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Neuroinformatics

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https://www.readbyqxmd.com/read/30006920/a-web-based-atlas-combining-mri-and-histology-of-the-squirrel-monkey-brain
#1
Kurt G Schilling, Yurui Gao, Matthew Christian, Vaibhav Janve, Iwona Stepniewska, Bennett A Landman, Adam W Anderson
The squirrel monkey (Saimiri sciureus) is a commonly-used surrogate for humans in biomedical research. In the neuroimaging community, MRI and histological atlases serve as valuable resources for anatomical, physiological, and functional studies of the brain; however, no digital MRI/histology atlas is currently available for the squirrel monkey. This paper describes the construction of a web-based multi-modal atlas of the squirrel monkey brain. The MRI-derived information includes anatomical MRI contrast (i...
July 13, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29956131/using-deep-learning-algorithms-to-automatically-identify-the-brain-mri-contrast-implications-for-managing-large-databases
#2
Ricardo Pizarro, Haz-Edine Assemlal, Dante De Nigris, Colm Elliott, Samson Antel, Douglas Arnold, Amir Shmuel
Neuroimaging science has seen a recent explosion in dataset size driving the need to develop database management with efficient processing pipelines. Multi-center neuroimaging databases consistently receive magnetic resonance imaging (MRI) data with unlabeled or incorrectly labeled contrast. There is a need to automatically identify the contrast of MRI scans to save database-managing facilities valuable resources spent by trained technicians required for visual inspection. We developed a deep learning (DL) algorithm with convolution neural network architecture to automatically infer the contrast of MRI scans based on the image intensity of multiple slices...
June 29, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29956130/qmodeling-a-multiplatform-easy-to-use-and-open-source-toolbox-for-pet-kinetic-analysis
#3
Francisco J López-González, José Paredes-Pacheco, Karl Thurnhofer-Hemsi, Carlos Rossi, Manuel Enciso, Daniel Toro-Flores, Belén Murcia-Casas, Antonio L Gutiérrez-Cardo, Núria Roé-Vellvé
Kinetic modeling is at the basis of most quantification methods for dynamic PET data. Specific software is required for it, and a free and easy-to-use kinetic analysis toolbox can facilitate routine work for clinical research. The relevance of kinetic modeling for neuroimaging encourages its incorporation into image processing pipelines like those of SPM, also providing preprocessing flexibility to match the needs of users. The aim of this work was to develop such a toolbox: QModeling. It implements four widely-used reference-region models: Simplified Reference Tissue Model (SRTM), Simplified Reference Tissue Model 2 (SRTM2), Patlak Reference and Logan Reference...
June 28, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29946897/user-guided-segmentation-of-multi-modality-medical-imaging-datasets-with-itk-snap
#4
Paul A Yushkevich, Artem Pashchinskiy, Ipek Oguz, Suyash Mohan, J Eric Schmitt, Joel M Stein, Dženan Zukić, Jared Vicory, Matthew McCormick, Natalie Yushkevich, Nadav Schwartz, Yang Gao, Guido Gerig
ITK-SNAP is an interactive software tool for manual and semi-automatic segmentation of 3D medical images. This paper summarizes major new features added to ITK-SNAP over the last decade. The main focus of the paper is on new features that support semi-automatic segmentation of multi-modality imaging datasets, such as MRI scans acquired using different contrast mechanisms (e.g., T1, T2, FLAIR). The new functionality uses decision forest classifiers trained interactively by the user to transform multiple input image volumes into a foreground/background probability map; this map is then input as the data term to the active contour evolution algorithm, which yields regularized surface representations of the segmented objects of interest...
June 27, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29948844/pypns-multiscale-simulation-of-a-peripheral-nerve-in-python
#5
Carl H Lubba, Yann Le Guen, Sarah Jarvis, Nick S Jones, Simon C Cork, Amir Eftekhar, Simon R Schultz
Bioelectronic Medicines that modulate the activity patterns on peripheral nerves have promise as a new way of treating diverse medical conditions from epilepsy to rheumatism. Progress in the field builds upon time consuming and expensive experiments in living organisms. To reduce experimentation load and allow for a faster, more detailed analysis of peripheral nerve stimulation and recording, computational models incorporating experimental insights will be of great help. We present a peripheral nerve simulator that combines biophysical axon models and numerically solved and idealised extracellular space models in one environment...
