More Like this

1. Computing Functional Brain Connectivity in Neurological Disorders: Efficient Processing and Retrieval of Electrophysiological Signal Data

   Gershon, A; Devulapalli, P; Zonjy, B; Ghosh, K; Tatsuoka, C; Sahoo, SS (April 2019, AMIA Jt Summits Transl Sci Proc.)

   Brain functional network connectivity is an important measure for characterizing changes in a variety of neurological disorders, for example Alzheimer’s Disease, Parkinson Disease, and Epilepsy. Epilepsy is a serious neurological disorder affecting more than 50 million persons worldwide with severe impact on the quality of life of patients and their family members due to recurrent seizures. More than 30% of epilepsy patients are refractive to pharmacotherapy and are considered for resection to disrupt epilepsy seizure networks. However, 20-50% of these patients continue to have seizures after surgery. Therefore, there is a critical need to gain new insights into the characteristics of epilepsy seizure networks involving one of more brain regions and accurately delineate epileptogenic zone as a target for surgery. Although there is growing availability of large volume of high resolution stereotactic electroencephalogram (SEEG) data recorded from intracranial electrodes during presurgical evaluation of patients, there are significant informatics challenges associated with processing and analyzing this large signal dataset for characterizing epilepsy seizure networks. In this paper, we describe the development and application of a high-performance indexing structure for efficient retrieval of large-scale SEEG signal data to compute seizure network patterns corresponding to brain functional connectivity networks. This novel Neuro-Integrative Connectivity (NIC) search and retrieval method has been developed by extending the red-black tree index model together with an efficient lookup algorithm. We systematically perform a comparative evaluation of the proposed NIC index using de-identified SEEG data from a patient with temporal lobe epilepsy to retrieve segments of signal data corresponding to multiple seizure events and demonstrate the significant advantages of the NIC index as compared to existing methods. This new NIC Index enables faster computation of brain functional connectivity measures in epilepsy patients for large-scale network analysis and potentially provide new insights into the organization as well as evolution of seizure networks in epilepsy patients. 

   more » « less
2. Topological Analysis of Mouse Brain Vasculature via 3D Light-sheet Microscopy Images

   Yao, Jiachen; Hagemann, Nina; Xiong, Qiaojie; Chen, Jianxu; Hermann, Dirk M; Chen, Chao (May 2024, IEEE International Symposium on Biomedical Imaging (ISBI))

   Vascular networks play a crucial role in understanding brain functionalities. Brain integrity and function, neuronal activity and plasticity, which are crucial for learning, are actively modulated by their local environments, specifically vascular networks. With recent developments in high-resolution 3D light-sheet microscopy imaging together with tissue processing techniques, it becomes feasible to obtain and examine large-scale brain vasculature in mice. To establish a structural foundation for functional study, however, we need advanced image analysis and structural modeling methods. Existing works use geometric features such as thickness, tortuosity, etc. However, geometric features cannot fully capture structural characteristics such as the richness of branches, connectivity, etc. In this paper, we study the morphology of brain vasculature through a topological lens. We extract topological features based on the theory of topological data analysis. Comparing of these robust and multi-scale topological structural features across different brain anatomical structures and between normal and obese populations sheds light on their promising future in studying neurological diseases. 

   more » « less
3. Characterizing Focal and Generalized Epileptic Networks Using Interictal Functional Connectivity

   https://doi.org/10.1109/CSCI51800.2020.00285  

   Zarafshan, Elaheh; Rajaei, Hoda; Forouzannezhad, Parisa; Morar, Ulyana; Cabrerizo, Mercedes; Adjouadi, Malek (December 2020, 2020 International Conference on Computational Science and Computational Intelligence (CSCI))

   null (Ed.)

   Using electroencephalography (EEG) data from epileptic patients 1 , we investigated and compared functional connectivity networks of three various types of epileptiform discharges (ED; single, complex & repetitive spikes) in 4 regions of the brain. Our results showed different connectivity patterns among three ED types within-and between-brain regions. The one-way ANOVA test indicated significant differences between the mean of the average connectivity matrices (ACMs) of the single spike, which characterize focal epilepsy, and the other two ED types (complex & repetitive) which characterize generalized epilepsy. The interictal EEG segments, through the connectivity patterns they yield, could be considered as one of the key indicators for the diagnosis of focal or generalized epilepsy. 

