scholarly journals Axonal T2 estimation using the spherical variance of the strongly diffusion-weighted MRI signal

2021 ◽  
Author(s):  
Marco Pizzolato ◽  
Mariam Andersson ◽  
Erick Jorge Canales-Rodriguez ◽  
Jean-Philippe Thiran ◽  
Tim B Dyrby
Keyword(s):  
White Matter ◽  
Ex Vivo ◽  
Transverse Relaxation Time ◽  
Cell Nuclei ◽  
Fixed Tissue ◽  
Diffusion Weighted ◽  
Spherical Mean ◽  
Diffusion Weighting ◽  
Strong Diffusion

In magnetic resonance imaging, the application of a strong diffusion weighting suppresses the signal contributions from the less diffusion-restricted constituents of the brain's white matter, thus enabling the estimation of the transverse relaxation time T2 that arises from the more diffusion-restricted constituents such as the axons. However, the presence of cell nuclei and vacuoles can confound the estimation of the axonal T2, as diffusion within those structures is also restricted, causing the corresponding signal to survive the strong diffusion weighting. We devise an estimator of the axonal T2 based on the directional spherical variance of the strongly diffusion-weighted signal. The spherical variance T2 estimates are insensitive to the presence of isotropic contributions to the signal like those provided by cell nuclei and vacuoles. We show that with a strong diffusion weighting these estimates differ from those obtained using the directional spherical mean of the signal which contains both axonal and isotropically-restricted contributions. Our findings hint at the presence of an MRI-visible isotropically-restricted contribution to the signal in the white matter ex vivo fixed tissue (monkey) at 7T, and do not allow us to discard such a possibility also for in vivo human data collected with a clinical 3T system.

scholarly journals Diffusion-weighted tractography in the common marmoset monkey at 9.4T

2017 ◽  
Vol 118 (2) ◽  
pp. 1344-1354 ◽  
Author(s):  
David J. Schaeffer ◽  
Ramina Adam ◽  
Kyle M. Gilbert ◽  
Joseph S. Gati ◽  
Alex X. Li ◽  
...  
Keyword(s):  
White Matter ◽  
Ex Vivo ◽  
Common Marmoset ◽  
Fiber Tracts ◽  
Marmoset Monkey ◽  
Diffusion Weighted ◽  
Ultrahigh Field Mri ◽  
White Matter Fiber Tracts ◽  
Tracing Techniques

Although significant progress has been made in mapping white matter connections in the marmoset brain using ex vivo tracing techniques, the application of in vivo virtual dissection of major white matter fiber tracts has been established by few studies in the marmoset literature. Here, we demonstrate the feasibility of whole-brain diffusion-weighted tractography in anesthetized marmosets at ultrahigh-field MRI (9.4T) and propose protocols for isolating nine major white matter fiber tracts in the marmoset brain.

[P2-420]: A COMPARISON OF BRAIN WHITE MATTER HYPERINTENSITY BURDEN ASSESSED IN VIVO AND EX VIVO

2017 ◽  
Vol 13 (7S_Part_16) ◽  
pp. P794-P795
Author(s):  
Arman P. Kulkarni ◽  
Arnold M. Evia ◽  
Julie A. Schneider ◽  
David A. Bennett ◽  
Konstantinos Arfanakis
Keyword(s):  
White Matter ◽  
Ex Vivo ◽  
White Matter Hyperintensity ◽  
Brain White Matter

scholarly journals In vivo diffusion tensor imaging and ex vivo histologic characterization of white matter pathology in a post-status epilepticus model of temporal lobe epilepsy

Epilepsia ◽  
2011 ◽  
Vol 52 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Pieter van Eijsden ◽  
Wim M. Otte ◽  
W. Saskia van der Hel ◽  
Onno van Nieuwenhuizen ◽  
Rick M. Dijkhuizen ◽  
...  
Keyword(s):  
Diffusion Tensor Imaging ◽  
Status Epilepticus ◽  
White Matter ◽  
Temporal Lobe Epilepsy ◽  
Temporal Lobe ◽  
Diffusion Tensor ◽  
Ex Vivo ◽  
White Matter Pathology

scholarly journals Does powder averaging remove dispersion bias in diffusion MRI diameter estimates within real 3D axonal architectures?

