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.

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 Characterization of ex vivo healthy human axillary lymph nodes with high resolution 7 Tesla MRI

2010 ◽  
Vol 21 (2) ◽  
pp. 310-317 ◽  
Author(s):  
M. A. Korteweg ◽  
J. J. M. Zwanenburg ◽  
P. J. van Diest ◽  
M. A. A. J. van den Bosch ◽  
P. R. Luijten ◽  
...  
Keyword(s):  
High Resolution ◽  
Lymph Nodes ◽  
Ex Vivo ◽  
7 Tesla ◽  
Axillary Lymph Nodes ◽  
Axillary Lymph ◽  
Healthy Human ◽  
7 Tesla Mri

Parallel-transmission-enabled three-dimensional T2-weighted imaging of the human brain at 7 Tesla

2014 ◽  
Vol 73 (6) ◽  
pp. 2195-2203 ◽  
Author(s):  
Aurélien Massire ◽  
Alexandre Vignaud ◽  
Benjamin Robert ◽  
Denis Le Bihan ◽  
Nicolas Boulant ◽  
...  
Keyword(s):  
Human Brain ◽  
Three Dimensional ◽  
7 Tesla ◽  
Parallel Transmission

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 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.

Ex Vivo and In Vivo Imaging of the Inner Ear at 7 Tesla MRI

2014 ◽  
Vol 35 (4) ◽  
pp. 725-729 ◽  
Author(s):  
Sylvia L. van Egmond ◽  
Fredy Visser ◽  
Frank A. Pameijer ◽  
Wilko Grolman
Keyword(s):  
Inner Ear ◽  
In Vivo Imaging ◽  
Ex Vivo ◽  
7 Tesla ◽  
7 Tesla Mri

Ischaemic Cavities in the Cerebellum: An ex vivo 7-Tesla MRI Study with Pathological Correlation

2014 ◽  
Vol 38 (1) ◽  
pp. 17-23 ◽  
Author(s):  
Laurens J.L. De Cocker ◽  
Susanne J. van Veluw ◽  
Geert Jan Biessels ◽  
Wim G.M. Spliet ◽  
Isabel E. Thunnissen ◽  
...  
Keyword(s):  
Ex Vivo ◽  
7 Tesla ◽  
Pathological Correlation ◽  
7 Tesla Mri ◽  
Mri Study

scholarly journals A scalable method to improve gray matter segmentation at ultra high field MRI

2018 ◽  
Author(s):  
Omer Faruk Gulban ◽  
Marian Schneider ◽  
Ingo Marquardt ◽  
Roy A.M. Haast ◽  
Federico De Martino
Keyword(s):  
Gray Matter ◽  
Compositional Data ◽  
Three Dimensional ◽  
Ground Truth ◽  
7 Tesla ◽  
Compositional Data Analysis ◽  
Two Dimensional ◽  
Anatomical Images ◽  
7 Tesla Mri ◽  
Magnetic Resonance Imaging Mri

AbstractHigh-resolution (functional) magnetic resonance imaging (MRI) at ultra high magnetic fields (7 Tesla and above) enables researchers to study how anatomical and functional properties change within the cortical ribbon, along surfaces and across cortical depths. These studies require an accurate delineation of the gray matter ribbon, which often suffers from inclusion of blood vessels, dura mater and other non-brain tissue. Residual segmentation errors are commonly corrected by browsing the data slice-by-slice and manually changing labels. This task becomes increasingly laborious and prone to error at higher resolutions since both work and error scale with the number of voxels. Here we show that many mislabeled, non-brain voxels can be corrected more efficiently and semi-automatically by representing three-dimensional anatomical images using two-dimensional histograms. We propose both a uni-modal (based on first spatial derivative) and multi-modal (based on compositional data analysis) approach to this representation and quantify the benefits in 7 Tesla MRI data of nine volunteers. We present an openly accessible Python implementation of these approaches and demonstrate that editing cortical segmentations using two-dimensional histogram representations as an additional post-processing step aids existing algorithms and yields improved gray matter borders. By making our data and corresponding expert (ground truth) segmentations openly available, we facilitate future efforts to develop and test segmentation algorithms on this challenging type of data.

scholarly journals Studying magnetic susceptibility, microstructural compartmentalisation and chemical exchange in a formalin-fixed ex vivo human brain specimen

2021 ◽  
Author(s):  
Kwok-Shing Chan ◽  
Renaud Hedouin ◽  
Jeroen Mollink ◽  
Anne-Marie van Cappellen van Walsum ◽  
Jose P Marques
Keyword(s):  
Magnetic Susceptibility ◽  
White Matter ◽  
Human Brain ◽  
In Vivo Imaging ◽  
Chemical Exchange ◽  
Ex Vivo ◽  
Signal Phase ◽  
Brain Specimen ◽  
Formalin Fixed

Purpose: Ex vivo imaging is a preferable method to study the biophysical mechanism of white matter orientation-dependent signal phase evolution. Yet, how formalin fixation, commonly used for tissue preservation, affects the phase measurement is not fully known. We, therefore, study the impacts of formalin fixation on magnetic susceptibility, microstructural compartmentalisation and chemical exchange measurement on human brain tissue. Methods: A formalin-fixed, post-mortem human brain specimen was scanned with multiple orientations with respect to the main magnetic field direction for robust bulk magnetic susceptibility measurement with conventional quantitative susceptibility imaging models. Homogeneous white matter tissues were subsequently excised from the whole-brain specimen and scanned in multiple rotations on an MRI scanner to measure the anisotropic magnetic susceptibility and microstructure-related contributions in the signal phase. Electron microscopy was used to validate the MRI findings. Results: The bulk isotropic magnetic susceptibility of ex vivo whole-brain imaging is comparable to in vivo imaging, with noticeable enhanced non-susceptibility contributions. The excised specimen experiment reveals that anisotropic magnetic susceptibility and compartmentalisation phase effect were considerably reduced in formalin-fixed white matter tissue. Conclusions: Despite formalin-fixed white matter tissue has comparable bulk isotropic magnetic susceptibility to those measured via in vivo imaging, its orientation-dependent components in the signal phase related to the tissue microstructure is substantially weaker, making it less favourable in white matter microstructure studies using phase imaging.

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