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.

scholarly journals A data-driven approach to optimising the encoding for multi-shell diffusion MRI with application to neonatal imaging

2019 ◽  
Author(s):  
J-Donald Tournier ◽  
Daan Christiaens ◽  
Jana Hutter ◽  
Anthony N. Price ◽  
Lucilio Cordero-Grande ◽  
...  
Keyword(s):  
Information Content ◽  
Diffusion Mri ◽  
Data Driven ◽  
Abnormal Development ◽  
Quality Data ◽  
List Type ◽  
Reconstruction Methods ◽  
Human Connectome Project ◽  
Data Driven Approach

AbstractDiffusion MRI has the potential to provide important information about the connectivity and microstructure of the human brain during normal and abnormal development, non-invasively and in vivo. Recent developments in MRI hardware and reconstruction methods now permit the acquisition of large amounts of data within relatively short scan times. This makes it possible to acquire more informative multi-shell data, with diffusion-sensitisation applied along many directions over multiple b-value shells. Such schemes are characterised by the number of shells acquired, and the specific b-value and number of directions sampled for each shell. However, there is currently no clear consensus as to how to optimise these parameters. In this work, we propose a means of optimising multi-shell acquisition schemes by estimating the information content of the diffusion MRI signal, and optimising the acquisition parameters for sensitivity to the observed effects, in a manner agnostic to any particular diffusion analysis method that might subsequently be applied to the data. This method was used to design the acquisition scheme for the neonatal diffusion MRI sequence used in the developing Human Connectome Project, which aims to acquire high quality data and make it freely available to the research community. The final protocol selected by the algorithm, and currently in use within the dHCP, consists of b = 0, 400, 1000, 2600 s/mm2 with 20, 64, 88 & 128 DW directions per shell respectively.HighlightsA data driven method is presented to design multi-shell diffusion MRI acquisition schemes (b-values and no. directions).This method optimises the multi-shell scheme for maximum sensitivity to the information content in the signal.When applied in neonates, the data suggest that a b=0 + 3 shell strategy is appropriate

scholarly journals Improving the Quality of Positive Datasets for the Establishment of Machine Learning Models for pre-microRNA Detection

2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Müşerref Duygu Saçar Demirci ◽  
Jens Allmer
Keyword(s):  
Machine Learning ◽  
Training Data ◽  
Quality Data ◽  
Virus Infections ◽  
High Quality ◽  
Disease States ◽  
Positive Data ◽  
Mirna Detection ◽  
Post Transcriptional Regulation

AbstractMicroRNAs (miRNAs) are involved in the post-transcriptional regulation of protein abundance and thus have a great impact on the resulting phenotype. It is, therefore, no wonder that they have been implicated in many diseases ranging from virus infections to cancer. This impact on the phenotype leads to a great interest in establishing the miRNAs of an organism. Experimental methods are complicated which led to the development of computational methods for pre-miRNA detection. Such methods generally employ machine learning to establish models for the discrimination between miRNAs and other sequences. Positive training data for model establishment, for the most part, stems from miRBase, the miRNA registry. The quality of the entries in miRBase has been questioned, though. This unknown quality led to the development of filtering strategies in attempts to produce high quality positive datasets which can lead to a scarcity of positive data. To analyze the quality of filtered data we developed a machine learning model and found it is well able to establish data quality based on intrinsic measures. Additionally, we analyzed which features describing pre-miRNAs could discriminate between low and high quality data. Both models are applicable to data from miRBase and can be used for establishing high quality positive data. This will facilitate the development of better miRNA detection tools which will make the prediction of miRNAs in disease states more accurate. Finally, we applied both models to all miRBase data and provide the list of high quality hairpins.

scholarly journals FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution

2021 ◽  
Author(s):  
Rui Zeng ◽  
Jinglei Lv ◽  
He Wang ◽  
Luping Zhou ◽  
Michael Barnett ◽  
...  
Keyword(s):  
Deep Learning ◽  
Angular Resolution ◽  
Super Resolution ◽  
Orientation Distribution ◽  
Quality Data ◽  
High Angular Resolution ◽  
Clinical Protocols ◽  
High Quality ◽  
Human Connectome Project ◽  
Fiber Orientation Distribution