June 15, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29907892/a-robust-reduced-rank-graph-regression-method-for-neuroimaging-genetic-analysis
#6
Xiaofeng Zhu, Weihong Zhang, Yong Fan
To characterize associations between genetic and neuroimaging data, a variety of analytic methods have been proposed in neuroimaging genetic studies. These methods have achieved promising performance by taking into account inherent correlation in either the neuroimaging data or the genetic data alone. In this study, we propose a novel robust reduced rank graph regression based method in a linear regression framework by considering correlations inherent in neuroimaging data and genetic data jointly. Particularly, we model the association analysis problem in a reduced rank regression framework with the genetic data as a feature matrix and the neuroimaging data as a response matrix by jointly considering correlations among the neuroimaging data as well as correlations between the genetic data and the neuroimaging data...
June 15, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29948843/predict-mirna-disease-association-with-collaborative-filtering
#7
Yatong Jiang, Bingtao Liu, Linghui Yu, Chenggang Yan, Hujun Bian
The era of human brain science research is dawning. Researchers utilize the various multi-disciplinary knowledge to explore the human brain,such as physiology and bioinformatics. The emerging disease association prediction technology can speed up the study of diseases, so as to better understanding the structure and function of human body. There are increasing evidences that miRNA plays a significant role in nervous system development, adult function, plasticity, and vulnerability to neurological disease states...
June 8, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29802511/cognitive-assessment-prediction-in-alzheimer-s-disease-by-multi-layer-multi-target-regression
#8
Xiaoqian Wang, Xiantong Zhen, Quanzheng Li, Dinggang Shen, Heng Huang
Accurate and automatic prediction of cognitive assessment from multiple neuroimaging biomarkers is crucial for early detection of Alzheimer's disease. The major challenges arise from the nonlinear relationship between biomarkers and assessment scores and the inter-correlation among them, which have not yet been well addressed. In this paper, we propose multi-layer multi-target regression (MMR) which enables simultaneously modeling intrinsic inter-target correlations and nonlinear input-output relationships in a general compositional framework...
May 25, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29785624/longitudinal-neuroimaging-hippocampal-markers-for-diagnosing-alzheimer-s-disease
#9
Carlos Platero, Lin Lin, M Carmen Tobar
Hippocampal atrophy measures from magnetic resonance imaging (MRI) are powerful tools for monitoring Alzheimer's disease (AD) progression. In this paper, we introduce a longitudinal image analysis framework based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two innovative parts: a longitudinal segmentation and a longitudinal classification step. The results show that both steps of the longitudinal pipeline improved the reliability and the accuracy of the discrimination between clinical groups...
May 21, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29725916/segan-adversarial-network-with-multi-scale-l-1-loss-for-medical-image-segmentation
#10
Yuan Xue, Tao Xu, Han Zhang, L Rodney Long, Xiaolei Huang
Inspired by classic Generative Adversarial Networks (GANs), we propose a novel end-to-end adversarial neural network, called SegAN, for the task of medical image segmentation. Since image segmentation requires dense, pixel-level labeling, the single scalar real/fake output of a classic GAN's discriminator may be ineffective in producing stable and sufficient gradient feedback to the networks. Instead, we use a fully convolutional neural network as the segmentor to generate segmentation label maps, and propose a novel adversarial critic network with a multi-scale L1 loss function to force the critic and segmentor to learn both global and local features that capture long- and short-range spatial relationships between pixels...
May 3, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29721680/the-decision-decoding-toolbox-ddtbox-a-multivariate-pattern-analysis-toolbox-for-event-related-potentials
#11
Stefan Bode, Daniel Feuerriegel, Daniel Bennett, Phillip M Alday
In recent years, neuroimaging research in cognitive neuroscience has increasingly used multivariate pattern analysis (MVPA) to investigate higher cognitive functions. Here we present DDTBOX, an open-source MVPA toolbox for electroencephalography (EEG) data. DDTBOX runs under MATLAB and is well integrated with the EEGLAB/ERPLAB and Fieldtrip toolboxes (Delorme and Makeig 2004; Lopez-Calderon and Luck 2014; Oostenveld et al. 2011). It trains support vector machines (SVMs) on patterns of event-related potential (ERP) amplitude data, following or preceding an event of interest, for classification or regression of experimental variables...
May 2, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29705977/new-features-for-neuron-classification
#12
Leonardo A Hernández-Pérez, Duniel Delgado-Castillo, Rainer Martín-Pérez, Rubén Orozco-Morales, Juan V Lorenzo-Ginori
This paper addresses the problem of obtaining new neuron features capable of improving results of neuron classification. Most studies on neuron classification using morphological features have been based on Euclidean geometry. Here three one-dimensional (1D) time series are derived from the three-dimensional (3D) structure of neuron instead, and afterwards a spatial time series is finally constructed from which the features are calculated. Digitally reconstructed neurons were separated into control and pathological sets, which are related to three categories of alterations caused by epilepsy, Alzheimer's disease (long and local projections), and ischemia...
