P. Agrawal, R. T. Whitaker, S. Y. Elhabian. Learning Deep Features for Shape Correspondence with Domain Invariance, Subtitled arXiv preprint arXiv:2102.10493, 2021.
Correspondence-based shape models are key to various medical imaging applications that rely on a statistical analysis of anatomies. Such shape models are expected to represent consistent anatomical features across the population for population-specific shape statistics. Early approaches for correspondence placement rely on nearest neighbor search for simpler anatomies. Coordinate transformations for shape correspondence hold promise to address the increasing anatomical complexities. Nonetheless, due to the inherent shape-level geometric complexity and population-level shape variation, the coordinate-wise correspondence often does not translate to the anatomical correspondence. An alternative, group-wise approach for correspondence placement explicitly models the trade-off between geometric description and the population's statistical compactness. However, these models achieve limited success in resolving nonlinear shape correspondence. Recent works have addressed this limitation by adopting an application-specific notion of correspondence through lifting positional data to a higher dimensional feature space. However, they heavily rely on manual expertise to create domain-specific features and consistent landmarks. This paper proposes an automated feature learning approach, using deep convolutional neural networks to extract correspondence-friendly features from shape ensembles. Further, an unsupervised domain adaptation scheme is introduced to augment the pretrained geometric features with new anatomies. Results on anatomical datasets of human scapula, femur, and pelvis bones demonstrate that …
We present a nonparametric statistical framework for the quantification, analysis, and propagation of data uncertainty in direct volume rendering (DVR). The state-of-the-art statistical DVR framework allows for preserving the transfer function (TF) of the ground truth function when visualizing uncertain data; however, the existing framework is restricted to parametric models of uncertainty. In this paper, we address the limitations of the existing DVR framework by extending the DVR framework for nonparametric distributions. We exploit the quantile interpolation technique to derive probability distributions representing uncertainty in viewing-ray sample intensities in closed form, which allows for accurate and efficient computation. We evaluate our proposed nonparametric statistical models through qualitative and quantitative comparisons with the mean-field and parametric statistical models, such as uniform and Gaussian, as well as Gaussian mixtures. In addition, we present an extension of the state-of-the-art rendering parametric framework to 2D TFs for improved DVR classifications. We show the applicability of our uncertainty quantification framework to ensemble, downsampled, and bivariate versions of scalar field datasets.
P. R. Atkins, P. Agrawal, J. D. Mozingo, K. Uemura, K. Tokunaga, C. L. Peters, S. Y. Elhabian, R. T. Whitaker, A. E. Anderson.
Prediction of Femoral Head Coverage from Articulated Statistical Shape Models of Patients with Developmental Dysplasia of the Hip, In Journal of Orthopaedic Research, Wiley, 2021.
Developmental dysplasia of the hip (DDH) is commonly described as reduced femoral head coverage due to anterolateral acetabular deficiency. Although reduced coverage is the defining trait of DDH, more subtle and localized anatomic features of the joint are also thought to contribute to symptom development and degeneration. These features are challenging to identify using conventional approaches. Herein, we assessed the morphology of the full femur and hemi-pelvis using an articulated statistical shape model (SSM). The model determined the morphological and pose-based variations associated with DDH in a population of Japanese females and established which of these variations predict coverage. Computed tomography images of 83 hips from 47 patients were segmented for input into a correspondence-based SSM. The dominant modes of variation in the model initially represented scale and pose. After removal of these factors through individual bone alignment, femoral version and neck-shaft angle, pelvic curvature, and acetabular version dominated the observed variation. Femoral head oblateness and prominence of the acetabular rim and various muscle attachment sites of the femur and hemi-pelvis were found to predict 3D CT-based coverage measurements (R2=0.5-0.7 for the full bones, R2=0.9 for the joint).
Electrocardiographic forward problems are crucial components for noninvasive electrocardiographic imaging (ECGI) that compute torso potentials from cardiac source measurements. Forward problems have few sources of error as they are physically well posed and supported by mature numerical and computational techniques. However, the residual errors reported from experimental validation studies between forward computed and measured torso signals remain surprisingly high.
