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Frontiers in Neuroinformatics, Volume 8
Volume 8, 2014
- Michael Wibral
, Joseph T. Lizier
, Sebastian Vögler, Viola Priesemann
, Ralf Galuske:
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
, Hans J. Johnson
, Martin Andreas Styner:
DTIPrep: quality control of diffusion-weighted images. 4 - Izabela M. Zakiewicz, Jan G. Bjaalie
, Trygve B. Leergaard
:
Brain-wide map of efferent projections from rat barrel cortex. 5 - Marcel Stimberg
, Dan F. M. Goodman, Victor Benichoux, Romain Brette
:
Equation-oriented specification of neural models for simulations. 6 - Jiahui Wang, Clement Vachet
, Ashley Rumple, Sylvain Gouttard, Clementine Ouziel, Emilie Perrot, Guangwei Du, Xuemei Huang, Guido Gerig
, Martin Andreas Styner:
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
, Joseph Troy Lizier
, Michael Schaum, Patricia Wollstadt
, Christine Grützner, Peter Uhlhaas
, Christine M. Freitag
, Sabine Schlitt, Sven Bölte
, Roberto Hornero
, Michael Wibral
:
Reduced predictable information in brain signals in autism spectrum disorder. 9 - Samuel Garcia
, Domenico Guarino
, Florent Jaillet
, Todd R. Jennings, Robert Pröpper, Philipp L. Rautenberg, Chris C. Rodgers
, Andrey Sobolev, Thomas Wachtler
, Pierre Yger
, Andrew P. Davison
:
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
, Satoshi Hirose, Hiroyuki Wada, Yoshio Imai, Toru Machida, Ichiro Shirouzu, Seiki Konishi, Yasushi Miyashita
, Naoki Masuda
:
Energy landscapes of resting-state brain networks. 12 - Matthew McCormick
, Xiaoxiao Liu, Luis Ibáñez, Julien Jomier, Charles Marion:
ITK: enabling reproducible research and open science. 13 - Alexandre Abraham, Fabian Pedregosa, Michael Eickenberg, Philippe Gervais, Andreas Mueller, Jean Kossaifi
, Alexandre Gramfort
, Bertrand Thirion, Gaël Varoquaux
:
Machine learning for neuroimaging with scikit-learn. 14 - Andrey Sobolev, Adrian Stoewer, Michael Pereira
, Christian Johannes Kellner
, Christian Garbers, Philipp L. Rautenberg, Thomas Wachtler
:
Data management routines for reproducible research using the G-Node Python Client library. 15 - Segundo Jose Guzman
, Alois Schlögl
, Christoph Schmidt-Hieber
:
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
, Anne B. Newman, Eleanor M. Simonsick, Dane R. Van Domelen, Fridtjof Thomas
, Kristine Yaffe, Caterina Rosano:
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
, Petr Bruha
, Petr Jezek
, Pavel Mautner, Jiri Novotny, Václav Papez, Tomás Prokop, Tomás Rondík, Jan Stebeták, Lukás Vareka:
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
, Paul Dufort, Mattias Villani, Stephen LaConte:
BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs. 24 - Hauke Bartsch
, Wesley K. Thompson, Terry L. Jernigan, Anders M. Dale:
A web-portal for interactive data exploration, visualization, and hypothesis testing. 25 - Mufti Mahmud
, Rocco Pulizzi, Eleni Vasilaki
, Michele Giugliano
:
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
, Ben Jeurissen
, Daniele Perrone, Jan Aelterman, Alexander Leemans
, Wilfried Philips, Jan Sijbers
:
Isotropic non-white matter partial volume effects in constrained spherical deconvolution. 28 - Jingyu Liu
, Vince D. Calhoun
:
A review of multivariate analyses in imaging genetics. 29 - Wojtek Goscinski
, Paul McIntosh
, Ulrich Claus Felzmann, Anton Maksimenko, Christopher Hall, Timur Gureyev
, Darren Thompson
, Andrew L. Janke
, Graham J. Galloway
, Neil E. B. Killeen, Parnesh Raniga
, Owen Kaluza
, Amanda Ng, Govinda R. Poudel
, David G. Barnes
, Toàn D. Nguyên, C. Paul Bonnington
, Gary F. Egan
:
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
, Gaël Varoquaux