April 28, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29691798/gpu-accelerated-browser-for-neuroimaging-genomics
#13
Bob Zigon, Huang Li, Xiaohui Yao, Shiaofen Fang, Mohammad Al Hasan, Jingwen Yan, Jason H Moore, Andrew J Saykin, Li Shen
Neuroimaging genomics is an emerging field that provides exciting opportunities to understand the genetic basis of brain structure and function. The unprecedented scale and complexity of the imaging and genomics data, however, have presented critical computational bottlenecks. In this work we present our initial efforts towards building an interactive visual exploratory system for mining big data in neuroimaging genomics. A GPU accelerated browsing tool for neuroimaging genomics is created that implements the ANOVA algorithm for single nucleotide polymorphism (SNP) based analysis and the VEGAS algorithm for gene-based analysis, and executes them at interactive rates...
April 25, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29644547/sacmda-mirna-disease-association-prediction-with-short-acyclic-connections-in-heterogeneous-graph
#14
Biyao Shao, Bingtao Liu, Chenggang Yan
MiRNA-disease association is important to disease diagnosis and treatment. Prediction of miRNA-disease associations is receiving increasing attention. Using the huge number of known databases to predict potential associations between miRNAs and diseases is an important topic in the field of biology and medicine. In this paper, we propose a novel computational method of with Short Acyclic Connections in Heterogeneous Graph (SACMDA). SACMDA obtains AUCs of 0.8770 and 0.8368 during global and local leave-one-out cross validation, respectively...
April 11, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29796969/wilfrid-rall
#15
EDITORIAL
Gordon M Shepherd
No abstract text is available yet for this article.
April 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29704208/neuroimaging-neuroinformatics-sample-size-and-other-evolutionary-topics
#16
EDITORIAL
David N Kennedy
No abstract text is available yet for this article.
April 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29594711/validation-and-optimization-of-bianca-for-the-segmentation-of-extensive-white-matter-hyperintensities
#17
Yifeng Ling, Eric Jouvent, Louis Cousyn, Hugues Chabriat, François De Guio
White matter hyperintensities (WMH) are a hallmark of small vessel diseases (SVD). Yet, no automated segmentation method is readily and widely used, especially in patients with extensive WMH where lesions are close to the cerebral cortex. BIANCA (Brain Intensity AbNormality Classification Algorithm) is a new fully automated, supervised method for WMH segmentation. In this study, we optimized and compared BIANCA against a reference method with manual editing in a cohort of patients with extensive WMH. This was achieved in two datasets: a clinical protocol with 90 patients having 2-dimensional FLAIR and an advanced protocol with 66 patients having 3-dimensional FLAIR...
April 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29564729/fast-accurate-and-stable-feature-selection-using-neural-networks
#18
James Deraeve, William H Alexander
Multi-voxel pattern analysis often necessitates feature selection due to the high dimensional nature of neuroimaging data. In this context, feature selection techniques serve the dual purpose of potentially increasing classification accuracy and revealing sets of features that best discriminate between classes. However, feature selection techniques in current, widespread use in the literature suffer from a number of deficits, including the need for extended computational time, lack of consistency in selecting features relevant to classification, and only marginal increases in classifier accuracy...
April 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29516302/optimal-model-parameter-estimation-from-eeg-power-spectrum-features-observed-during-general-anesthesia
#19
Meysam Hashemi, Axel Hutt, Laure Buhry, Jamie Sleigh
Mathematical modeling is a powerful tool that enables researchers to describe the experimentally observed dynamics of complex systems. Starting with a robust model including model parameters, it is necessary to choose an appropriate set of model parameters to reproduce experimental data. However, estimating an optimal solution of the inverse problem, i.e., finding a set of model parameters that yields the best possible fit to the experimental data, is a very challenging problem. In the present work, we use different optimization algorithms based on a frequentist approach, as well as Monte Carlo Markov Chain methods based on Bayesian inference techniques to solve the considered inverse problems...
April 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29508123/a-bit-encoding-based-new-data-structure-for-time-and-memory-efficient-handling-of-spike-times-in-an-electrophysiological-setup
#20
Bengt Ljungquist, Per Petersson, Anders J Johansson, Jens Schouenborg, Martin Garwicz
Recent neuroscientific and technical developments of brain machine interfaces have put increasing demands on neuroinformatic databases and data handling software, especially when managing data in real time from large numbers of neurons. Extrapolating these developments we here set out to construct a scalable software architecture that would enable near-future massive parallel recording, organization and analysis of neurophysiological data on a standard computer. To this end we combined, for the first time in the present context, bit-encoding of spike data with a specific communication format for real time transfer and storage of neuronal data, synchronized by a common time base across all unit sources...
April 2018: Neuroinformatics
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