To test the hypothesis that incomplete cardiac source sampling, especially above the atrioventricular (AV) plane is a major contributor to forward solution errors.
We used a modified Langendorff preparation suspended in a human-shaped electrolytic torso-tank and a novel pericardiac-cage recording array to thoroughly sample the cardiac potentials. With this carefully controlled experimental preparation, we minimized possible sources of error, including geometric error and torso inhomogeneities. We progressively removed recorded signals from above the atrioventricular plane to determine how the forward-computed torso-tank potentials were affected by incomplete source sampling.
We studied 240 beats total recorded from three different activation sequence types (sinus, and posterior and anterior left-ventricular free-wall pacing) in each of two experiments. With complete sampling by the cage electrodes, all correlation metrics between computed and measured torso-tank potentials were above 0.93 (maximum 0.99). The mean root-mean-squared error across all beat types was also low, less than or equal to 0.10 mV. A precipitous drop in forward solution accuracy was observed when we included only cage measurements below the AV plane.
First, our forward computed potentials using complete cardiac source measurements set a benchmark for similar studies. Second, this study validates the importance of complete cardiac source sampling above the AV plane to produce accurate forward computed torso potentials. Testing ECGI systems and techniques with these more complete and highly accurate datasets will improve inverse techniques and noninvasive detection of cardiac electrical abnormalities.
R. Bhalodia, S. Elhabian, L. Kavan, R. Whitaker. Leveraging Unsupervised Image Registration for Discovery of Landmark Shape Descriptor, In Medical Image Analysis, Elsevier, pp. 102157. 2021.
In current biological and medical research, statistical shape modeling (SSM) provides an essential framework for the characterization of anatomy/morphology. Such analysis is often driven by the identification of a relatively small number of geometrically consistent features found across the samples of a population. These features can subsequently provide information about the population shape variation. Dense correspondence models can provide ease of computation and yield an interpretable low-dimensional shape descriptor when followed by dimensionality reduction. However, automatic methods for obtaining such correspondences usually require image segmentation followed by significant preprocessing, which is taxing in terms of both computation as well as human resources. In many cases, the segmentation and subsequent processing require manual guidance and anatomy specific domain expertise. This paper proposes a self-supervised deep learning approach for discovering landmarks from images that can directly be used as a shape descriptor for subsequent analysis. We use landmark-driven image registration as the primary task to force the neural network to discover landmarks that register the images well. We also propose a regularization term that allows for robust optimization of the neural network and ensures that the landmarks uniformly span the image domain. The proposed method circumvents segmentation and preprocessing and directly produces a usable shape descriptor using just 2D or 3D images. In addition, we also propose two variants on the training loss function that allows for prior shape information to be integrated into the model. We apply this framework on several 2D and 3D datasets to obtain their shape descriptors. We analyze these shape descriptors in their efficacy of capturing shape information by performing different shape-driven applications depending on the data ranging from shape clustering to severity prediction to outcome diagnosis.
R. Bhalodia, S. Elhabian, J. Adams, W. Tao, L. Kavan, R. Whitaker. DeepSSM: A Blueprint for Image-to-Shape Deep Learning Models, Subtitled arXiv preprint arXiv:2110.07152, 2021.
Statistical shape modeling (SSM) characterizes anatomical variations in a population of shapes generated from medical images. SSM requires consistent shape representation across samples in shape cohort. Establishing this representation entails a processing pipeline that includes anatomy segmentation, re-sampling, registration, and non-linear optimization. These shape representations are then used to extract low-dimensional shape descriptors that facilitate subsequent analyses in different applications. However, the current process of obtaining these shape descriptors from imaging data relies on human and computational resources, requiring domain expertise for segmenting anatomies of interest. Moreover, this same taxing pipeline needs to be repeated to infer shape descriptors for new image data using a pre-trained/existing shape model. Here, we propose DeepSSM, a deep learning-based framework for learning the functional mapping from images to low-dimensional shape descriptors and their associated shape representations, thereby inferring statistical representation of anatomy directly from 3D images. Once trained using an existing shape model, DeepSSM circumvents the heavy and manual pre-processing and segmentation and significantly improves the computational time, making it a viable solution for fully end-to-end SSM applications. In addition, we introduce a model-based data-augmentation strategy to address data scarcity. Finally, this paper presents and analyzes two different architectural variants of DeepSSM with different loss functions using three medical datasets and their downstream clinical application. Experiments showcase that DeepSSM performs comparably or better to the state-of-the-art SSM both quantitatively and on application-driven downstream tasks. Therefore, DeepSSM aims to provide a comprehensive blueprint for deep learning-based image-to-shape models.
