Article
Neurosciences
Jason Kai, Ali R. Khan, Roy Am Haast, Jonathan C. Lau
Summary: This study investigated the feasibility and reliability of mapping subcortical connectivity using tractography. The results demonstrated that a data-driven tractography-based approach can accurately depict the connections within the subcortex.
Article
Neurosciences
Tanzil Mahmud Arefin, Choong Heon Lee, Zifei Liang, Harikrishna Rallapalli, Youssef Z. Wadghiri, Daniel H. Turnbull, Jiangyang Zhang
Summary: In this study, we aimed to optimize the imaging and computational pipeline to achieve the best possible spatial overlaps between dMRI tractography and tracer-based axonal projection maps in the mouse brain corticothalamic network. We developed a dMRI-based atlas of the mouse forebrain and reconstructed detailed corticothalamic structural connectivity matrices using different imaging and tractography parameters. Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain.
Article
Neurosciences
Zifei Liang, Tanzil Mahmud Arefin, Choong H. Lee, Jiangyang Zhang
Summary: Diffusion MRI (dMRI) tractography is the only non-invasive tool for mapping macroscopic structural connectivity. This study demonstrated that a deep learning network trained on mesoscopic tract-tracing data can improve the estimation of fiber orientation distributions (FODs) in mouse brain dMRI data, leading to enhanced specificity in tractography results without compromising sensitivity.
Article
Neurosciences
Ahmed M. Radwan, Stefan Sunaert, Kurt Schilling, Maxime Descoteaux, Bennett A. Landman, Mathieu Vandenbulcke, Tom Theys, Patrick Dupont, Louise Emsell
Summary: The virtual dissection of white matter using diffusion MRI tractography has poor reproducibility, but this study provides a comprehensive description of white matter anatomy using a reproducible automated subject-specific parcellation-based approach with probabilistic CSD tractography. The study demonstrates high inter-session similarity and provides a WM atlas that can be useful for mapping white matter fasciculi in healthy adults.
Article
Multidisciplinary Sciences
Norio Takata, Nobuhiko Sato, Yuji Komaki, Hideyuki Okano, Kenji F. Tanaka
Summary: The study constructed a flexible annotation atlas (FAA) of the mouse brain using public resources from the Allen Institute for Brain Science, allowing for objective combination or division of nodes while maintaining the anatomical hierarchy of brain structures. The FAA demonstrated unique characteristics in analyzing resting-state functional connectivity (FC) across the anatomical hierarchy and among different brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling researchers' various requests with its flexibility and reproducibility.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Uzair Hussain, Corey A. Baron, Ali R. Khan
Summary: Coordinate invariance of physical laws is crucial in physics, allowing freedom to express observations in computationally convenient coordinate systems. Transitioning from Cartesian to curvilinear coordinates in medical imaging can simplify visualization and operation. Introducing tools to enhance existing diffusion tractography approaches, testing showed that tracts from curvilinear coordinates generally have improved sensitivity and specificity compared to Cartesian coordinates. As an application, harmonic coordinates can enhance tractography for the hippocampus.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Neurosciences
Andrada Ianu, Joana Carvalho, Francisca F. Fernandes, Renata Cruz, Cristina Chavarrias, Marco Palombo, Noam Shemesh
Summary: Diffusion MRI (dMRI) provides unique insights into the neural tissue milieu. The SANDI methodology enables the characterization of cellular and neurite densities. This study validates SANDI using in-vivo preclinical imaging and compares its metrics with cellular density reflected by the Allen mouse brain atlas. The findings demonstrate good reproducibility and correlation, indicating the potential of SANDI in brain tissue microstructure research.
