scholarly journals The visual white matter: The application of diffusion MRI and fiber tractography to vision science

2017 ◽  
Vol 17 (2) ◽  
pp. 4 ◽  
Author(s):  
Ariel Rokem ◽  
Hiromasa Takemura ◽  
Andrew S. Bock ◽  
K. Suzanne Scherf ◽  
Marlene Behrmann ◽  
...  
Keyword(s):  
White Matter ◽  
Diffusion Mri ◽  
Fiber Tractography ◽  
Vision Science

scholarly journals The visual white matter: The application of diffusion MRI and fiber tractography to vision science

2016 ◽  
Author(s):  
Ariel Rokem ◽  
Hiromasa Takemura ◽  
Andrew Bock ◽  
K. Suzanne Scherf ◽  
Marlene Behrmann ◽  
...  
Keyword(s):  
White Matter ◽  
Visual Information ◽  
Diffusion Mri ◽  
Brain Connectivity ◽  
Open Data ◽  
Data Sets ◽  
Fiber Tractography ◽  
Vision Science ◽  
Visual Neuroscience

AbstractVisual neuroscience has traditionally focused much of its attention on understanding the response properties of neurons along the visual pathways. This review focuses instead on the properties of the white matter connections between these neurons. Specifically, we provide an introduction to methods to study the human visual white matter using diffusion MRI (dMRI). This method allows us to measure the white matter connections in individual visual systems in vivo, allows us to trace long-range connections between different parts of the visual system, and to measure the biophysical properties of these connections. We explain the principles underlying dMRI measurements and the basics of modeling these data. We review a range of findings from recent studies on connections between different visual field maps, on the effects of visual impairment on the white matter, and on the properties underlying networks that process visual information that supports visual face recognition. Finally, we discuss a few promising directions for future studies. These include new methods for analysis of MRI data, open data-sets that are becoming available to study brain connectivity and white matter properties, and open-source software for the analysis of these data.

scholarly journals Pandora: 4-D White Matter Bundle Population-Based Atlases Derived from Diffusion MRI Fiber Tractography

2020 ◽  
Author(s):  
Colin B Hansen ◽  
Qi Yang ◽  
Ilwoo Lyu ◽  
Francois Rheault ◽  
Cailey Kerley ◽  
...  
Keyword(s):  
White Matter ◽  
Diffusion Mri ◽  
Population Based ◽  
Fiber Tractography

scholarly journals Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography

2021 ◽  
Author(s):  
Kurt Schilling ◽  
Chantal M.W. Tax ◽  
Francois M.W. Rheault ◽  
Bennett A Landman ◽  
Adam W Anderson ◽  
...  
Keyword(s):  
White Matter ◽  
Human Brain ◽  
Diffusion Mri ◽  
Brain Connectivity ◽  
False Negative ◽  
Fiber Tractography ◽  
Single Voxel ◽  
Ill Posed ◽  
Pass Through

Characterizing and understanding the limitations of diffusion MRI fiber tractography is a prerequisite for methodological advances and innovations which will allow these techniques to accurately map the connections of the human brain. The so-called "crossing fiber problem" has received tremendous attention and has continuously triggered the community to develop novel approaches for disentangling distinctly oriented fiber populations. Perhaps an even greater challenge occurs when multiple white matter bundles converge within a single voxel, or throughout a single brain region, and share the same parallel orientation, before diverging and continuing towards their final cortical or sub-cortical terminations. These so-called "bottleneck" regions contribute to the ill-posed nature of the tractography process, and lead to both false positive and false negative estimated connections. Yet, as opposed to the extent of crossing fibers, a thorough characterization of bottleneck regions has not been performed. The aim of this study is to quantify the prevalence of bottleneck regions. To do this, we use diffusion tractography to segment known white matter bundles of the brain, and assign each bundle to voxels they pass through and to specific orientations within those voxels (i.e. fixels). We demonstrate that bottlenecks occur in greater than 50-70% of fixels in the white matter of the human brain. We find that all projection, association, and commissural fibers contribute to, and are affected by, this phenomenon, and show that even regions traditionally considered "single fiber voxels" often contain multiple fiber populations. Together, this study shows that a majority of white matter presents bottlenecks for tractography which may lead to incorrect or erroneous estimates of brain connectivity or quantitative tractography (i.e., tractometry), and underscores the need for a paradigm shift in the process of tractography and bundle segmentation for studying the fiber pathways of the human brain.

scholarly journals Pandora: 4-D white matter bundle population-based atlases derived from diffusion MRI fiber tractography

2020 ◽  
Author(s):  
Colin B Hansen ◽  
Qi Yang ◽  
Ilwoo Lyu ◽  
Francois Rheault ◽  
Cailey Kerley ◽  
...  
Keyword(s):  
White Matter ◽  
Diffusion Mri ◽  
State Of The Art ◽  
Population Based ◽  
Small Sample ◽  
Fiber Tractography ◽  
Statistical Inferences ◽  
Small Sample Sizes ◽  
The Brain ◽  
Brain Atlases

AbstractBrain atlases have proven to be valuable neuroscience tools for localizing regions of interest and performing statistical inferences on populations. Although many human brain atlases exist, most do not contain information about white matter structures, often neglecting them completely or labelling all white matter as a single homogenous substrate. While few white matter atlases do exist based on diffusion MRI fiber tractography, they are often limited to descriptions of white matter as spatially separate “regions” rather than as white matter “bundles” or fascicles, which are well-known to overlap throughout the brain. Additional limitations include small sample sizes, few white matter pathways, and the use of outdated diffusion models and techniques. Here, we present a new population-based collection of white matter atlases represented in both volumetric and surface coordinates in a standard space. These atlases are based on 2443 subjects, and include 216 white matter bundles derived from 6 different state-of-the-art tractography techniques. This atlas is freely available and will be a useful resource for parcellation and segmentation.

scholarly journals Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?

