scholarly journals Insights from the IronTract challenge: optimal methods for mapping brain pathways from multi-shell diffusion MRI

2021 ◽  
Author(s):  
Chiara Maffei ◽  
Gabriel Girard ◽  
Kurt Schilling ◽  
Baran Aydogan ◽  
Nagesh Aduluru ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Ex Vivo ◽  
Analysis Methods ◽  
Processing Strategies ◽  
Human Connectome Project ◽  
Grid Scheme ◽  
Technical Advances ◽  
Brain Pathways ◽  
Similar Accuracy ◽  
Validation Tool

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.

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.

scholarly journals Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data

2021 ◽  
Author(s):  
Chiara Maffei ◽  
Christine Lee ◽  
Michael Planich ◽  
Manisha Ramprasad ◽  
Nivedita Ravi ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Region Of Interest ◽  
Training Data ◽  
Quality Data ◽  
High Quality ◽  
Scanning Time ◽  
Human Connectome Project ◽  
High Gradients ◽  
Comprehensive Comparison

The development of scanners with ultra-high gradients, spearheaded by the Human Connectome Project, has led to dramatic improvements in the spatial, angular, and diffusion resolution that is feasible for in vivo diffusion MRI acquisitions. The improved quality of the data can be exploited to achieve higher accuracy in the inference of both microstructural and macrostructural anatomy. However, such high-quality data can only be acquired on a handful of Connectom MRI scanners worldwide, while remaining prohibitive in clinical settings because of the constraints imposed by hardware and scanning time. In this study, we first update the classical protocols for tractography-based, manual annotation of major white-matter pathways, to adapt them to the much greater volume and variability of the streamlines that can be produced from today's state-of-the-art diffusion MRI data. We then use these protocols to annotate 42 major pathways manually in data from a Connectom scanner. Finally, we show that, when we use these manually annotated pathways as training data for global probabilistic tractography with anatomical neighborhood priors, we can perform highly accurate, automated reconstruction of the same pathways in much lower-quality, more widely available diffusion MRI data. The outcomes of this work include both a new, comprehensive atlas of WM pathways from Connectom data, and an updated version of our tractography toolbox, TRActs Constrained by UnderLying Anatomy (TRACULA), which is trained on data from this atlas. Both the atlas and TRACULA are distributed publicly as part of FreeSurfer. We present the first comprehensive comparison of TRACULA to the more conventional, multi-region-of-interest approach to automated tractography, and the first demonstration of training TRACULA on high-quality, Connectom data to benefit studies that use more modest acquisition protocols.

Diffusion MRI analysis methods

2021 ◽  
pp. 147-156
Author(s):  
Szabolcs David ◽  
Joost Verhoeff ◽  
Alexander Leemans
Keyword(s):  
Diffusion Mri ◽  
Analysis Methods

scholarly journals Ex vivo diffusion MRI of the human brain: Technical challenges and recent advances

2018 ◽  
Vol 32 (4) ◽  
pp. e3941 ◽  
Author(s):  
Alard Roebroeck ◽  
Karla L. Miller ◽  
Manisha Aggarwal
Keyword(s):  
Human Brain ◽  
Diffusion Mri ◽  
Ex Vivo ◽  
Recent Advances ◽  
Technical Challenges

scholarly journals Awake functional MRI detects neural circuit dysfunction in a mouse model of autism

2020 ◽  
Vol 6 (6) ◽  
pp. eaav4520 ◽  
Author(s):  
Tomokazu Tsurugizawa ◽  
Kota Tamada ◽  
Nobukazu Ono ◽  
Sachise Karakawa ◽  
Yuko Kodama ◽  
...  
Keyword(s):  
Functional Mri ◽  
Brain Function ◽  
Copy Number ◽  
Diffusion Mri ◽  
Neural Circuit ◽  
Ex Vivo ◽  
Disease Model ◽  
Wild Type ◽  
Number Variation ◽  
Translational Approach

MRI has potential as a translational approach from rodents to humans. However, given that mouse functional MRI (fMRI) uses anesthetics for suppression of motion, it has been difficult to directly compare the result of fMRI in “unconsciousness” disease model mice with that in “consciousness” patients. We develop awake fMRI to investigate brain function in 15q dup mice, a copy number variation model of autism. Compared to wild-type mice, we find that 15q dup is associated with whole-brain functional hypoconnectivity and diminished fMRI responses to odors of stranger mice. Ex vivo diffusion MRI reveals widespread anomalies in white matter ultrastructure in 15q dup mice, suggesting a putative anatomical substrate for these functional hypoconnectivity. We show that d-cycloserine (DCS) treatment partially normalizes these anormalies in the frontal cortex of 15q dup mice and rescues some social behaviors. Our results demonstrate the utility of awake rodent fMRI and provide a rationale for further investigation of DCS therapy.

