scholarly journals Mapping the human subcortical auditory system using histology, post mortem MRI and in vivo MRI at 7T

2019 ◽  
Author(s):  
Kevin Richard Sitek ◽  
Omer Faruk Gulban ◽  
Evan Calabrese ◽  
G. Allan Johnson ◽  
Agustin Lage-Castellanos ◽  
...  
Keyword(s):  
Auditory System ◽  
Structural Connectivity ◽  
Three Dimensional ◽  
Auditory Pathway ◽  
7 Tesla ◽  
Post Mortem ◽  
Subcortical Structures ◽  
Isotropic Resolution ◽  
Histological Data

AbstractStudying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. We addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and post mortem MRI (50 μm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 μm isotropic resolution) and post mortem (200 μm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.

scholarly journals Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Kevin R Sitek ◽  
Omer Faruk Gulban ◽  
Evan Calabrese ◽  
G Allan Johnson ◽  
Agustin Lage-Castellanos ◽  
...  
Keyword(s):  
Auditory System ◽  
Structural Connectivity ◽  
Three Dimensional ◽  
Auditory Pathway ◽  
7 Tesla ◽  
Post Mortem ◽  
Subcortical Structures ◽  
Isotropic Resolution ◽  
Postmortem Mri

Studying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. Wfe addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and postmortem MRI (50 µm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2 mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 µm isotropic resolution) and post mortem (200 µm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.

scholarly journals Alteration within the Hippocampal Volume in Patients with LHON Disease—7 Tesla MRI Study

2020 ◽  
Vol 10 (1) ◽  
pp. 14
Author(s):  
Cezary Grochowski ◽  
Kamil Jonak ◽  
Marcin Maciejewski ◽  
Andrzej Stępniewski ◽  
Mansur Rahnama-Hezavah
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Molecular Layer ◽  
Three Dimensional ◽  
Hippocampal Volume ◽  
7 Tesla ◽  
Diagnostic Process ◽  
Resonance Imaging ◽  
The Right

Purpose: The aim of this study was to assess the volumetry of the hippocampus in the Leber’s hereditary optic neuropathy (LHON) of blind patients. Methods: A total of 25 patients with LHON were randomly included into the study from the national health database. A total of 15 patients were selected according to the inclusion criteria. The submillimeter segmentation of the hippocampus was based on three-dimensional spoiled gradient recalled acquisition in steady state (3D-SPGR) BRAVO 7T magnetic resonance imaging (MRI) protocol. Results: Statistical analysis revealed that compared to healthy controls (HC), LHON subjects had multiple significant differences only in the right hippocampus, including a significantly higher volume of hippocampal tail (p = 0.009), subiculum body (p = 0.018), CA1 body (p = 0.002), hippocampal fissure (p = 0.046), molecular layer hippocampus (HP) body (p = 0.014), CA3 body (p = 0.006), Granule Cell (GC) and Molecular Layer (ML) of the Dentate Gyrus (DG)–GC ML DG body (p = 0.003), CA4 body (p = 0.001), whole hippocampal body (p = 0.018), and the whole hippocampus volume (p = 0.023). Discussion: The ultra-high-field magnetic resonance imaging allowed hippocampus quality visualization and analysis, serving as a powerful in vivo diagnostic tool in the diagnostic process and LHON disease course assessment. The study confirmed previous reports regarding volumetry of hippocampus in blind individuals.

scholarly journals A probabilistic atlas of the human ventral tegmental area (VTA) based on 7 Tesla MRI data

2021 ◽  
Vol 226 (4) ◽  
pp. 1155-1167 ◽  
Author(s):  
Anne C. Trutti ◽  
Laura Fontanesi ◽  
Martijn J. Mulder ◽  
Pierre-Louis Bazin ◽  
Bernhard Hommel ◽  
...  
Keyword(s):  
Ventral Tegmental Area ◽  
Region Of Interest ◽  
Reward Processing ◽  
7 Tesla ◽  
Subcortical Structures ◽  
7 Tesla Mri ◽  
Subcortical Nuclei ◽  
Ventral Tegmental ◽  
The Brain

AbstractFunctional magnetic resonance imaging (fMRI) BOLD signal is commonly localized by using neuroanatomical atlases, which can also serve for region of interest analyses. Yet, the available MRI atlases have serious limitations when it comes to imaging subcortical structures: only 7% of the 455 subcortical nuclei are captured by current atlases. This highlights the general difficulty in mapping smaller nuclei deep in the brain, which can be addressed using ultra-high field 7 Tesla (T) MRI. The ventral tegmental area (VTA) is a subcortical structure that plays a pivotal role in reward processing, learning and memory. Despite the significant interest in this nucleus in cognitive neuroscience, there are currently no available, anatomically precise VTA atlases derived from 7 T MRI data that cover the full region of the VTA. Here, we first provide a protocol for multimodal VTA imaging and delineation. We then provide a data description of a probabilistic VTA atlas based on in vivo 7 T MRI data.