S. R. Black, A. Janson, M. Mahan, J. Anderson, C. R. Butson. Identification of Deep Brain Stimulation Targets for Neuropathic Pain After Spinal Cord Injury Using Localized Increases in White Matter Fiber Cross‐Section, In Neuromodulation: Technology at the Neural Interface, John Wiley & Sons, Inc., 2021.
The spinal cord injury (SCI) patient population is overwhelmingly affected by neuropathic pain (NP), a secondary condition for which therapeutic options are limited and have a low degree of efficacy. The objective of this study was to identify novel deep brain stimulation (DBS) targets that may theoretically benefit those with NP in the SCI patient population. We hypothesize that localized changes in white matter identified in SCI subjects with NP compared to those without NP could be used to develop an evidence‐based approach to DBS target identification.
W. W. Good, B. Zenger, J. A. Bergquist, L. C. Rupp, K. K. Gillette, M. A.F. Gsell, G. Plank, R. S. MacLeod. Quantifying the spatiotemporal influence of acute myocardial ischemia on volumetric conduction velocity, In Journal of Electrocardiology, Vol. 66, Churchill Livingstone, pp. 86-94. 2021.
Acute myocardial ischemia occurs when coronary perfusion to the heart is inadequate, which can perturb the highly organized electrical activation of the heart and can result in adverse cardiac events including sudden cardiac death. Ischemia is known to influence the ST and repolarization phases of the ECG, but it also has a marked effect on propagation (QRS); however, studies investigating propagation during ischemia have been limited.
Objective: In this study, we have used whole heart simulations parameterized with large animal experiments to validate three techniques (two from the literature and one novel) for estimating epicardial and volumetric conduction velocity (CV). Methods: We used an eikonal-based simulation model to generate ground truth activation sequences with prescribed CVs. Using the sampling density achieved experimentally we examined the accuracy with which we could reconstruct the wavefront, and then examined the robustness of three CV estimation techniques to reconstruction related error. We examined a triangulation-based, inverse-gradient-based, and streamline-based techniques for estimating CV cross the surface and within the volume of the heart. Results: The reconstructed activation times agreed closely with simulated values, with 50-70% of the volumetric nodes and 97-99% of the epicardial nodes were within 1 ms of the ground truth. We found close agreement between the CVs calculated using reconstructed versus ground truth activation times, with differences in the median estimated CV on the order of 3-5% volumetrically and 1-2% superficially, regardless of what technique was used. Conclusion: Our results indicate that the wavefront reconstruction and CV estimation techniques are accurate, allowing us to examine changes in propagation induced by experimental interventions such as acute ischemia, ectopic pacing, or drugs. Significance: We implemented, validated, and compared the performance of a number of CV estimation techniques. The CV estimation techniques implemented in this study produce accurate, high-resolution CV fields that can be used to study propagation in the heart experimentally and clinically.
W. W. Good, B. Zenger, J. A. Bergquist, L. C. Rupp, K. Gillett, N. Angel, D. Chou, G. Plank, R. S. MacLeod.
Combining endocardial mapping and electrocardiographic imaging (ECGI) for improving PVC localization: A feasibility study, In Journal of Electrocardiology, 2021.