, Goetz Brasche, Patricia J. Conrod, Hervé Lemaître, Tomás Paus, Marcella Rietschel, Vincent Frouin, Jean-Baptiste Poline, Gabriel Antoniu, Bertrand Thirion:
Generic Machine Learning Pattern for Neuroimaging-Genetic Studies in the Cloud. 31 - Andrey Sobolev, Adrian Stoewer, Aljoscha Pascal Leonhardt
, Philipp L. Rautenberg, Christian Johannes Kellner
, Christian Garbers, Thomas Wachtler
:
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
, Ryan Kennedy, Stephen M. Plaza, Anirban Chakraborty, William T. Katz
:
Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages. 34 - Anand D. Sarwate
, Sergey M. Plis
, Jessica A. Turner
, Mohammad Arbabshirani, Vince D. Calhoun
:
Sharing privacy-sensitive access to neuroimaging and genetics data: a review and preliminary validation. 35 - Michael Marmaduke Woodman
, Laurent Pezard, Lia Domide, Stuart Knock, Paula Leon
, Jochen Mersmann, Anthony Randal McIntosh
, Viktor K. Jirsa
:
Integrating neuroinformatics tools in TheVirtualBrain. 36 - Weiliang Chen
, Erik De Schutter:
Python-based geometry preparation and simulation visualization toolkits for STEPS. 37 - Michael Vella, Robert C. Cannon, Sharon M. Crook, Andrew P. Davison
, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver, Padraig Gleeson
:
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
, Judith Savitskaya, Shawn D. Burton
, Nathaniel N. Urban
, Richard C. Gerkin
:
NeuroElectro: a window to the world's neuron electrophysiology data. 40 - Ivo D. Dinov
, Petros Petrosyan, Zhizhong Liu, Paul R. Eggert, Sam Hobel, Seok Woo Moon, John D. Van Horn, Joe Franco, Arthur W. Toga:
High-throughput neuroimaging-genetics computational infrastructure. 41 - Claudia Hänel, Peter Pieperhoff, Bernd Hentschel, Katrin Amunts
, Torsten W. Kuhlen:
Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome. 42 - Mikael Djurfeldt, Andrew P. Davison
, Jochen Martin Eppler:
Efficient generation of connectivity in neuronal networks from simulator-independent descriptions. 43 - Brian B. Avants
, Nicholas J. Tustison
, James C. Gee, Gang Song, Baohua Wu, Michael Stauffer:
The Insight ToolKit image registration framework. 44 - Martin Luessi, S. Derin Babacan, Rafael Molina
, James R. Booth, Aggelos K. Katsaggelos
:
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
, Steven M. Hodge
, Jean A. Frazier, David N. Kennedy:
Structure-centered portal for child psychiatry research. 47 - Sukhbinder Kumar
, William D. Penny:
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
, Matilde Leonardi, Ludovico D'Incerti, Ludovico Minati:
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
, Jean-Baptiste Poline, David N. Kennedy:
A simple tool for neuroimaging data sharing. 52 - David A. Gutman, William D. Dunn, Jake Cobb, Richard Martin Stoner, Jayashree Kalpathy-Cramer
, Bradley J. Erickson:
Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer. 53 - Tarek Sherif, Pierre Rioux, Marc-Etienne Rousseau
, Nicolas Kassis, Natacha Beck, Reza Adalat, Samir Das, Tristan Glatard, Alan C. Evans
:
CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. 54 - Philipp L. Rautenberg, Ajayrama Kumaraswamy
, Álvaro Tejero-Cantero, Christoph Doblander, Mohammad Norouzian, Kazuki Kai, Hans-Arno Jacobsen, Hiroyuki Ai
, Thomas Wachtler
, Hidetoshi Ikeno
:
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
, Payam Saisan:
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
, Hisako Fujiwara, Nat Hemasilpin, Douglas F. Rose:
Accumulated source imaging of brain activity with both low and high-frequency neuromagnetic signals. 57 - Luis N. Marenco, Rixin Wang, Anita E. Bandrowski
, Jeffrey S. Grethe
, Gordon M. Shepherd, Perry L. Miller:
Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. 58 - Maxime Chamberland
