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Frontiers in Neuroinformatics, Volume 8
Volume 8, 2014
- Michael Wibral
, Joseph T. Lizier
Local active information storage as a tool to understand distributed neural information processing. 1 - Jukka-Pekka Kauppi, Juha Pajula, Jussi Tohka
A versatile software package for inter-subject correlation based analyses of fMRI. 2 - Luke Campagnola, Megan B. Kratz, Paul B. Manis
ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research. 3 - Ipek Oguz, Mahshid Farzinfar, Joy T. Matsui, François Budin, Zhexing Liu, Guido Gerig
DTIPrep: quality control of diffusion-weighted images. 4 - Izabela M. Zakiewicz, Jan G. Bjaalie
Brain-wide map of efferent projections from rat barrel cortex. 5 - Marcel Stimberg
Equation-oriented specification of neural models for simulations. 6 - Jiahui Wang, Clement Vachet
Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline. 7 - Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stéfan van der Walt, Maxime Descoteaux, Ian Nimmo-Smith:
Dipy, a library for the analysis of diffusion MRI data. 8 - Carlos Gómez
Reduced predictable information in brain signals in autism spectrum disorder. 9 - Samuel Garcia
Neo: an object model for handling electrophysiology data in multiple formats. 10 - Fotis Drakopoulos, Yixun Liu, Panagiotis A. Foteinos, Nikos P. Chrisochoides:
Toward a real time multi-tissue Adaptive Physics-Based Non-Rigid Registration framework for brain tumor resection. 11 - Takamitsu Watanabe
Energy landscapes of resting-state brain networks. 12 - Matthew McCormick
ITK: enabling reproducible research and open science. 13 - Alexandre Abraham, Fabian Pedregosa, Michael Eickenberg, Philippe Gervais, Andreas Mueller, Jean Kossaifi
Machine learning for neuroimaging with scikit-learn. 14 - Andrey Sobolev, Adrian Stoewer, Michael Pereira
Data management routines for reproducible research using the G-Node Python Client library. 15 - Segundo Jose Guzman
Stimfit: quantifying electrophysiological data with Python. 16 - Corey M. Thibeault, Michael John O'Brien, Narayan Srinivasa:
Analyzing large-scale spiking neural data with HRLAnalysis™. 17 - MeganOlson Hunt, Lisa A. Weissfeld, Robert Boudreau, Howard Aizenstein
A variant of sparse partial least squares for variable selection and data exploration. 18 - S. Y. Matt Goh, Andrei Irimia, Carinna M. Torgerson, John D. Van Horn:
Neuroinformatics challenges to the structural, connectomic, functional and electrophysiological multimodal imaging of human traumatic brain injury. 19 - Roman Moucek
Software and hardware infrastructure for research in electrophysiology. 20 - Sudeshna Das, Patricia G. Mccaffrey, Megan Talkington, Neil Andrews, Stephane Corlosquet, Adrian Ivinson, Tim Clark
Pain Research Forum: application of scientific social media frameworks in neuroscience. 21 - Martin Billinger, Clemens Brunner, Gernot R. Müller-Putz
SCoT: a Python toolbox for EEG source connectivity. 22 - Yury V. Zaytsev, Abigail Morrison
CyNEST: a maintainable Cython-based interface for the NEST simulator. 23 - Anders Eklund
BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs. 24 - Hauke Bartsch
A web-portal for interactive data exploration, visualization, and hypothesis testing. 25 - Mufti Mahmud
QSpike tools: a generic framework for parallel batch preprocessing of extracellular neuronal signals recorded by substrate microelectrode arrays. 26 - Yen-Nan Lin, Po-Yen Chang, Pao-Yueh Hsiao, Chung-Chuan Lo
Polarity-specific high-level information propagation in neural networks. 27 - Timo Roine
Isotropic non-white matter partial volume effects in constrained spherical deconvolution. 28 - Jingyu Liu
A review of multivariate analyses in imaging genetics. 29 - Wojtek Goscinski
The multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) high performance computing infrastructure: applications in neuroscience and neuroinformatics research. 30 - Benoit Da Mota, Radu Tudoran, Alexandru Costan
Generic Machine Learning Pattern for Neuroimaging-Genetic Studies in the Cloud. 31 - Andrey Sobolev, Adrian Stoewer, Aljoscha Pascal Leonhardt
Integrated platform and API for electrophysiological data. 32 - Yixun Liu, Andriy Kot, Fotis Drakopoulos, Chengjun Yao, Andriy Fedorov, Andinet Enquobahrie, Olivier Clatz, Nikos P. Chrisochoides:
An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery. 33 - Juan Nunez-Iglesias
Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages. 34 - Anand D. Sarwate
Sharing privacy-sensitive access to neuroimaging and genetics data: a review and preliminary validation. 35 - Michael Marmaduke Woodman
Integrating neuroinformatics tools in TheVirtualBrain. 36 - Weiliang Chen
Python-based geometry preparation and simulation visualization toolkits for STEPS. 37 - Michael Vella, Robert C. Cannon, Sharon M. Crook, Andrew P. Davison
libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. 38 - Nicolas Rey-Villamizar:
Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python. 39 - Shreejoy J. Tripathy
NeuroElectro: a window to the world's neuron electrophysiology data. 40 - Ivo D. Dinov
High-throughput neuroimaging-genetics computational infrastructure. 41 - Claudia Hänel, Peter Pieperhoff, Bernd Hentschel, Katrin Amunts
Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome. 42 - Mikael Djurfeldt, Andrew P. Davison
Efficient generation of connectivity in neuronal networks from simulator-independent descriptions. 43 - Brian B. Avants
The Insight ToolKit image registration framework. 44 - Martin Luessi, S. Derin Babacan, Rafael Molina