Accurate reconstruction of cardiac activation wavefronts is crucial for clinical diagnosis, management, and treatment of cardiac arrhythmias. Furthermore, reconstruction of activation profiles within the intramural myocardium has long been impossible because electrical mapping was only performed on the endocardial surface. Recent advancements in electrocardiographic imaging (ECGI) have made endocardial and epicardial activation mapping possible. We propose a novel approach to use both endocardial and epicardial mapping in a combined approach to reconstruct intramural activation times.
Deep Adaptive Electrocardiographic Imaging with Generative Forward Model for Error Reduction, In Functional Imaging and Modeling of the Heart: 11th International Conference, In Functional Imaging and Modeling of the Heart: 11th International Conference, Vol. 12738, Springer Nature, pp. 471. 2021.X. Jiang, J. C. Font, J. A. Bergquist, B. Zenger, W. W. Good, D. H. Brooks, R. S. MacLeod, L. Wang.
Accuracy of estimating the heart’s electrical activity with Electrocardiographic Imaging (ECGI) is challenging due to using an error-prone physics-based model (forward model). While getting better results than the traditional numerical methods following the underlying physics, modern deep learning approaches ignore the physics behind the electrical propagation in the body and do not allow the use of patientspecific geometry. We introduce a deep-learning-based ECGI framework capable of understanding the underlying physics, aware of geometry, and adjustable to patient-specific data. Using a variational autoencoder (VAE), we uncover the forward model’s parameter space, and when solving the inverse problem, these parameters will be optimized to reduce the errors in the forward model. In both simulation and real data experiments, we demonstrated the ability of the presented framework to provide accurate reconstruction of the heart’s electrical potentials and localization of the earliest activation sites.
Several severity metrics have been developed for metopic craniosynostosis, including a recent machine learning-derived algorithm. This study assessed the diagnostic concordance between machine learning and previously published severity indices.
Area Available for Atrial Fibrillation to Propagate Is an Important Determinant of Recurrence After Ablation, In JACC: Clinical Electrophysiology, Elsevier, 2021.R. Kamali, J. Kump, E. Ghafoori, M. Lange, N. Hu, T. J. Bunch, D. J. Dosdall, R. S. Macleod, R. Ranjan.
This study sought to evaluate atrial fibrillation (AF) ablation outcomes based on scar patterns and contiguous area available for AF wavefronts to propagate.
A.S. Rababah, L.R. Bear, Y.S. Dogrusoz, W. Good, J. Bergquist, J. Stoks, R. MacLeod, K. Rjoob, M. Jennings, J. Mclaughlin, D. D. Finlay. Reducing Line-of-block Artifacts in Cardiac Activation Maps Estimated Using ECG Imaging: A Comparison of Source Models and Estimation Methods, In Computers in Biology and Medicine, Vol. 136, pp. 104666. 2021.
Electrocardiographic imaging is an imaging modality that has been introduced recently to help in visualizing the electrical activity of the heart and consequently guide the ablation therapy for ventricular arrhythmias. One of the main challenges of this modality is that the electrocardiographic signals recorded at the torso surface are contaminated with noise from different sources. Low amplitude leads are more affected by noise due to their low peak-to-peak amplitude. In this paper, we have studied 6 datasets from two torso tank experiments (Bordeaux and Utah experiments) to investigate the impact of removing or interpolating these low amplitude leads on the inverse reconstruction of cardiac electrical activity. Body surface potential maps used were calculated by using the full set of recorded leads, removing 1, 6, 11, 16, or 21 low amplitude leads, or interpolating 1, 6, 11, 16, or 21 low amplitude leads using one of the three interpolation methods – Laplacian interpolation, hybrid interpolation, or the inverse-forward interpolation. The epicardial potential maps and activation time maps were computed from these body surface potential maps and compared with those recorded directly from the heart surface in the torso tank experiments. There was no significant change in the potential maps and activation time maps after the removal of up to 11 low amplitude leads. Laplacian interpolation and hybrid interpolation improved the inverse reconstruction in some datasets and worsened it in the rest. The inverse forward interpolation of low amplitude leads improved it in two out of 6 datasets and at least remained the same in the other datasets. It was noticed that after doing the inverse-forward interpolation, the selected lambda value was closer to the optimum lambda value that gives the inverse solution best correlated with the recorded one.