2021 ◽  
Author(s):  
Mariam Andersson ◽  
Marco Pizzolato ◽  
Hans Martin Kjer ◽  
Katrine Forum Skodborg ◽  
Henrik Lundell ◽  
...  
Keyword(s):  
White Matter ◽  
Diffusion Mri ◽  
Ex Vivo ◽  
Dynamic Properties ◽  
High Signal ◽  
Axon Diameter ◽  
Signal To Noise ◽  
B Values ◽  
Wide Range

Noninvasive estimation of axon diameter with diffusion MRI holds potential to investigate the dynamic properties of the brain network and pathology of neurodegenerative diseases. Recent methods use powder averaging to account for complex white matter architectures, such as fibre crossing regions, but these have not been validated for real axonal geometries. Here, we present 120-313 μm long segmented axons from X-ray nano-holotomography volumes of a splenium and crossing fibre region of a vervet monkey brain. We show that the axons in the complex crossing fibre region, which contains callosal, association, and corticospinal connections, are larger and exhibit a wider distribution than those of the splenium region. To accurately estimate the axon diameter in these regions, therefore, sensitivity to a wide range of diameters is required. We demonstrate how the q-value, b-value, signal-to-noise ratio and the assumed intra-axonal parallel diffusivity influence the range of measurable diameters with powder average approaches. Furthermore, we show how Gaussian distributed noise results in a wider range of measurable diameter at high b-values than with Rician distributed noise, even at high signal-to-noise ratios of 100. The number of gradient directions is also shown to impose a lower bound on measurable diameter. Our results indicate that axon diameter estimation can be performed with only few b-shells, and that additional shells do not improve the accuracy of the estimate. Through Monte Carlo simulations of diffusion, we show that powder averaging techniques succeed in providing accurate estimates of axon diameter across a range of sequence parameters and diffusion times, even in complex white matter architectures. At sufficiently low b-values, the acquisition becomes sensitive to axonal microdispersion and the intra-axonal parallel diffusivity shows time dependency at both in vivo and ex vivo intrinsic diffusivities.

scholarly journals In vivo pulse-labeling of isochronic cohorts of cells in the central nervous system using FlashTag

2018 ◽  
Author(s):  
Subashika Govindan ◽  
Polina Oberst ◽  
Denis Jabaudon
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Cell Sorting ◽  
Ex Vivo ◽  
Live Cells ◽  
Fixed Tissue ◽  
System A ◽  
M Phase ◽  
The Central Nervous System

AbstractThis protocol describes a fluorescence birthdating technique to label, track and isolate isochronic cohorts of newborn cells in the central nervous system in vivo. Injection of carboxyfluorescein esters into the cerebral ventricle allows pulse-labeling of M-phase progenitors in touch with the ventricle and their progeny across the central nervous system, a procedure we termed FlashTag. Labeled cells can be imaged ex vivo or in fixed tissue, targeted for electrophysiological experiments, or isolated using Fluorescence-Activated Cell Sorting (FACS) for cell culture or (single-cell) RNA-sequencing. The dye is retained for several weeks, allowing labeled cells to be identified postnatally. This protocol describes the labeling procedure using in utero injection, the isolation of live cells using FACS, as well as the processing of labeled tissue using immunohistochemistry.

Morphometry of in vivo human white matter association pathways with diffusion-weighted magnetic resonance imaging

1997 ◽  
Vol 42 (6) ◽  
pp. 951-962 ◽  
Author(s):  
N. Makris ◽  
A. J. Worth ◽  
G. M. Papadimitriou ◽  
J. W. Stakes ◽  
V. S. Caviness ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
White Matter ◽  
Magnetic Resonance ◽  
Resonance Imaging ◽  
Diffusion Weighted ◽  
Weighted Magnetic Resonance Imaging

scholarly journals Superficial white matter fiber systems impede detection of long-range cortical connections in diffusion MR tractography

