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ORCIDFrontiers 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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