Gao Y, Zhu L, Cates J, MacLeod RS, Bouix S, Tannenbaum A. A Kalman Filtering Perspective for Multiatlas Segmentation. SIAM J Imaging Sci 2015;8(2):1007-29.
In multiatlas segmentation, one typically registers several atlases to the novel image, and their respective segmented label images are transformed and fused to form the final segmentation. In this work, we provide a new dynamical system perspective for multiatlas segmentation, inspired by the following fact: The transformation that aligns the current atlas to the novel image can be not only computed by direct registration but also inferred from the transformation that aligns the previous atlas to the image together with the transformation between the two atlases. This process is similar to the global positioning system on a vehicle, which gets position by inquiring from the satellite and by employing the previous location and velocity-neither answer in isolation being perfect. To solve this problem, a dynamical system scheme is crucial to combine the two pieces of information; for example, a Kalman filtering scheme is used. Accordingly, in this work, a Kalman multiatlas segmentation is proposed to stabilize the global/affine registration step. The contributions of this work are twofold. First, it provides a new dynamical systematic perspective for standard independent multiatlas registrations, and it is solved by Kalman filtering. Second, with very little extra computation, it can be combined with most existing multiatlas segmentation schemes for better registration/segmentation accuracy.
Wang D, Buckner RL, Fox MD, Holt DJ, Holmes AJ, Stoecklein S, Langs G, Pan R, Qian T, Li K, Baker JT, Stufflebeam SM, Wang K, Wang X, Hong B, Liu H. Parcellating Cortical Functional Networks in Individuals. Nat Neurosci 2015;18(12):1853-60.
The capacity to identify the unique functional architecture of an individual’s brain is a crucial step toward personalized medicine and understanding the neural basis of variation in human cognition and behavior. Here we developed a cortical parcellation approach to accurately map functional organization at the individual level using resting-state functional magnetic resonance imaging (fMRI). A population-based functional atlas and a map of inter-individual variability were employed to guide the iterative search for functional networks in individual subjects. Functional networks mapped by this approach were highly reproducible within subjects and effectively captured the variability across subjects, including individual differences in brain lateralization. The algorithm performed well across different subject populations and data types, including task fMRI data. The approach was then validated by invasive cortical stimulation mapping in surgical patients, suggesting potential for use in clinical applications.
Vaughan T, Lasso A, Ungi T, Fichtinger G. Hole filling with oriented sticks in ultrasound volume reconstruction. J Med Imaging (Bellingham) 2015;2(3):034002.
Volumes reconstructed from tracked planar ultrasound images often contain regions where no information was recorded. Existing interpolation methods introduce image artifacts and tend to be slow in filling large missing regions. Our goal was to develop a computationally efficient method that fills missing regions while adequately preserving image features. We use directional sticks to interpolate between pairs of known opposing voxels in nearby images. We tested our method on 30 volumetric ultrasound scans acquired from human subjects, and compared its performance to that of other published hole-filling methods. Reconstruction accuracy, fidelity, and time were improved compared with other methods.
Garlapati RR, Mostayed A, Joldes GR, Wittek A, Doyle B, Miller K. Towards measuring neuroimage misalignment. Comput Biol Med 2015;64:12-23.
To enhance neuro-navigation, high quality pre-operative images must be registered onto intra-operative configuration of the brain. Therefore evaluation of the degree to which structures may remain misaligned after registration is critically important. We consider two Hausdorff Distance (HD)-based evaluation approaches: the edge-based HD (EBHD) metric and the Robust HD (RHD) metric as well as various commonly used intensity-based similarity metrics such as Mutual Information (MI), Normalised Mutual Information (NMI), Entropy Correlation Coefficient (ECC), Kullback-Leibler Distance (KLD) and Correlation Ratio (CR). We conducted the evaluation by applying known deformations to simple sample images and real cases of brain shift. We conclude that the intensity-based similarity metrics such as MI, NMI, ECC, KLD and CR do not correlate well with actual alignment errors, and hence are not useful for assessing misalignment. On the contrary, the EBHD and the RHD metrics correlated well with actual alignment errors; however, they have been found to underestimate the actual misalignment. We also note that it is beneficial to present HD results as a percentile-HD curve rather than a single number such as the 95-percentile HD. Percentile-HD curves present the full range of alignment errors and also facilitate the comparison of results obtained using different approaches. Furthermore, the qualities that should be possessed by an ideal evaluation metric were highlighted. Future studies could focus on developing such an evaluation metric.