2015 ◽  
Vol 112 (21) ◽  
pp. E2820-E2828 ◽  
Author(s):  
Colin Reveley ◽  
Anil K. Seth ◽  
Carlo Pierpaoli ◽  
Afonso C. Silva ◽  
David Yu ◽  
...  
Keyword(s):  
White Matter ◽  
High Resolution ◽  
Human Brain ◽  
Long Range ◽  
Ex Vivo ◽  
Cortical Surface ◽  
Tracer Injection ◽  
Axonal Projections ◽  
Probabilistic Tracking

In vivo tractography based on diffusion magnetic resonance imaging (dMRI) has opened new doors to study structure–function relationships in the human brain. Initially developed to map the trajectory of major white matter tracts, dMRI is used increasingly to infer long-range anatomical connections of the cortex. Because axonal projections originate and terminate in the gray matter but travel mainly through the deep white matter, the success of tractography hinges on the capacity to follow fibers across this transition. Here we demonstrate that the complex arrangement of white matter fibers residing just under the cortical sheet poses severe challenges for long-range tractography over roughly half of the brain. We investigate this issue by comparing dMRI from very-high-resolution ex vivo macaque brain specimens with histological analysis of the same tissue. Using probabilistic tracking from pure gray and white matter seeds, we found that ∼50% of the cortical surface was effectively inaccessible for long-range diffusion tracking because of dense white matter zones just beneath the infragranular layers of the cortex. Analysis of the corresponding myelin-stained sections revealed that these zones colocalized with dense and uniform sheets of axons running mostly parallel to the cortical surface, most often in sulcal regions but also in many gyral crowns. Tracer injection into the sulcal cortex demonstrated that at least some axonal fibers pass directly through these fiber systems. Current and future high-resolution dMRI studies of the human brain will need to develop methods to overcome the challenges posed by superficial white matter systems to determine long-range anatomical connections accurately.

scholarly journals Superoanterior Fasciculus (SAF): Novel fiber tract revealed by diffusion MRI fiber tractography

2018 ◽  
Author(s):  
Szabolcs David ◽  
Anneriet M. Heemskerk ◽  
Francesco Corrivetti ◽  
Michel Thiebaut de Schotten ◽  
Silvio Sarubbo ◽  
...  
Keyword(s):  
White Matter ◽  
Polarized Light ◽  
Region Of Interest ◽  
Diffusion Weighted Mri ◽  
Fiber Tractography ◽  
Cingulum Bundle ◽  
Diffusion Weighted ◽  
Substantial Progress ◽  
Shaped Fibers

AbstractSubstantial progress in acquisition, processing, and analysis boosted the reliability of diffusion-weighted MRI and increased the accuracy of mapping white matter pathways with fiber tractography. Since the introduction of ‘region of interest’ (ROI) based virtual dissection by Conturo et al. in 1999, researchers have used tractography to identify white matter pathways, which faithfully represented previously known structures revealed by dyeing studies or post-mortem descriptions. The reconstructed streamlines are subjects of bundle-specific in vivo investigations to show differences between groups (e.g., comparing fractional anisotropy (FA) between patients and healthy controls) or to describe the relation between diffusion scalars and metrics of interest (e.g.: normal aging or changes due to learning). By applying a reverse strategy in using diffusion-weighted MRI tractography first, then supporting the findings with other techniques, we have identified a bilateral tract in the frontal cortex - the superoanterior fasciculus (SAF). The tract resembles the anterior shape of the cingulum bundle, but is located more frontally. To erase the chance that our findings are confounded by acquisition, processing or modeling artifacts, we analyzed a total of 421 subjects from four cohorts with different acquisition schemes and diverse processing pipelines. The findings were also completed with other non-MRI techniques, such as polarized light microscopy and dissection. Tractography results demonstrate a long pathway and are consistent among cohorts, while dissection indicates a series of U-shaped fibers connecting adjacent gyri. In conclusion, we hypothesize that these consecutive U-shaped fibers emerge to form a pathway, thereby resulting in a multicomponent bundle.

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