Human Connectome-Based Tractographic Atlas of the Brainstem Connections and Surgical Approaches

Neurosurgery ◽  
2016 ◽  
Vol 79 (3) ◽  
pp. 437-455 ◽  
Author(s):  
Antonio Meola ◽  
Fang-Cheng Yeh ◽  
Wendy Fellows-Mayle ◽  
Jared Weed ◽  
Juan C. Fernandez-Miranda
Keyword(s):  
Spatial Resolution ◽  
Diffusion Mri ◽  
Diffusion Tensor ◽  
Population Based ◽  
Medial Longitudinal Fasciculus ◽  
Surgical Approaches ◽  
Medial Lemniscus ◽  
Spinothalamic Tract ◽  
Rubrospinal Tract ◽  
Human Connectome Project

Abstract BACKGROUND The brainstem is one of the most challenging areas for the neurosurgeon because of the limited space between gray matter nuclei and white matter pathways. Diffusion tensor imaging-based tractography has been used to study the brainstem structure, but the angular and spatial resolution could be improved further with advanced diffusion magnetic resonance imaging (MRI). OBJECTIVE To construct a high-angular/spatial resolution, wide-population-based, comprehensive tractography atlas that presents an anatomical review of the surgical approaches to the brainstem. METHODS We applied advanced diffusion MRI fiber tractography to a population-based atlas constructed with data from a total of 488 subjects from the Human Connectome Project-488. Five formalin-fixed brains were studied for surgical landmarks. Luxol Fast Blue-stained histological sections were used to validate the results of tractography RESULTS We acquired the tractography of the major brainstem pathways and validated them with histological analysis. The pathways included the cerebellar peduncles, corticospinal tract, corticopontine tracts, medial lemniscus, lateral lemniscus, spinothalamic tract, rubrospinal tract, central tegmental tract, medial longitudinal fasciculus, and dorsal longitudinal fasciculus. Then, the reconstructed 3-dimensional brainstem structure was sectioned at the level of classic surgical approaches, namely supracollicular, infracollicular, lateral mesencephalic, perioculomotor, peritrigeminal, anterolateral (to the medulla), and retro-olivary approaches. CONCLUSION The advanced diffusion MRI fiber tracking is a powerful tool to explore the brainstem neuroanatomy and to achieve a better understanding of surgical approaches.

scholarly journals Local connectome phenotypes predict social, health, and cognitive factors

2018 ◽  
Vol 2 (1) ◽  
pp. 86-105 ◽  
Author(s):  
Michael A. Powell ◽  
Javier O. Garcia ◽  
Fang-Cheng Yeh ◽  
Jean M. Vettel ◽  
Timothy Verstynen
Keyword(s):  
White Matter ◽  
Diffusion Mri ◽  
Social Health ◽  
Cognitive Factors ◽  
High Dimensional ◽  
Cognitive Measures ◽  
Human Connectome Project ◽  
Low Dimensional ◽  
The Brain ◽  
Over Time

The unique architecture of the human connectome is defined initially by genetics and subsequently sculpted over time with experience. Thus, similarities in predisposition and experience that lead to similarities in social, biological, and cognitive attributes should also be reflected in the local architecture of white matter fascicles. Here we employ a method known as local connectome fingerprinting that uses diffusion MRI to measure the fiber-wise characteristics of macroscopic white matter pathways throughout the brain. This fingerprinting approach was applied to a large sample ( N = 841) of subjects from the Human Connectome Project, revealing a reliable degree of between-subject correlation in the local connectome fingerprints, with a relatively complex, low-dimensional substructure. Using a cross-validated, high-dimensional regression analysis approach, we derived local connectome phenotype (LCP) maps that could reliably predict a subset of subject attributes measured, including demographic, health, and cognitive measures. These LCP maps were highly specific to the attribute being predicted but also sensitive to correlations between attributes. Collectively, these results indicate that the local architecture of white matter fascicles reflects a meaningful portion of the variability shared between subjects along several dimensions.