Salinet et al. Electrocardiographic Imaging for Atrial Fibrillation treatment guidance (for example, localization of AF triggers and sustaining mechanisms), and we discuss the technological requirements and validation. We address experimental and clinical results, limitations, and future challenges for fruitful application of ECGI for AF understanding and management. We pay attention to existing techniques and clinical application, to computer models and (animal or human) experiments, to challenges of methodological and clinical validation. The overall objective of the study is to provide a consensus on valuable directions that ECGI research may take to provide future improvements in AF characterization and treatment guidance.
S. Sane, A. Yenpure, R. Bujack, M. Larsen, K. Moreland, C. Garth, C. R. Johnson,, H. Childs.
Scalable In Situ Computation of Lagrangian Representations via Local Flow Maps, In Eurographics Symposium on Parallel Graphics and Visualization, The Eurographics Association, 2021.
In situ computation of Lagrangian flow maps to enable post hoc time-varying vector field analysis has recently become an active area of research. However, the current literature is largely limited to theoretical settings and lacks a solution to address scalability of the technique in distributed memory. To improve scalability, we propose and evaluate the benefits and limitations of a simple, yet novel, performance optimization. Our proposed optimization is a communication-free model resulting in local Lagrangian flow maps, requiring no message passing or synchronization between processes, intrinsically improving scalability, and thereby reducing overall execution time and alleviating the encumbrance placed on simulation codes from communication overheads. To evaluate our approach, we computed Lagrangian flow maps for four time-varying simulation vector fields and investigated how execution time and reconstruction accuracy are impacted by the number of GPUs per compute node, the total number of compute nodes, particles per rank, and storage intervals. Our study consisted of experiments computing Lagrangian flow maps with up to 67M particle trajectories over 500 cycles and used as many as 2048 GPUs across 512 compute nodes. In all, our study contributes an evaluation of a communication-free model as well as a scalability study of computing distributed Lagrangian flow maps at scale using in situ infrastructure on a modern supercomputer.
Uncertainty Quantification of the Effects of Segmentation Variability in ECGI, In Functional Imaging and Modeling of the Heart, Springer International Publishing, pp. 515--522. 2021.
Despite advances in many of the techniques used in Electrocardiographic Imaging (ECGI), uncertainty remains insufficiently quantified for many aspects of the pipeline. The effect of geometric uncertainty, particularly due to segmentation variability, may be the least explored to date. We use statistical shape modeling and uncertainty quantification (UQ) to compute the effect of segmentation variability on ECGI solutions. The shape model was made with Shapeworks from nine segmentations of the same patient and incorporated into an ECGI pipeline. We computed uncertainty of the pericardial potentials and local activation times (LATs) using polynomial chaos expansion (PCE) implemented in UncertainSCI. Uncertainty in pericardial potentials from segmentation variation mirrored areas of high variability in the shape model, near the base of the heart and the right ventricular outflow tract, and that ECGI was less sensitive to uncertainty in the posterior region of the heart. Subsequently LAT calculations could vary dramatically due to segmentation variability, with a standard deviation as high as 126ms, yet mainly in regions with low conduction velocity. Our shape modeling and UQ pipeline presented possible uncertainty in ECGI due to segmentation variability and can be used by researchers to reduce said uncertainty or mitigate its effects. The demonstrated use of statistical shape modeling and UQ can also be extended to other types of modeling pipelines.
J. Tate, S. Rampersad, C. Charlebois, Z. Liu, J. Bergquist, D. White, L. Rupp, D. Brooks, A. Narayan, R. MacLeod. Uncertainty Quantification in Brain Stimulation using UncertainSCI, In Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, Vol. 14, No. 6, Elsevier, pp. 1659-1660. 2021.