Article
Neurosciences
Mark D. Grier, Essa Yacoub, Gregor Adriany, Russell L. Lagoreb, Noam Harel, Ru-Yuan Zhang, Christophe Lenglet, Kamil Ugurbil, Jan Zimmermann, Sarah R. Heilbronner
Summary: Diffusion-weighted magnetic resonance imaging (dMRI) provides information about water molecule diffusion barriers in tissue, particularly in the brain. While useful for studying brain disorders and white matter organization, dMRI faces challenges like biological validation difficulties and low signal-to-noise ratios. Utilizing ultra-high field scanners and denoising techniques can improve the quality of dMRI data.
Article
Biology
Jun Takatoh, Jae Hong Park, Jinghao Lu, Shun Li, P. M. Thompson, Bao-Xia Han, Shengli Zhao, David Kleinfeld, Beth Friedman, Fan Wang
Summary: This study developed a new method to track premotor circuits in the adult mouse, revealing unique spatial organizations of different premotor circuits and identifying premotor neurons that simultaneously innervate multiple motor nuclei.
Article
Neurosciences
Zhiyong Zhao, Lei Zhang, Wanrong Luo, Zuozhen Cao, Qinfeng Zhu, Xueqian Kong, Keqing Zhu, Jing Zhang, Dan Wu
Summary: This study used high-resolution dMRI to investigate the microstructural characteristics of the anterior hippocampus in patients with Alzheimer's disease (AD). The results showed significant variability in microstructural features across different layers and subfields, and these features were associated with protein deposition in AD patients' anterior hippocampus.
HUMAN BRAIN MAPPING
(2023)
Article
Multidisciplinary Sciences
Yasser Aleman-Gomez, Alessandra Griffa, Jean-Christophe Houde, Elena Najdenovska, Stefano Magon, Meritxell Bach Cuadra, Maxime Descoteaux, Patric Hagmann
Summary: In this work, a whole-brain multi-scale structural connectome atlas is presented, which can provide valuable network information for imaging studies. This tool is derived from healthy subject data, using extensively validated processing and segmentation tools, and it offers user-friendly code to extract connection-specific quantitative information from individual brain imaging data. This method contributes to analyzing the network-level consequences of regional changes.
Article
Psychology, Developmental
Judit Ciarrusta, Daan Christiaens, Sean P. Fitzgibbon, Ralica Dimitrova, Jana Hutter, Emer Hughes, Eugene Duff, Anthony N. Price, Lucilio Cordero-Grande, J. -Donald Tournier, Daniel Rueckert, Joseph V. Hajnal, Tomoki Arichi, Grainne McAlonan, David Edwards, Dafnis Batalle
Summary: The study found that structural connectivity in early life is more stable and can represent a potential connectome fingerprint of an individual. In contrast, the similarity between functional connectomes of the same subject at different time points is low.
DEVELOPMENTAL COGNITIVE NEUROSCIENCE
(2022)
Article
Neurosciences
Harm Jan van der Horn, Namrata R. Mangina, Sandra E. Rakers, Jelmer G. Kok, Marieke E. Timmerman, Alexander Leemans, Jacoba M. Spikman, Joukje van Der Naalt
Summary: This longitudinal tractography study found microstructural changes in emotion regulation tracts among patients with mild traumatic brain injury, particularly in those without complications. However, the presence of symptoms could not be explained by these changes.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2021)
Article
Neurosciences
Syed M. Adil, Evan Calabrese, Lefko T. Charalambous, James J. Cook, Shervin Rahimpour, Ahmet F. Atik, Gary P. Cofer, Beth A. Parente, G. Allan Johnson, Shivanand P. Lad, Leonard E. White
Summary: This study successfully constructed an atlas of the human brainstem using high-resolution MRI technology, which is available online for interactive use, providing a new tool for neuroanatomical education and research.
Article
Neurosciences
Xuehu Wei, Helyne Adamson, Matthias Schwendemann, Tomas Goucha, Angela D. Friederici, Alfred Anwander
Summary: The current study investigated the differences in brain white matter connections between native speakers of German and Arabic. German speakers showed stronger connectivity in a language network associated with complex syntax processing, while Arabic speakers exhibited stronger connectivity between semantic language regions and inter-hemispheric connections. These findings suggest that the structural language connectome is influenced by the linguistic characteristics of the native language.
