icaOcularCorrection: Independent Components Analysis (ICA) based artifact correction.

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Removes eye-movement and other types of known (i.e., recorded) or unknown (i.e., not recorded) artifacts using the fastICA package. The correction method proposed in this package is largely based on the method described in on Flexer, Bauer, Pripfl, and Dorffner (2005). The process of correcting electro- and magneto-encephalographic data (EEG/MEG) begins by running function ``icac'', which first performs independent components analysis (ICA) to decompose the data frame into independent components (ICs) using function ``fastICA'' from the package of the same name. It then calculates for each trial the correlation between each IC and each one of the noise signals -- there can be one or more, e.g., vertical and horizontal electro-oculograms (VEOG and HEOG), electro-myograms (EMG), electro-cardiograms (ECG), galvanic skin responses (GSR), and other noise signals. Subsequently, portions of an IC corresponding to trials at which the correlation between it and a noise signal was at or above threshold (set to 0.4 by default; Flexer et al., 2005, p. 1001) are zeroed-out in the source matrix, ``S''. The user can then identify which ICs correlate with the noise signals the most by looking at the summary of the ``icac'' object (using function ``summary.icac''), the scalp topography of the ICs (using function ``topo_ic''), the time courses of the ICs (using functions ``plot_tric'' and ``plot_nic''), and other diagnostic plots. Once these ICs have been identified, they can be completely zeroed-out using function ``update.icac'' and the resulting correction checked using functions ``plot_avgba'' and ``plot_trba''. Some worked-out examples with R code are provided in the package vignette.

Author
Antoine Tremblay, NeuroCognitive Imaging Lab, Dalhousie University
Date of publication
2013-07-12 18:51:58
Maintainer
Antoine Tremblay <trea26@gmail.com>
License
GPL-2
Version
3.0.0

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Man pages

get.peaks
Get the time value of one or more peaks.
icac
ICA noise correction.
icaOcularCorrection-package
Independent Components Analysis (ICA) based eye-movement...
mwd.thrsh
Multiple wavelet decomposition thresholding.
plot_avgba
Plot the average waveforms at each channel before and after...
plot_nic
Plot an independent component with superimposed noise signal...
plot_trba
Plot the corrected and uncorrected time course at a specific...
plot_tric
Plot the time course of an independent component at each...
summary.icac
Print and/or return the correction summary of an "icac"...
topo_ic
Plot the topographic map of an independent component.
update.icac
Update the correction performed by function 'icac'.

Files in this package

icaOcularCorrection
icaOcularCorrection/MD5
icaOcularCorrection/vignettes
icaOcularCorrection/vignettes/vignette.Rnw
icaOcularCorrection/vignettes/uncorrectedCorrected5.pdf
icaOcularCorrection/vignettes/uncorrectedCorrected3.pdf
icaOcularCorrection/vignettes/uncorrectedCorrected12.pdf
icaOcularCorrection/vignettes/uncorrectedCorrected0.pdf
icaOcularCorrection/vignettes/topomapIC6.pdf
icaOcularCorrection/vignettes/topomapIC52.pdf
icaOcularCorrection/vignettes/topomapIC43.pdf
icaOcularCorrection/vignettes/smryEGI129IC6.rda
icaOcularCorrection/vignettes/smryEGI129IC52.rda
icaOcularCorrection/vignettes/smryEGI129IC43.rda
icaOcularCorrection/vignettes/smryEGI129.rda
icaOcularCorrection/vignettes/plotNICIC6E126.pdf
icaOcularCorrection/vignettes/plotNICIC52E14.pdf
icaOcularCorrection/vignettes/plotNICIC43E21.pdf
icaOcularCorrection/vignettes/beforeAfter5IC.pdf
icaOcularCorrection/vignettes/ICNumTrials5.pdf
icaOcularCorrection/vignettes/ICNumTrials3.pdf
icaOcularCorrection/vignettes/ICNumTrials12.pdf
icaOcularCorrection/vignettes/IC6E126.pdf
icaOcularCorrection/vignettes/IC52E14.pdf
icaOcularCorrection/vignettes/IC43E21.pdf
icaOcularCorrection/vignettes/EEGLABvsICAocularCorrection.pdf
icaOcularCorrection/vignettes/EEGLABuncorrectedCorrected.pdf
icaOcularCorrection/man
icaOcularCorrection/man/update.icac.Rd
icaOcularCorrection/man/topo_ic.Rd
icaOcularCorrection/man/summary.icac.Rd
icaOcularCorrection/man/plot_tric.Rd
icaOcularCorrection/man/plot_trba.Rd
icaOcularCorrection/man/plot_nic.Rd
icaOcularCorrection/man/plot_avgba.Rd
icaOcularCorrection/man/mwd.thrsh.Rd
icaOcularCorrection/man/icac.Rd
icaOcularCorrection/man/icaOcularCorrection-package.Rd
icaOcularCorrection/man/get.peaks.Rd
icaOcularCorrection/inst
icaOcularCorrection/inst/doc
icaOcularCorrection/inst/doc/vignette.pdf
icaOcularCorrection/inst/doc/vignette.Rnw
icaOcularCorrection/inst/doc/vignette.R
icaOcularCorrection/R
icaOcularCorrection/R/update.icac.R
icaOcularCorrection/R/topo_ic.R
icaOcularCorrection/R/summary.icac.R
icaOcularCorrection/R/plot_tric.R
icaOcularCorrection/R/plot_trba.R
icaOcularCorrection/R/plot_nic.R
icaOcularCorrection/R/plot_avgba.R
icaOcularCorrection/R/mwd.thrsh.R
icaOcularCorrection/R/icac.R
icaOcularCorrection/R/get.peaks.R
icaOcularCorrection/NEWS
icaOcularCorrection/NAMESPACE
icaOcularCorrection/DESCRIPTION