Chen Z, Tie Y, Olubiyi O, Rigolo L, Mehrtash A, Norton I, Pasternak O, Rathi Y, Golby AJ, Donnell LJO. Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography. Neuroimage Clin 2015;7:815-22.
BACKGROUND: Diffusion imaging tractography is increasingly used to trace critical fiber tracts in brain tumor patients to reduce the risk of post-operative neurological deficit. However, the effects of peritumoral edema pose a challenge to conventional tractography using the standard diffusion tensor model. The aim of this study was to present a novel technique using a two-tensor unscented Kalman filter (UKF) algorithm to track the arcuate fasciculus (AF) in brain tumor patients with peritumoral edema. METHODS: Ten right-handed patients with left-sided brain tumors in the vicinity of language-related cortex and evidence of significant peritumoral edema were retrospectively selected for the study. All patients underwent 3-Tesla magnetic resonance imaging (MRI) including a diffusion-weighted dataset with 31 directions. Fiber tractography was performed using both single-tensor streamline and two-tensor UKF tractography. A two-regions-of-interest approach was applied to perform the delineation of the AF. Results from the two different tractography algorithms were compared visually and quantitatively. RESULTS: Using single-tensor streamline tractography, the AF appeared disrupted in four patients and contained few fibers in the remaining six patients. Two-tensor UKF tractography delineated an AF that traversed edematous brain areas in all patients. The volume of the AF was significantly larger on two-tensor UKF than on single-tensor streamline tractography (p 
Li M, Miller K, Joldes GR, Doyle B, Garlapati RR, Kikinis R, Wittek A. Patient-specific biomechanical model as whole-body CT image registration tool. Med Image Anal 2015;22(1):22-34.
Whole-body computed tomography (CT) image registration is important for cancer diagnosis, therapy planning and treatment. Such registration requires accounting for large differences between source and target images caused by deformations of soft organs/tissues and articulated motion of skeletal structures. The registration algorithms relying solely on image processing methods exhibit deficiencies in accounting for such deformations and motion. We propose to predict the deformations and movements of body organs/tissues and skeletal structures for whole-body CT image registration using patient-specific non-linear biomechanical modelling. Unlike the conventional biomechanical modelling, our approach for building the biomechanical models does not require time-consuming segmentation of CT scans to divide the whole body into non-overlapping constituents with different material properties. Instead, a Fuzzy C-Means (FCM) algorithm is used for tissue classification to assign the constitutive properties automatically at integration points of the computation grid. We use only very simple segmentation of the spine when determining vertebrae displacements to define loading for biomechanical models. We demonstrate the feasibility and accuracy of our approach on CT images of seven patients suffering from cancer and aortic disease. The results confirm that accurate whole-body CT image registration can be achieved using a patient-specific non-linear biomechanical model constructed without time-consuming segmentation of the whole-body images.
Sandhu R, Georgiou T, Reznik E, Zhu L, Kolesov I, Senbabaoglu Y, Tannenbaum A. Graph Curvature for Differentiating Cancer Networks. Sci Rep 2015;5:12323.
Cellular interactions can be modeled as complex dynamical systems represented by weighted graphs. The functionality of such networks, including measures of robustness, reliability, performance, and efficiency, are intrinsically tied to the topology and geometry of the underlying graph. Utilizing recently proposed geometric notions of curvature on weighted graphs, we investigate the features of gene co-expression networks derived from large-scale genomic studies of cancer. We find that the curvature of these networks reliably distinguishes between cancer and normal samples, with cancer networks exhibiting higher curvature than their normal counterparts. We establish a quantitative relationship between our findings and prior investigations of network entropy. Furthermore, we demonstrate how our approach yields additional, non-trivial pair-wise (i.e. gene-gene) interactions which may be disrupted in cancer samples. The mathematical formulation of our approach yields an exact solution to calculating pair-wise changes in curvature which was computationally infeasible using prior methods. As such, our findings lay the foundation for an analytical approach to studying complex biological networks.