Article
Multidisciplinary Sciences
Wei Shao, Jiajun Yang, Ming He, Xiang-Yu Yu, Choong Heon Lee, Zhaohui Yang, Alexandra L. Joyner, Kathryn V. Anderson, Jiangyang Zhang, Meng-Fu Bryan Tsou, Hang Shi, Song-Hai Shi
Article
Endocrinology & Metabolism
Fusheng Gao, Xiaoxia Shen, Hongxi Zhang, Ruicheng Ba, Xiaolu Ma, Can Lai, Jiangyang Zhang, Yi Zhang, Dan Wu
Summary: The study investigates the clinical feasibility and value of t(d)-dependent diffusion MRI in neonatal hypoxic-ischemic encephalopathy (HIE). Results show that t(d)-dependent dMRI provides high sensitivity in detecting moderate-to-severe HIE and can offer more information on brain microstructure.
JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM
(2021)
Article
Biology
Jordon D. White, Tanzil M. Arefin, Alexa Pugliese, Choong H. Lee, Jeff Gassen, Jiangyang Zhang, Arie Kaffman
Article
Neurosciences
Jennifer K. Lee, Dapeng Liu, Dengrong Jiang, Ewa Kulikowicz, Aylin Tekes, Peiying Liu, Qin Qin, Raymond C. Koehler, Manisha Aggarwal, Jiangyang Zhang, Lee J. Martin
Summary: The changes in FA and MD after neonatal hypoxia-ischemia are associated with cytotoxic edema in astrocytes and oligodendrocyte processes, as well as myelin injury. MD can detect glial cell death and loss, but may not discern subtle pathology in swollen astrocytes, oligodendrocytes, or myelin. This study provides a cytopathologic basis for interpreting DTI in the neonatal brain after hypoxia-ischemia.
JOURNAL OF COMPARATIVE NEUROLOGY
(2021)
Article
Multidisciplinary Sciences
Marios Georgiadis, Aileen Schroeter, Zirui Gao, Manuel Guizar-Sicairos, Marianne Liebi, Christoph Leuze, Jennifer A. McNab, Aleezah Balolia, Jelle Veraart, Benjamin Ades-Aron, Sunglyoung Kim, Timothy Shepherd, Choong H. Lee, Piotr Walczak, Shirish Chodankar, Phillip DiGiacomo, Gergely David, Mark Augath, Valerio Zerbi, Stefan Sommer, Ivan Rajkovic, Thomas Weiss, Oliver Bunk, Lin Yang, Jiangyang Zhang, Dmitry S. Novikov, Michael Zeineh, Els Fieremans, Markus Rudin
Summary: This study demonstrates the use of small-angle X-ray scattering tensor tomography (SAXS-TT) to quantify myelin levels, nanostructural integrity, and axon orientations in nervous tissue. The method was successfully applied to whole mouse brain, mouse spinal cord, and human white and gray matter samples, showcasing its potential in studying myelination in development, aging, disease, and treatment.
NATURE COMMUNICATIONS
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Hongyu Li, Zifei Liang, Chaoyi Zhang, Ruiying Liu, Jing Li, Weihong Zhang, Dong Liang, Bowen Shen, Xiaoliang Zhang, Yulin Ge, Jiangyang Zhang, Leslie Ying
Summary: The SuperDTI framework developed using deep learning is capable of generating fractional anisotropy, mean diffusivity maps, and fiber tractography from as few as six raw DWIs with a quantification error of less than 5% in all regions of interest. It demonstrates robustness to noises and motions in testing data and has the potential for clinical applications.