, Kevin Whittingstall, David Mathieu
, David Fortin, Maxime Descoteaux:
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
, Vince D. Calhoun
:
Automated collection of imaging and phenotypic data to centralized and distributed data repositories. 60 - Daniel P. Holschneider
, Zhuo Wang
, Raina D. Pang:
Functional connectivity-based parcellation and connectome of cortical midline structures in the mouse: a perfusion autoradiography study. 61 - Janna Hastings
, Gwen A. Frishkoff, Barry Smith
, Mark Jensen, Russell A. Poldrack
, Jane Lomax
, Anita E. Bandrowski
, Fahim T. Imam
, Jessica A. Turner, Maryann E. Martone
:
Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. 62 - Péter Friedrich, Michael Vella, Attila I. Gulyás
, Tamás F. Freund, Szabolcs Káli:
A flexible, interactive software tool for fitting the parameters of neuronal models. 63 - Daniel Chicharro
, Stefano Panzeri
:
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
, Martijn P. van den Heuvel
, Alessandra Griffa
, Patric Hagmann, Luis M. Rocha
, Olaf Sporns
, Joaquín Goñi:
Multi-scale integration and predictability in resting state brain activity. 66 - Miriam Friedel, Matthijs C. van Eede, Jon Pipitone
, M. Mallar Chakravarty, Jason P. Lerch:
Pydpiper: a flexible toolkit for constructing novel registration pipelines. 67 - Stephan Grein
, Martin Stepniewski, Sebastian Reiter, Markus M. Knodel
, Gillian Queisser:
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
, Vince D. Calhoun
:
Harnessing modern web application technology to create intuitive and efficient data visualization and sharing tools. 71 - Daniela Adolf, Snezhana Weston, Sebastian Baecke, Michael Luchtmann
, Johannes Bernarding, Siegfried Kropf:
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
, Giacomo Indiveri
:
PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems. 73 - Ilya Zaslavsky, Richard A. Baldock
, Jyl Boline:
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
, Wulfram Gerstner
:
Limits to high-speed simulations of spiking neural networks using general-purpose computers. 76 - Susanne Kunkel
, Maximilian Schmidt
, Jochen Martin Eppler, Hans Ekkehard Plesser, Gen Masumoto
, Jun Igarashi
, Shin Ishii
, Tomoki Fukai
, Abigail Morrison
, Markus Diesmann
, Moritz Helias
:
Spiking network simulation code for petascale computers. 78 - Robert C. Cannon, Padraig Gleeson
, Sharon M. Crook, Gautham Ganapathy, Bóris Marin
, Eugenio Piasini
, R. Angus Silver:
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. 79 - Patrick Kaifosh
, Jeffrey Zaremba
, Nathan Danielson
, Attila Losonczy:
SIMA: Python software for analysis of dynamic fluorescence imaging data. 80 - Christian Haselgrove
, Jean-Baptiste Poline, David N. Kennedy:
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
, Björn Kampa
:
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
, Daniele Marinazzo
, Miguel Ángel Muñoz:
Editorial for the research topic: information-based methods for neuroimaging: analyzing structure, function and dynamics. 86 - Luca Dodero, Sebastiano Vascon
, Vittorio Murino
, Angelo Bifone, Alessandro Gozzi
, Diego Sona
:
Automated multi-subject fiber clustering of mouse brain using dominant sets. 87 - Martin N. Hebart
, Kai Görgen
, John-Dylan Haynes
:
The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data. 88 - Tarek Sherif, Nicolas Kassis, Marc-Etienne Rousseau
, Reza Adalat, Alan C. Evans
:
BrainBrowser: distributed, web-based neurological data visualization. 89 - Rhodri Cusack
, Alejandro Vicente-Grabovetsky, Daniel J. Mitchell
, Conor James Wild
, Tibor Auer
, Annika C. Linke, Jonathan E. Peelle
:
Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML. 90
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