ABSTRACTMapping the human connectome using fibre-tracking permits the study of brain connectivity and yields new insights into neuroscience. However, reliable connectome reconstruction using diffusion magnetic resonance imaging (dMRI) data acquired by widely available clinical protocols remains challenging, thus limiting the connectome/tractography clinical applications. Here we develop fibre orientation distribution (FOD) network (FOD-Net), a deep-learning-based framework for FOD angular super-resolution. Our method enhances the angular resolution of FOD images computed from common clinical-quality dMRI data, to obtain FODs with quality comparable to those produced from advanced research scanners. Super-resolved FOD images enable superior tractography and structural connectome reconstruction from clinical protocols. The method was trained and tested with high-quality data from the Human Connectome Project (HCP) and further validated with a local clinical 3.0T scanner. Using this method, we improve the angular resolution of FOD images acquired with typical single-shell low-angular-resolution dMRI data (e.g., 32 directions, b=1000 s/mm2) to approximate the quality of FODs derived from time-consuming, multi-shell high-angular-resolution dMRI research protocols. We also demonstrate tractography improvement, removing spurious connections and bridging missing connections. We further demonstrate that connectomes reconstructed by super-resolved FOD achieve comparable results to those obtained with more advanced dMRI acquisition protocols, on both HCP and clinical 3T data. Advances in deep-learning approaches used in FOD-Net facilitate the generation of high quality tractography/connectome analysis from existing clinical MRI environments.

scholarly journals Dialog State Tracking with Reinforced Data Augmentation

2020 ◽  
Vol 34 (05) ◽  
pp. 9474-9481
Author(s):  
Yichun Yin ◽  
Lifeng Shang ◽  
Xin Jiang ◽  
Xiao Chen ◽  
Qun Liu
Keyword(s):  
Data Augmentation ◽  
State Of The Art ◽  
The State ◽  
Training Data ◽  
Quality Data ◽  
Specific Context ◽  
High Quality ◽  
High Quality Data ◽  
Fine Grained ◽  
State Tracking

Neural dialog state trackers are generally limited due to the lack of quantity and diversity of annotated training data. In this paper, we address this difficulty by proposing a reinforcement learning (RL) based framework for data augmentation that can generate high-quality data to improve the neural state tracker. Specifically, we introduce a novel contextual bandit generator to learn fine-grained augmentation policies that can generate new effective instances by choosing suitable replacements for specific context. Moreover, by alternately learning between the generator and the state tracker, we can keep refining the generative policies to generate more high-quality training data for neural state tracker. Experimental results on the WoZ and MultiWoZ (restaurant) datasets demonstrate that the proposed framework significantly improves the performance over the state-of-the-art models, especially with limited training data.

scholarly journals The Forget-Me-Not dHCP study: 7 Tesla high resolution diffusion imaging in the unfixed post-mortem neonatal brain

2021 ◽  
Author(s):  
Wenchuan Wu ◽  
Luke Baxter ◽  
Sebastian W Rieger ◽  
Eleri Adams ◽  
Jesper L. R. Andersson ◽  
...  
Keyword(s):  
High Resolution ◽  
Diffusion Mri ◽  
Care Pathway ◽  
7 Tesla ◽  
Cortical Plate ◽  
Post Mortem ◽  
Ethical Challenges ◽  
Neonatal Brain ◽  
High Quality ◽  
Human Connectome Project

Diffusion MRI of the neonatal brain allows investigation of the organisational structure of maturing fibres during brain development. Post-mortem imaging has the potential to achieve high resolution by using long scan times, enabling precise assessment of small structures. The Forget-Me-Not study, part of the Developing Human Connectome Project (dHCP), aims to acquire and publicly distribute high-resolution diffusion MRI data for unfixed post-mortem neonatal brain at 7T with a custom-built head coil. This paper describes how the study addressed logistical, technical and ethical challenges relating to recruitment pipeline, care pathway, tissue preservation, scan setup and protocol optimisation. Results from the first subject recruited to the study demonstrate high-quality diffusion MRI data. Preliminary voxel-wise and tractography-based analyses are presented for the cortical plate, subplate and white matter pathways, with comparison to age-matched in vivo dHCP data. These results demonstrate that high quality post-mortem data can be acquired and provide a sensitive means to explore the developing human brain, as well as altered diffusion properties consistent with post-mortem changes, at high resolution.

