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Neurophysiological Biomarker Toolbox

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Template:Infobox software

The Neurophysiological Biomarker Toolbox (NBT) is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers (e.g., biomarkers based on EEG or MEG recordings).[1] The NBT toolbox has so far been used in three peer-reviewed research articles, and has a broad user base of more than 340 users. The NBT toolbox provides unique features for analysis of resting-state EEG or MEG recordings. NBT offers a pipeline from data storage to statistics including artifact rejection, signal visualization, biomarker computation, statistical testing, and biomarker databasing. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki (the NBTwiki[2]) that aims at facilitating collaboration among NBT users including extensive help and tutorials. The standardised way of data storage and analysis that NBT proposes allow different research projects to merge, compare, or share their data and biomarker algorithms.[3]

Features Edit

Neuronal oscillations are generated at many spatial and temporal scales of neuronal organization, and thought to provide a network-level mechanism for the coordination of spatio-temporally distributed spiking activity. For an adequate understanding of quantitative changes in neurophysiological signals, such as electroencephalography (EEG) or magnetoencephalography (MEG), as a consequence of disease, experimental manipulations, or genetic variability there is a need to apply multiple biomarker algorithms.

The aim of the NBT toolbox is to make biomarker research easier at all levels. From having raw data, cleaning it, calculating biomarkers, to performing advanced statistics.

The NBT toolbox includes biomarkers, such as:

The toolbox has a standard template for how biomarkers should be implemented, which makes it relatively easy to implement new biomarkers. Originally the toolbox was aimed at biomarkers based on EEG or MEG signals, recently however the toolbox has moved towards supporting almost any type of biomarker data.

The biomarker data and associated meta information is stored in a Matlab based database; the NBT elements database.

The NBT toolbox works as a plugin to the open-source Matlab toolbox EEGLAB

HistoryEdit

The development of the NBT toolbox was started in 2008 by Simon-Shlomo Poil and Klaus Linkenkaer-Hansen from the VU University Amsterdam. Later the developer team was joined by Rick Jansen, Richard Hardstone, and Giuseppina Schiavone. The toolbox has also received contributions from many other people.

The toolbox and its associated tutorial website has served as a major part of courses at the VU University Amsterdam; such as, the Human Neurophysiology course (with on average 100 students each year), and the advanced human neurophysiology.

18. April 2012 the first public release of the toolbox was made (release candidate R1). The toolbox has been downloaded more than 590 times (April 2013).[4] The most recent public version of the NBT toolbox is RC3b (released 2 August 2013)[5] .

Scientific publications using the NBT toolboxEdit

  • O'Gorman et al., Coupling Between Resting Cerebral Perfusion and EEG, Brain Topography, 2012 [6]
  • Hardstone et al., Detrended fluctuation analysis: A scale-free view on neuronal oscillations, Frontiers in Fractal Physiology, 2012 [3]

See alsoEdit

Other open-source toolboxes for analysis of M/EEG recordings:

  • Fieldtrip

ReferencesEdit

  1. Poil, Simon-Shlomo (2013). Neurophysiological Biomarkers of cognitive decline: from criticality to toolbox.
  2. (2012). NBTwiki.net. NBTwiki.net. URL accessed on 2013-07-21.
  3. 3.0 3.1 3.2 Hardstone, Richard, Poil, Simon-Shlomo; Schiavone, Giuseppina; Jansen, Rick; Nikulin, Vadim V.; Mansvelder, Huibert D.; Linkenkaer-Hansen, Klaus (1 January 2012). Detrended Fluctuation Analysis: A Scale-Free View on Neuronal Oscillations. Frontiers in Physiology 3.
  4. Poil, Simon-Shlomo One year release birthday of NBT. poil.dk. URL accessed on 22 July 2013.
  5. Error on call to template:cite web: Parameters url and title must be specified URL accessed on 2 August 2013.
  6. O'Gorman, RL, Poil, SS; Brandeis, D; Klaver, P; Bollmann, S; Ghisleni, C; Lüchinger, R; Martin, E; Shankaranarayanan, A; Alsop, DC; Michels, L (2013 Jul). Coupling between resting cerebral perfusion and EEG.. Brain topography 26 (3): 442–57.


[[Category:|Electrophysiology software]]
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