MAGNETIC RESONANCE IN MEDICINE
(2021)
Article
Multidisciplinary Sciences
Dan Wu, Linda J. Richards, Zhiyong Zhao, Zuozhen Cao, Wanrong Luo, Wei Shao, Song-Hai Shi, Michael Miller, Susumu Mori, Seth Blackshaw, Jiangyang Zhang
Summary: The study reconstructed a four-dimensional continuum of the embryonic mouse brain from E10.5 to E15.5, revealing morphological and microscopic changes in the developing brain and correlating gene expression data with neuroanatomical changes. By identifying developmental modes and regional clusters, it demonstrates how this method can be used to analyze interactions between upstream genetic events and anatomical changes in brain development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Zifei Liang, Choong H. Lee, Tanzil M. Arefin, Zijun Dong, Piotr Walczak, Song-Hai Shi, Florian Knoll, Yulin Ge, Leslie Ying, Jiangyang Zhang
Summary: This study demonstrates the use of deep convolutional neural networks to estimate histological staining intensity directly from MRI signals, providing three-dimensional images that closely mimic target histology and enhanced sensitivity and specificity compared to conventional MRI markers. Additionally, the relative contribution of each MRI contrast within the networks can be used to optimize multi-contrast MRI acquisition, serving as a resource for validating novel MRI techniques.
Article
Radiology, Nuclear Medicine & Medical Imaging
Choong Heon Lee, Piotr Walczak, Jiangyang Zhang
Summary: In this study, we investigated the ability of ihMT MRI to detect white matter structures in the hypomyelinated shiverer mouse brain. Our results showed that ihMT can provide clear visualization of the hypomyelinated corpus callosum, with higher myelin contrast compared to conventional MT. These findings suggest the potential use of ihMT as a marker for early myelination or myelin repair.
MAGNETIC RESONANCE IN MEDICINE
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Zuozhen Cao, Huijia Lin, Fusheng Gao, Xiaoxia Shen, Hongxi Zhang, Jiangyang Zhang, Lizhong Du, Can Lai, Xiaolu Ma, Dan Wu
Summary: This study systematically characterized the microstructural alterations in neonates with hypoxic-ischemic encephalopathy (HIE) using advanced diffusion MRI. The results showed extensive microstructural injury in severe HIE, and association fiber injury with rightward lateralization in moderate and mild HIE.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Chenyang Li, Els Fieremans, Dmitry S. S. Novikov, Yulin Ge, Jiangyang Zhang
Summary: FEXI and DKI(t) show similar sensitivity to exchange processes in white matter but are affected by tissue microstructure in gray matter.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Neurosciences
Zifei Liang, Tanzil Mahmud Arefin, Choong H. Lee, Jiangyang Zhang
Summary: Diffusion MRI (dMRI) tractography is the only non-invasive tool for mapping macroscopic structural connectivity. This study demonstrated that a deep learning network trained on mesoscopic tract-tracing data can improve the estimation of fiber orientation distributions (FODs) in mouse brain dMRI data, leading to enhanced specificity in tractography results without compromising sensitivity.
Article
Neurosciences
Tanzil Mahmud Arefin, Choong Heon Lee, Zifei Liang, Harikrishna Rallapalli, Youssef Z. Wadghiri, Daniel H. Turnbull, Jiangyang Zhang
Summary: In this study, we aimed to optimize the imaging and computational pipeline to achieve the best possible spatial overlaps between dMRI tractography and tracer-based axonal projection maps in the mouse brain corticothalamic network. We developed a dMRI-based atlas of the mouse forebrain and reconstructed detailed corticothalamic structural connectivity matrices using different imaging and tractography parameters. Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain.
Article
Neurosciences
Jose Sanchez-Bornot, Roberto C. Sotero, J. A. Scott Kelso, Ozguer Simsek, Damien Coyle
Summary: This study proposes a multi-penalized state-space model for analyzing unobserved dynamics, using a data-driven regularization method. Novel algorithms are developed to solve the model, and a cross-validation method is introduced to evaluate regularization parameters. The effectiveness of this method is validated through simulations and real data analysis, enabling a more accurate exploration of cognitive brain functions.