scholarly journals Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning

2018 ◽  
Author(s):  
Naihui Zhou ◽  
Zachary D Siegel ◽  
Scott Zarecor ◽  
Nigel Lee ◽  
Darwin A Campbell ◽  
...  
Keyword(s):  
Machine Learning ◽  
Image Analysis ◽  
Best Practices ◽  
Ground Truth ◽  
Training Data ◽  
Quality Data ◽  
High Quality ◽  
Ground Truth Data ◽  
Plant Phenomics

AbstractThe accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good quality. We explore an image analysis task involving the segmentation of corn tassels from images taken in a field setting. We investigate the accuracy, speed and other quality metrics when this task is performed by students for academic credit, Amazon MTurk workers, and Master Amazon MTurk workers. We conclude that the Amazon MTurk and Master Mturk workers perform significantly better than the for-credit students, but with no significant difference between the two MTurk worker types. Furthermore, the quality of the segmentation produced by Amazon MTurk workers rivals that of an expert worker. We provide best practices to assess the quality of ground truth data, and to compare data quality produced by different sources. We conclude that properly managed crowdsourcing can be used to establish large volumes of viable ground truth data at a low cost and high quality, especially in the context of high throughput plant phenotyping. We also provide several metrics for assessing the quality of the generated datasets.Author SummaryFood security is a growing global concern. Farmers, plant breeders, and geneticists are hastening to address the challenges presented to agriculture by climate change, dwindling arable land, and population growth. Scientists in the field of plant phenomics are using satellite and drone images to understand how crops respond to a changing environment and to combine genetics and environmental measures to maximize crop growth efficiency. However, the terabytes of image data require new computational methods to extract useful information. Machine learning algorithms are effective in recognizing select parts of images, butthey require high quality data curated by people to train them, a process that can be laborious and costly. We examined how well crowdsourcing works in providing training data for plant phenomics, specifically, segmenting a corn tassel – the male flower of the corn plant – from the often-cluttered images of a cornfield. We provided images to students, and to Amazon MTurkers, the latter being an on-demand workforce brokered by Amazon.com and paid on a task-by-task basis. We report on best practices in crowdsourcing image labeling for phenomics, and compare the different groups on measures such as fatigue and accuracy over time. We find that crowdsourcing is a good way of generating quality labeled data, rivaling that of experts.

scholarly journals Test-retest reproducibility of in vivo oscillating gradient and microscopic anisotropy diffusion MRI in mice at 9.4 Tesla

2021 ◽  
Author(s):  
Naila Rahman ◽  
Kathy Xu ◽  
Mohammad Omer ◽  
Matthew Budde ◽  
Arthur Brown ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Spin Echo ◽  
Spatial Scales ◽  
Mean Diffusivity ◽  
Region Of Interest ◽  
Sample Sizes ◽  
High Reproducibility ◽  
Microstructural Changes ◽  
Increased Sensitivity