scholarly journals Sex-Based Differences in Cortical and Subcortical Development in 436 Individuals Aged 4–54 Years

2019 ◽  
Vol 30 (5) ◽  
pp. 2854-2866 ◽  
Author(s):  
Emma G Duerden ◽  
M Mallar Chakravarty ◽  
Jason P Lerch ◽  
Margot J Taylor
Keyword(s):  
Surface Area ◽  
Ex Vivo ◽  
Automatic Segmentation ◽  
Structural Connectivity ◽  
In Vivo Studies ◽  
Brain Maturation ◽  
Subcortical Structures ◽  
Cross Sectional ◽  
Area Expansion

Abstract Sex-based differences in brain development have long been established in ex vivo studies. Recent in vivo studies using magnetic resonance imaging (MRI) have offered considerable insight into sex-based variations in brain maturation. However, reports of sex-based differences in cortical volumes and thickness are inconsistent. We examined brain maturation in a cross-sectional, single-site cohort of 436 individuals (201 [46%] males) aged 4–54 years (median = 16 years). Cortical thickness, cortical surface area, subcortical surface area, volumes of the cerebral cortex, white matter (WM), cortical and subcortical gray matter (GM), including the thalamic subnuclei, basal ganglia, and hippocampi were calculated using automatic segmentation pipelines. Subcortical structures demonstrated distinct curvilinear trajectories from the cortex, in both volumetric maturation and surface-area expansion in relation to age. Surface-area analysis indicated that dorsal regions of the thalamus, globus pallidus and striatum, regions demonstrating structural connectivity with frontoparietal cortices, exhibited extensive expansion with age, and were inversely related to changes seen in cortical maturation, which contracted with age. Furthermore, surface-area expansion was more robust in males in comparison to females. Age- and sex-related maturational changes may reflect alterations in dendritic and synaptic architecture known to occur during development from early childhood through to mid-adulthood.

scholarly journals 7 Tesla MRI of the ex vivo human brain at 100 micron resolution

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Brian L. Edlow ◽  
Azma Mareyam ◽  
Andreas Horn ◽  
Jonathan R. Polimeni ◽  
Thomas Witzel ◽  
...  
Keyword(s):  
Human Brain ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Academic Community ◽  
7 Tesla ◽  
Brain Anatomy ◽  
Isotropic Resolution ◽  
Scan Time ◽  
Brain Specimen ◽  
7 Tesla Mri

Abstract We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.

scholarly journals Improving robustness of 3D multi-shot EPI by structured low-rank reconstruction of segmented CAIPI sampling for fMRI at 7T

2021 ◽  
Author(s):  
Xi Chen ◽  
Wenchuan Wu ◽  
Mark Chiew
Keyword(s):  
Temporal Stability ◽  
Three Dimensional ◽  
Low Rank ◽  
Reconstruction Method ◽  
Isotropic Resolution ◽  
Resonance Effects ◽  
Temporal Variance ◽  
Phase Variations ◽  
Recovery Simulation

Three-dimensional (3D) encoding methods are increasingly being explored as alternatives to multi-slice two-dimensional (2D) acquisitions in fMRI, particularly in cases where high isotropic resolution is needed. 3D multi-shot EPI is the most popular 3D fMRI acquisition method, but is susceptible to physiological fluctuations which can induce inter-shot phase variations, and thus reducing the achievable tSNR, negating some of the benefit of 3D encoding. This issue can be particularly problematic at ultra-high fields like 7T, which have more severe off-resonance effects. In this work, we aim to improve the temporal stability of 3D multi-shot EPI at 7T by improving its robustness to inter-shot phase variations. We presented a 3D segmented CAIPI sampling trajectory ("seg-CAIPI") and an improved reconstruction method based on Hankel structured low-rank matrix recovery. Simulation and in-vivo results demonstrate that the combination of the seg-CAIPI sampling scheme and the proposed structured low-rank reconstruction is a promising way to effectively reduce the unwanted temporal variance induced by inter-shot physiological fluctuations, and thus improve the robustness of 3D multi-shot EPI for fMRI.

scholarly journals High resolution atlas of the venous brain vasculature from 7 T quantitative susceptibility maps

2018 ◽  
Author(s):  
Julia Huck ◽  
Yvonne Wanner ◽  
Audrey P. Fan ◽  
Anna-Thekla Jäger ◽  
Sophia Grahl ◽  
...  
Keyword(s):  
Human Brain ◽  
Blood Oxygen Level Dependent ◽  
7 Tesla ◽  
Cerebral Vein ◽  
Registration Method ◽  
Isotropic Resolution ◽  
Common Location ◽  
Susceptibility Maps ◽  
Venous Vasculature