Variational Bayesian causal connectivity analysis for fMRI. 45 - Jeffrey T. Duda, Philip A. Cook, James C. Gee:
Reproducibility of graph metrics of human brain structural networks. 46 - Pallavi S. Rane, Christian Haselgrove
Structure-centered portal for child psychiatry research. 47 - Sukhbinder Kumar
Estimating Neural Response Functions from fMRI. 48 - Daniel Yasumasa Takahashi, Luiz A. Baccalá, Koichi Sameshima
Canonical information flow decomposition among neural structure subsets. 49 - Adrian Stefan Andronache, Cristina Rosazza, Davide Sattin
Corrigendum: Impact of functional MRI data preprocessing pipeline on default-mode network detectability in patients with disorders of consciousness. 50 - Andrew Zaldivar, Jeffrey L. Krichmar
Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool. 51 - Christian Haselgrove
A simple tool for neuroimaging data sharing. 52 - David A. Gutman, William D. Dunn, Jake Cobb, Richard Martin Stoner, Jayashree Kalpathy-Cramer
Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer. 53 - Tarek Sherif, Pierre Rioux, Marc-Etienne Rousseau
CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. 54 - Philipp L. Rautenberg, Ajayrama Kumaraswamy
NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications. 55 - Vishnu B. Sridhar, Peifang A. Tian, Anders M. Dale, Anna Devor
Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB® graphical user interface. 56 - Jing Xiang, Qian Luo, Rupesh Kotecha, Abraham Korman, Fawen Zhang, Huan Luo
Accumulated source imaging of brain activity with both low and high-frequency neuromagnetic signals. 57 - Luis N. Marenco, Rixin Wang, Anita E. Bandrowski
Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. 58 - Maxime Chamberland
Real-time multi-peak tractography for instantaneous connectivity display. 59 - Margaret D. King, Dylan Wood, Brittny Miller, Ross Kelly, William Courtney, Drew Landis, Runtang Wang, Jessica A. Turner
Automated collection of imaging and phenotypic data to centralized and distributed data repositories. 60 - Daniel P. Holschneider
Functional connectivity-based parcellation and connectome of cortical midline structures in the mouse: a perfusion autoradiography study. 61 - Janna Hastings
Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. 62 - Péter Friedrich, Michael Vella, Attila I. Gulyás
A flexible, interactive software tool for fitting the parameters of neuronal models. 63 - Daniel Chicharro
Algorithms of causal inference for the analysis of effective connectivity among brain regions. 64 - Rick Herrick, Michael McKay, Timothy R. Olsen, William Horton, Mark Florida, Charlie Moore, Daniel S. Marcus:
Data dictionary services in XNAT and the Human Connectome Project. 65 - Artemy Kolchinsky
Multi-scale integration and predictability in resting state brain activity. 66 - Miriam Friedel, Matthijs C. van Eede, Jon Pipitone
Pydpiper: a flexible toolkit for constructing novel registration pipelines. 67 - Stephan Grein
1D-3D hybrid modeling - from multi-compartment models to full resolution models in space and time. 68 - Moses O. Sokunbi
Sample entropy reveals high discriminative power between young and elderly adults in short fMRI data sets. 69 - Dejan Pecevski, David Kappel, Zeno Jonke:
NEVESIM: event-driven neural simulation framework with a Python interface. 70 - Dylan Wood, Margaret D. King, Drew Landis, William Courtney, Runtang Wang, Ross Kelly, Jessica A. Turner
Harnessing modern web application technology to create intuitive and efficient data visualization and sharing tools. 71 - Daniela Adolf, Snezhana Weston, Sebastian Baecke, Michael Luchtmann
Increasing the reliability of data analysis of functional magnetic resonance imaging by applying a new blockwise permutation method. 72 - Fabio Stefanini, Emre Neftci, Sadique Sheik
PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems. 73 - Ilya Zaslavsky, Richard A. Baldock
Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases. 74 - Roman Moucek
Corrigendum: Software and hardware infrastructure for research in electrophysiology. 75 - Friedemann Zenke
Limits to high-speed simulations of spiking neural networks using general-purpose computers. 76 - Susanne Kunkel
Spiking network simulation code for petascale computers. 78 - Robert C. Cannon, Padraig Gleeson
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. 79 - Patrick Kaifosh
SIMA: Python software for analysis of dynamic fluorescence imaging data. 80 - Christian Haselgrove
Comment on "A simple tool for neuroimaging data sharing". 82 - Carinna Margaret Torgerson, John Darrell Van Horn:
A case study in connectomics: the history, mapping, and connectivity of the claustrum. 83 - Sarah Katharina Schmitz, Philipp P. Hasselbach, Boris Ebisch, Anja Klein, Gordon Pipa, Ralf A. W. Galuske:
Application of Parallel Factor Analysis (PARAFAC) to electrophysiological data. 84 - Dylan Richard Muir
FocusStack and StimServer: A new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data. 85 - Jesús M. Cortés
Editorial for the research topic: information-based methods for neuroimaging: analyzing structure, function and dynamics. 86 - Luca Dodero, Sebastiano Vascon
Automated multi-subject fiber clustering of mouse brain using dominant sets. 87 - Martin N. Hebart
The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data. 88 - Tarek Sherif, Nicolas Kassis, Marc-Etienne Rousseau
BrainBrowser: distributed, web-based neurological data visualization. 89 - Rhodri Cusack
Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML. 90
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