Background and Purpose: Microstructure imaging with advanced diffusion MRI (dMRI) techniques have shown increased sensitivity and specificity to microstructural changes in various disease and injury models. Oscillating gradient spin echo (OGSE) dMRI, implemented by varying the oscillating gradient frequency, and microscopic anisotropy (µA) dMRI, implemented via tensor valued diffusion encoding, may provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The aims of this study were to characterize the test-retest reproducibility of in vivo OGSE and µA dMRI metrics in the mouse brain at 9.4 Tesla and provide estimates of required sample sizes for future investigations. Methods: Eight adult C57Bl/6 mice were scanned twice (5 days apart). Each imaging session consisted of multifrequency OGSE and µA dMRI protocols. Metrics investigated included µA, isotropic and anisotropic kurtosis, and the diffusion dispersion rate (Λ), which explores the power-law frequency dependence of mean diffusivity. The dMRI metric maps were analyzed with mean region-of-interest (ROI) and whole brain voxel-wise analysis. Bland-Altman plots and coefficients of variation (CV) were used to assess the reproducibility of OGSE and µA metrics. Furthermore, we estimated sample sizes required to detect a variety of effect sizes. Results: Bland-Altman plots showed negligible biases between test and retest sessions. ROI-based CVs revealed high reproducibility for both µA (CVs < 8 %) and Λ (CVs < 15 %). Voxel-wise CV maps revealed high reproducibility for µA (CVs ~ 10 %), but low reproducibility for OGSE metrics (CVs ~ 50 %). Conclusion: Most of the µA dMRI metrics are reproducible in both ROI-based and voxel-wise analysis, while the OGSE dMRI metrics are only reproducible in ROI-based analysis. µA and Λ may provide sensitivity to subtle microstructural changes (4 - 8 %) with feasible sample sizes (10 – 15).

scholarly journals Pushing the limits of in vivo diffusion MRI for the Human Connectome Project

NeuroImage ◽  
2013 ◽  
Vol 80 ◽  
pp. 220-233 ◽  
Author(s):  
K. Setsompop ◽  
R. Kimmlingen ◽  
E. Eberlein ◽  
T. Witzel ◽  
J. Cohen-Adad ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Human Connectome Project

scholarly journals A new method for counting reproductive structures in digitized herbarium specimens using Mask R-CNN

2020 ◽  
Author(s):  
Charles Davis ◽  
Julien Champ ◽  
Daniel S. Park ◽  
Ian Breckheimer ◽  
Goia M. Lyra ◽  
...  
Keyword(s):  
Machine Learning ◽  
Climatic Change ◽  
Morphological Variability ◽  
Scale Up ◽  
Training Data ◽  
Quality Data ◽  
Reproductive Phenology ◽  
Herbarium Specimens ◽  
High Quality ◽  
Binary Coding

AbstractPhenology–the timing of life-history events–is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from > 3000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with > 87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥ 90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant response to ongoing climatic change.

scholarly journals Reducing variability in along-tract analysis with diffusion profile realignment

2019 ◽  
Author(s):  
Samuel St-Jean ◽  
Maxime Chamberland ◽  
Max A. Viergever ◽  
Alexander Leemans
Keyword(s):  
White Matter ◽  
Fractional Anisotropy ◽  
Mean Diffusivity ◽  
Region Of Interest ◽  
Diffusion Profile ◽  
Fixed Number ◽  
Fiber Density ◽  
Human Connectome Project ◽  
Student’S T

AbstractDiffusion weighted magnetic resonance imaging (dMRI) provides a non invasive virtual reconstruction of the brain’s white matter structures through tractography. Analyzing dMRI measures along the trajectory of white matter bundles can provide a more specific investigation than considering a region of interest or tract-averaged measurements. However, performing group analyses with this along-tract strategy requires correspondence between points of tract pathways across subjects. This is usually achieved by creating a new common space where the representative streamlines from every subject are resampled to the same number of points. If the underlying anatomy of some subjects was altered due to, e.g., disease or developmental changes, such information might be lost by resampling to a fixed number of points. In this work, we propose to address the issue of possible misalignment, which might be present even after resampling, by realigning the representative streamline of each subject in this 1D space with a new method, coined diffusion profile realignment (DPR). Experiments on synthetic datasets show that DPR reduces the coefficient of variation for the mean diffusivity, fractional anisotropy and apparent fiber density when compared to the unaligned case. Using 100 in vivo datasets from the human connectome project, we simulated changes in mean diffusivity, fractional anisotropy and apparent fiber density. Pairwise Student’s t-tests between these altered subjects and the original subjects indicate that regional changes are identified after realignment with the DPR algorithm, while preserving differences previously detected in the unaligned case. This new correction strategy contributes to revealing effects of interest which might be hidden by misalignment and has the potential to improve the specificity in longitudinal population studies beyond the traditional region of interest based analysis and along-tract analysis workflows.

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