AbstractThe vascular organization of the human brain can determine neurological and neurophysiological functions, yet thus far it has not been comprehensively mapped. Aging and diseases such as dementia are known to be associated with changes to the vasculature and normative data could help detect these vascular changes in neuroimaging studies. Furthermore, given the well-known impact of venous vessels on the blood oxygen level dependent (BOLD) signal, information about the common location of veins could help detect biases in existing datasets. In this work, a quantitative atlas of the venous vasculature using quantitative susceptibility maps (QSM) acquired with a 0.6 mm isotropic resolution is presented. The Venous Neuroanatomy (VENAT) atlas was created from 5 repeated 7 Tesla MRI measurements in young and healthy volunteers (n = 20, 10 females, mean age = 25.1 ± 2.5 years) using a two-step registration method on 3D segmentations of the venous vasculature. This cerebral vein atlas includes the average vessel location, diameter (mean: 0.84 ± 0.33 mm) and curvature (0.11 ± 0.05 mm−1) from all participants and provides an in vivo measure of the angio-architectonic organization of the human brain and its variability. This atlas can be used as a basis to understand changes in the vasculature during aging and neurodegeneration, as well as vascular and physiological effects in neuroimaging.

scholarly journals Mapping the Human Visual Thalamus and its Cytoarchitectonic Subdivisions Using Quantitative MRI

2020 ◽  
Author(s):  
Christa Müller-Axt ◽  
Cornelius Eichner ◽  
Henriette Rusch ◽  
Louise Kauffmann ◽  
Pierre-Louis Bazin ◽  
...  
Keyword(s):  
High Resolution ◽  
Visual Information ◽  
Quantitative Mri ◽  
7 Tesla ◽  
Post Mortem ◽  
Non Invasive ◽  
Visual Thalamus ◽  
Processing Site ◽  
The Brain

AbstractThe human lateral geniculate nucleus (LGN) of the visual thalamus is a key subcortical processing site for visual information analysis. A non-invasive assessment of the LGN and its functionally and microstructurally distinct magnocellular (M) and parvocellular (P) subdivisions in-vivo in humans is challenging, because of its small size and location deep inside the brain. Here we tested whether recent advances in high-field structural quantitative MRI (qMRI) can enable MR-based mapping of human LGN subdivisions. We employed ultra-high resolution 7 Tesla qMRI of a post-mortem human LGN specimen and high-resolution 7 Tesla in-vivo qMRI in a large participant sample. We found that a quantitative assessment of the LGN and a differentiation of its subdivisions was possible based on microstructure-informed MR-contrast alone. In both the post-mortem and in-vivo qMRI data, we identified two components of shorter and longer longitudinal relaxation time (T1) within the LGN that coincided with the known anatomical locations of a dorsal P and a ventral M subdivision, respectively. Through a subsequent ground truth histological examination of the same post-mortem LGN specimen, we showed that the observed T1 contrast pertains to cyto- and myeloarchitectonic differences between LGN subdivisions. These differences were based on cell and myelin density, but not on iron content. Our qMRI-based mapping strategy overcomes shortcomings of previous fMRI-based mapping approaches. It paves the way for an in-depth understanding of the function and microstructure of the LGN in humans. It also enables investigations into the selective contributions of LGN subdivisions to human behavior in health and disease.Significance StatementThe lateral geniculate nucleus (LGN) is a key processing site for the analysis of visual information. Due to its small size and deep location within the brain, non-invasive mapping of the LGN and its microstructurally distinct subdivisions in humans is challenging. Using quantitative MRI methods that are sensitive to underlying microstructural tissue features, we show that a differentiation of the LGN and its microstructurally distinct subdivisions is feasible in humans non-invasively. These findings are important because they open up novel opportunities to assess the hitherto poorly understood complex role of the LGN in human perception and cognition, as well as the contribution of selective LGN subdivision impairments to various clinical conditions including developmental dyslexia, glaucoma and multiple sclerosis.

scholarly journals 7 Tesla MRI of the ex vivo human brain at 100 micron resolution

2019 ◽  
Author(s):  
Brian L. Edlow ◽  
Azma Mareyam ◽  
Andreas Horn ◽  
Jonathan R. Polimeni ◽  
Thomas Witzel ◽  
...  
Keyword(s):  
Human Brain ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Academic Community ◽  
7 Tesla ◽  
Brain Anatomy ◽  
Isotropic Resolution ◽  
Scan Time ◽  
Brain Specimen ◽  
7 Tesla Mri

AbstractWe present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 μm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of a T1 parameter map and synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.

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