions. Typically, the tumor volume is computed on a slice-by-slice basis using MRI scans obtained at regular intervals. (3D)Slicer - a free platform for biomedical research - provides an alternative to this manual slice-by-slice segmentation process, which is significantly faster and requires less user interaction. In this study, 4 physicians segmented GBMs in 10 patients, once using the competitive region-growing based GrowCut segmentation module of Slicer, and once purely by drawing boundaries completely manually on a slice-by-slice basis. Furthermore, we provide a variability analysis for three physicians for 12 GBMs. The time required for GrowCut segmentation was on an average 61% of the time required for a pure manual segmentation. A comparison of Slicer-based segmentation with manual slice-by-slice segmentation resulted in a Dice Similarity Coefficient of 88.43 ± 5.23% and a Hausdorff Distance of 2.32 ± 5.23 mm.

Chen GH, Wachinger C, Golland P. Sparse Projections of Medical Images onto Manifolds. Inf Process Med Imaging. 2013;23:292–303.

Manifold learning has been successfully applied to a variety of medical imaging problems. Its use in real-time applications requires fast projection onto the low-dimensional space. To this end, out-of-sample extensions are applied by constructing an interpolation function that maps from the input space to the low-dimensional manifold. Commonly used approaches such as the Nyström extension and kernel ridge regression require using all training points. We propose an interpolation function that only depends on a small subset of the input training data. Consequently, in the testing phase each new point only needs to be compared against a small number of input training data in order to project the point onto the low-dimensional space. We interpret our method as an out-of-sample extension that approximates kernel ridge regression. Our method involves solving a simple convex optimization problem and has the attractive property of guaranteeing an upper bound on the approximation error, which is crucial for medical applications. Tuning this error bound controls the sparsity of the resulting interpolation function. We illustrate our method in two clinical applications that require fast mapping of input images onto a low-dimensional space.