   more » « less
4. The dynamics of dynamic time warping in fMRI data: A method to capture inter-network stretching and shrinking via warp elasticity

   https://doi.org/10.1162/imag_a_00187  

   Wiafe, Sir-Lord; Faghiri, Ashkan; Fu, Zening; Miller, Robyn; Preda, Adrian; Calhoun, Vince D (May 2024, Imaging Neuroscience)

   Abstract In neuroimaging research, understanding the intricate dynamics of brain networks over time is paramount for unraveling the complexities of brain function. One approach commonly used to explore the dynamic nature of brain networks is functional connectivity analysis. However, while functional connectivity offers valuable insights, it fails to consider the diverse timescales of coupling between different brain regions. This gap in understanding leaves a significant aspect of brain dynamics unexplored in neuroimaging research. We propose an innovative approach that delves into the dynamic coupling/connectivity timescales of brain regions relative to one another, focusing on how brain region couplings stretch or shrink over time, rather than relying solely on functional connectivity measures. Our method introduces a novel metric called “warping elasticity,” which utilizes dynamic time warping (DTW) to capture the temporal nuances of connectivity. Unlike traditional methods, our approach allows for (potentially nonlinear) dynamic compression and expansion of the time series, offering a more intricate understanding of how coupling between brain regions evolves. Through the adaptive windows employed by the DTW method, we can effectively capture transient couplings within varying connectivity timescales of brain network pairs. In extensive evaluations, our method exhibits high replicability across subjects and diverse datasets, showcasing robustness against noise. More importantly, it uncovers statistically significant distinctions between healthy control (HC) and schizophrenia (SZ) groups through the identification of warp elasticity states. These states are cluster centroids, representing the warp elasticity across subjects and time, offering a novel perspective on the dynamic nature of brain connectivity, distinct from conventional metrics focused solely on functional connectivity. For instance, controls spend more time in a warp elasticity state characterized by timescale stretching of the visual domain relative to other domains, suggesting disruptions in the visual cortex. Conversely, patients show increased time spent in a warp elasticity state with stretching timescales in higher cognitive areas relative to sensory regions, indicative of prolonged cognitive processing of sensory input. Overall, our approach presents a promising avenue for investigating the temporal dynamics of brain network interactions in functional magnetic resonance imaging (fMRI) data. By focusing on the elasticity of connectivity timescales, rather than adhering to functional connectivity metrics, we pave the way for a deeper understanding of neuropsychiatric disorders in neuroscience research. 

   more » « less
5. A Flexible Constrained ICA Approach for Multisubject fMRI Analysis

   https://doi.org/10.1155/ijbi/2064944  

   Yang, Hanlu; Vu, Trung; Dhrubo, Ehsan_Ahmed; Calhoun, Vince_D; Adali, Tülay; Gallegos_Funes, ed., Francisco_Javier (March 2025, International Journal of Biomedical Imaging)

   Large‐scale analysis of functional connectivity within intrinsic brain networks using functional magnetic resonance imaging (fMRI) data has been widely used for identifying biomarkers in various psychiatric disorders. While the emerging access to large neuroimaging datasets provides unprecedented opportunities for exploring brain functions, they also pose significant computational complexity challenges due to the large amount of inherent variability across individuals and the complexity of brain activity patterns. To address these challenges, this paper introduces two novel constrained ICA methods, arc‐EBM and minc‐EBM, designed to overcome the computational complexity issue by incorporating prior information into the analysis framework. The proposed methods preserve the subject variability by adaptively selecting the constrained parameters for different functional networks and individuals, while also allowing estimation flexibility for activities not covered by the prior information through the concept of free components. Our methods are shown to enhance the precision of functional network estimation and improve the capture of subject variability across different cohorts. We evaluate the proposed methods using both synthetic and real fMRI data. By applying the proposed methods to a resting‐state fMRI dataset including 179 subjects, both algorithms successfully reveal significant group differences in functional network connectivity between healthy controls and schizophrenia patients. The observed group differences, particularly the abnormal connectivity alterations in networks involving the thalamus, subthalamus/hypothalamus, and superior temporal gyrus, align with findings from previous clinical studies. Furthermore, our results demonstrate that the constraint parameters adaptively selected by arc‐EBM reveal more diverse resting‐state network structures in individuals with schizophrenia compared with healthy controls. This finding is consistent with prior studies and suggests that the selected constraint parameters could serve as potential biomarkers for mental disorder diagnosis. 

   more » « less