scholarly journals Targeted In Situ Gene Correction of DysfunctionalAPOEAlleles to Produce Atheroprotective Plasma ApoE3 Protein

2012 ◽  
Vol 2012 ◽  
pp. 1-16 ◽  
Author(s):  
Ioannis Papaioannou ◽  
J. Paul Simons ◽  
James S. Owen
Keyword(s):  
Ex Vivo ◽  
Strand Break ◽  
Gene Correction ◽  
Cvd Risk ◽  
Transfer Strategies ◽  
Technical Advances ◽  
The Common ◽  
Induced Pluripotent

Cardiovascular disease is the leading worldwide cause of death. Apolipoprotein E (ApoE) is a 34-kDa circulating glycoprotein, secreted by the liver and macrophages with pleiotropic antiatherogenic functions and hence a candidate to treat hypercholesterolaemia and atherosclerosis. Here, we describe atheroprotective properties of ApoE, though also potential proatherogenic actions, and the prevalence of dysfunctional isoforms, outline conventional gene transfer strategies, and then focus on gene correction therapeutics that can repair defectiveAPOEalleles. In particular, we discuss the possibility and potential benefit of applying in combination two technical advances to repair aberrantAPOEgenes: (i) an engineered endonuclease to introduce a double-strand break (DSB) in exon 4, which contains the common, but dysfunctional,ε2 andε4 alleles; (ii) an efficient and selectable template for homologous recombination (HR) repair, namely, an adeno-associated viral (AAV) vector, which harbours wild-typeAPOEsequence. This technology is applicable ex vivo, for example to target haematopoietic or induced pluripotent stem cells, and also for in vivo hepatic gene targeting. It is to be hoped that such emerging technology will eventually translate to patient therapy to reduce CVD risk.

scholarly journals Diffantom: Whole-Brain Diffusion MRI Phantoms Derived from Real Datasets of the Human Connectome Project

2016 ◽  
Vol 10 ◽  
Author(s):  
Oscar Esteban ◽  
Emmanuel Caruyer ◽  
Alessandro Daducci ◽  
Meritxell Bach-Cuadra ◽  
María J. Ledesma-Carbayo ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Whole Brain ◽  
Human Connectome Project

scholarly journals Age, sex, and puberty related development of the corpus callosum: a multi-technique diffusion MRI study

2017 ◽  
Author(s):  
Sila Genc ◽  
Charles B Malpas ◽  
Gareth Ball ◽  
Timothy J Silk ◽  
Marc L Seal
Keyword(s):  
Corpus Callosum ◽  
Diffusion Mri ◽  
Diffusion Tensor ◽  
Ex Vivo ◽  
Profile Analysis ◽  
Pubertal Development ◽  
Strong Relationship ◽  
Childhood And Adolescence ◽  
Fibre Density ◽  
The Impact

AbstractPurposeThe corpus callosum is integral to the central nervous system, and continually develops with age by virtue of increasing axon diameter and ongoing myelination. Magnetic resonance imaging (MRI) techniques offer a means to disentangle these two aspects of white matter development. We investigate the profile of microstructural metrics across the corpus callosum, and assess the impact of age, sex and pubertal development on these processes.MethodsThis study made use of two independent paediatric populations. Multi-shell diffusion MRI data were analysed to produce a suite of diffusion tensor imaging (DTI), neurite orientation density and dispersion imaging (NODDI), and apparent fibre density (AFD) metrics. A multivariate profile analysis was performed for each diffusion metric across 10 subdivisions of the corpus callosum.ResultsAll diffusion metrics significantly varied across the length of the corpus callosum. AFD exhibited a strong relationship with age across the corpus callosum (partial η2 = .65), particularly in the posterior body of the corpus callosum (partial η2 = .72). In addition, females had significantly higher AFD compared with males, most markedly in the anterior splenium (partial η2 = .14) and posterior genu (partial η2 = .13). Age-matched pubertal group differences were localised to the splenium.ConclusionWe present evidence of a strong relationship between apparent fibre density and age, sex, and puberty during development. These results are consistent with ex vivo studies of fibre morphology, providing insights into the dynamics of axonal development in childhood and adolescence using diffusion MRI.Target journalsBrain Structure & Function; HBM; NeuroImage; Developmental Cognitive Neuroscience

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