Predicting the effects of brain stimulation with computer models presents many challenges, including estimating the possible error from the propagation of uncertain input parameters through the model. Quantification and control of these errors through uncertainty quantification (UQ) provide statistics on the likely impact of parameter variation on solution accuracy, including total variance and sensitivity associated to each parameter. While the need and importance of UQ in clinical modeling is generally accepted, tools for implementing UQ techniques remain limited or inaccessible for many researchers.
V. Vedam-Mai, K. Deisseroth, J. Giordano, G. Lazaro-Munoz, W. Chiong, N. Suthana, J. Langevin, J. Gill, W. Goodman, N. R. Provenza, C. H. Halpern, R. S. Shivacharan, T. N. Cunningham, S. A. Sheth, N. Pouratian, K. W. Scangos, H. S. Mayberg, A. Horn, K. A. Johnson, C. R. Butson, R. Gilron, C. de Hemptinne, R. Wilt, M. Yaroshinsky, S. Little, P. Starr, G. Worrell, P. Shirvalkar, E. Chang, J. Volkmann, M. Muthuraman, S. Groppa, A. A. Kühn, L. Li, M. Johnson, K. J. Otto, R. Raike, S. Goetz, C. Wu, P. Silburn, B. Cheeran, Y. J. Pathak, M. Malekmohammadi, A. Gunduz, J. K. Wong, S. Cernera, A. W. Shukla, A. Ramirez-Zamora, W. Deeb, A. Patterson, K. D. Foote, M. S. Okun.
Proceedings of the Eighth Annual Deep Brain Stimulation Think Tank: Advances in Optogenetics, Ethical Issues Affecting DBS Research, Neuromodulatory Approaches for Depression, Adaptive Neurostimulation, and Emerging DBS Technologies, In Frontiers in Human Neuroscience, Vol. 15, pp. 169. 2021.
We estimate that 208,000 deep brain stimulation (DBS) devices have been implanted to address neurological and neuropsychiatric disorders worldwide. DBS Think Tank presenters pooled data and determined that DBS expanded in its scope and has been applied to multiple brain disorders in an effort to modulate neural circuitry. The DBS Think Tank was founded in 2012 providing a space where clinicians, engineers, researchers from industry and academia discuss current and emerging DBS technologies and logistical and ethical issues facing the field. The emphasis is on cutting edge research and collaboration aimed to advance the DBS field. The Eighth Annual DBS Think Tank was held virtually on September 1 and 2, 2020 (Zoom Video Communications) due to restrictions related to the COVID-19 pandemic. The meeting focused on advances in: (1) optogenetics as a tool for comprehending neurobiology of diseases and on optogenetically-inspired DBS, (2) cutting edge of emerging DBS technologies, (3) ethical issues affecting DBS research and access to care, (4) neuromodulatory approaches for depression, (5) advancing novel hardware, software and imaging methodologies, (6) use of neurophysiological signals in adaptive neurostimulation, and (7) use of more advanced technologies to improve DBS clinical outcomes. There were 178 attendees who participated in a DBS Think Tank survey, which revealed the expansion of DBS into several indications such as obesity, post-traumatic stress disorder, addiction and Alzheimer’s disease. This proceedings summarizes the advances discussed at the Eighth Annual DBS Think Tank.
The main objective for understanding fluorescence microscopy data is to investigate and evaluate the fluorescent signal intensity distributions as well as their spatial relationships across multiple channels. The quantitative analysis of 3D fluorescence microscopy data needs interactive tools for researchers to select and focus on relevant biological structures. We developed an interactive tool based on volume visualization techniques and GPU computing for streamlining rapid data analysis. Our main contribution is the implementation of common data quantification functions on streamed volumes, providing interactive analyses on large data without lengthy preprocessing. Data segmentation and quantification are coupled with brushing and executed at an interactive speed. A large volume is partitioned into data bricks, and only user-selected structures are analyzed to constrain the computational load. We designed a framework to assemble a sequence of GPU programs to handle brick borders and stitch analysis results. Our tool was developed in collaboration with domain experts and has been used to identify cell types. We demonstrate a workflow to analyze cells in vestibular epithelia of transgenic mice.