2020 ◽  
Author(s):  
Kurt G. Schilling ◽  
François Rheault ◽  
Laurent Petit ◽  
Colin B. Hansen ◽  
Vishwesh Nath ◽  
...  
Keyword(s):  
White Matter ◽  
Diffusion Mri ◽  
External Validation ◽  
Reproducible Research ◽  
Clinical Settings ◽  
Complex Data ◽  
Fiber Tractography ◽  
Considerable Variability ◽  
Human Brains

AbstractWhite matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human wholebrain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.

scholarly journals Limits to anatomical accuracy of diffusion tractography using modern approaches

2018 ◽  
Author(s):  
Kurt G Schilling ◽  
Vishwesh Nath ◽  
Colin Hansen ◽  
Prasanna Parvathaneni ◽  
Justin Blaber ◽  
...  
Keyword(s):  
White Matter ◽  
Validation Studies ◽  
Diffusion Mri ◽  
Ex Vivo ◽  
Structural Connectivity ◽  
Fiber Tractography ◽  
Research Groups ◽  
Wide Range ◽  
Modern Methods ◽  
The Brain

AbstractDiffusion MRI fiber tractography is widely used to probe the structural connectivity of thebrain, with a range of applications in both clinical and basic neuroscience. Despite widespread use, tractography has well-known pitfalls that limits the anatomical accuracy of this technique. Numerous modern methods have been developed to address these shortcomings through advances in acquisition, modeling, and computation. To test whether these advances improve tractography accuracy, we organized the ISBI 2018 3D Validation of Tractography with Experimental MRI (3D-VoTEM) challenge. We made available three unique independent tractography validation datasets – a physical phantom and two ex vivo brain specimens - resulting in 176 distinct submissions from 9 research groups. By comparing results over a wide range of fiber complexities and algorithmic strategies, this challenge provides a more comprehensive assessment of tractography’s inherent limitations than has been reported previously. The central results were consistent across all sub-challenges in that, despite advances in tractography methods, the anatomical accuracy of tractography has not dramatically improved in recent years. Taken together, our results independently confirm findings from decades of tractography validation studies, demonstrate inherent limitations in reconstructing white matter pathways using diffusion MRI data alone, and highlight the need for alternative or combinatorial strategies to accurately map the fiber pathways of the brain.

Clustering of short association white matter fibers calculated from diffusion MRI

2014 ◽  
Author(s):  
C. Roman ◽  
D. Le Bihan ◽  
C. Poupon ◽  
P. Guevara ◽  
A. Lebois ◽  
...  
Keyword(s):  
White Matter ◽  
Diffusion Mri

scholarly journals Tractography Alterations in the Arcuate and Uncinate Fasciculi in Post-Stroke Aphasia

2021 ◽  
Vol 11 (1) ◽  
pp. 53
Author(s):  
Sara Kierońska ◽  
Milena Świtońska ◽  
Grzegorz Meder ◽  
Magdalena Piotrowska ◽  
Paweł Sokal
Keyword(s):  
White Matter ◽  
Brain Connectivity ◽  
Three Dimensional ◽  
Cerebral White Matter ◽  
Neural Pathways ◽  
Uncinate Fasciculus ◽  
Arcuate Fasciculus ◽  
Fiber Tractography ◽  
Post Stroke

Fiber tractography based on diffuse tensor imaging (DTI) can reveal three-dimensional white matter connectivity of the human brain. Tractography is a non-invasive method of visualizing cerebral white matter structures in vivo, including neural pathways surrounding the ischemic area. DTI may be useful for elucidating alterations in brain connectivity resulting from neuroplasticity after stroke. We present a case of a male patient who developed significant mixed aphasia following ischemic stroke. The patient had been treated by mechanical thrombectomy followed by an early rehabilitation, in conjunction with transcranial direct current stimulation (tDCS). DTI was used to examine the arcuate fasciculus and uncinate fasciculus upon admission and again at three months post-stroke. Results showed an improvement in the patient’s symptoms of aphasia, which was associated with changes in the volume and numbers of tracts in the uncinate fasciculus and the arcuate fasciculus.

scholarly journals Functional and diffusion MRI reveal the neurophysiological basis of neonates’ noxious-stimulus evoked brain activity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Luke Baxter ◽  
Fiona Moultrie ◽  
Sean Fitzgibbon ◽  
Marianne Aspbury ◽  
Roshni Mansfield ◽  
...  
Keyword(s):  
White Matter ◽  
Prediction Model ◽  
Resting State ◽  
Early Life ◽  
Diffusion Mri ◽  
Brain Activity ◽  
Noxious Stimulus ◽  
Noxious Stimulation ◽  
Human Connectome Project ◽  
And Diffusion

AbstractUnderstanding the neurophysiology underlying neonatal responses to noxious stimulation is central to improving early life pain management. In this neonatal multimodal MRI study, we use resting-state and diffusion MRI to investigate inter-individual variability in noxious-stimulus evoked brain activity. We observe that cerebral haemodynamic responses to experimental noxious stimulation can be predicted from separately acquired resting-state brain activity (n = 18). Applying this prediction model to independent Developing Human Connectome Project data (n = 215), we identify negative associations between predicted noxious-stimulus evoked responses and white matter mean diffusivity. These associations are subsequently confirmed in the original noxious stimulation paradigm dataset, validating the prediction model. Here, we observe that noxious-stimulus evoked brain activity in healthy neonates is coupled to resting-state activity and white matter microstructure, that neural features can be used to predict responses to noxious stimulation, and that the dHCP dataset could be utilised for future exploratory research of early life pain system neurophysiology.

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