Stamm JM, Koerte IK, Muehlmann M, Pasternak O, Bourlas AP, Baugh CM, Giwerc MY, Zhu A, Coleman MJ, Bouix S, Fritts NG, Martin BM, Chaisson C, McClean MD, Lin AP, Cantu RC, Tripodis Y, Stern RA, Shenton ME. Age at First Exposure to Football Is Associated with Altered Corpus Callosum White Matter Microstructure in Former Professional Football Players. J Neurotrauma 2015;32(22):1768-76.
Youth football players may incur hundreds of repetitive head impacts (RHI) in one season. Our recent research suggests that exposure to RHI during a critical neurodevelopmental period prior to age 12 may lead to greater later-life mood, behavioral, and cognitive impairments. Here, we examine the relationship between age of first exposure (AFE) to RHI through tackle football and later-life corpus callosum (CC) microstructure using magnetic resonance diffusion tensor imaging (DTI). Forty retired National Football League (NFL) players, ages 40-65, were matched by age and divided into two groups based on their AFE to tackle football: before age 12 or at age 12 or older. Participants underwent DTI on a 3 Tesla Siemens (TIM-Verio) magnet. The whole CC and five subregions were defined and seeded using deterministic tractography. Dependent measures were fractional anisotropy (FA), trace, axial diffusivity, and radial diffusivity. Results showed that former NFL players in the AFE
Radmanesh A, Zamani AA, Whalen S, Tie Y, Suarez RO, Golby AJ. Comparison of seeding methods for visualization of the corticospinal tracts using single tensor tractography. Clin Neurol Neurosurg 2015;129:44-9.
OBJECTIVES: To compare five different seeding methods to delineate hand, foot, and lip components of the corticospinal tract (CST) using single tensor tractography. METHODS: We studied five healthy subjects and 10 brain tumor patients. For each subject, we used five different seeding methods, from (1) cerebral peduncle (CP), (2) posterior limb of the internal capsule (PLIC), (3) white matter subjacent to functional MRI activations (fMRI), (4) whole brain and then selecting the fibers that pass through both fMRI and CP (WBF-CP), and (5) whole brain and then selecting the fibers that pass through both fMRI and PLIC (WBF-PLIC). Two blinded neuroradiologists rated delineations as anatomically successful or unsuccessful tractography. The proportions of successful trials from different methods were compared by Fisher’s exact test. RESULTS: To delineate hand motor tract, seeding through fMRI activation areas was more effective than through CP (p0.1). WBF-CP delineated hand motor tracts in a larger proportion of trials than CP alone (p
Ning L, Georgiou TT, Tannenbaum A, Boyd SP. Linear Models Based on Noisy Data and the Frisch Scheme. SIAM Rev Soc Ind Appl Math 2015;57(2):167-97.
We address the problem of identifying linear relations among variables based on noisy measurements. This is a central question in the search for structure in large data sets. Often a key assumption is that measurement errors in each variable are independent. This basic formulation has its roots in the work of Charles Spearman in 1904 and of Ragnar Frisch in the 1930s. Various topics such as errors-in-variables, factor analysis, and instrumental variables all refer to alternative viewpoints on this problem and on ways to account for the anticipated way that noise enters the data. In the present paper we begin by describing certain fundamental contributions by the founders of the field and provide alternative modern proofs to certain key results. We then go on to consider a modern viewpoint and novel numerical techniques to the problem. The central theme is expressed by the Frisch-Kalman dictum, which calls for identifying a noise contribution that allows a maximal number of simultaneous linear relations among the noise-free variables-a rank minimization problem. In the years since Frisch’s original formulation, there have been several insights, including trace minimization as a convenient heuristic to replace rank minimization. We discuss convex relaxations and theoretical bounds on the rank that, when met, provide guarantees for global optimality. A complementary point of view to this minimum-rank dictum is presented in which models are sought leading to a uniformly optimal quadratic estimation error for the error-free variables. Points of contact between these formalisms are discussed, and alternative regularization schemes are presented.