% Encoding: UTF-8
%
% If available, include a DOI (preferred) *or* a URL for a given reference, but
# not both, as the DOI turns into a link which is redundant with the URL.

% MNE-C reference
@article{GramfortEtAl2014,
  title = {{{MNE}} Software for Processing {{MEG}} and {{EEG}} Data},
  author = {Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis A. and Strohmeier, Daniel and Brodbeck, Christian and Parkkonen, Lauri and H{\"a}m{\"a}l{\"a}inen, Matti S.},
  year = {2014},
  volume = {86},
  pages = {446--460},
  doi = {10.1016/j.neuroimage.2013.10.027},
  journal = {NeuroImage},
}
% MNE-Python reference
@article{GramfortEtAl2013a,
  title = {{{MEG}} and {{EEG}} Data Analysis with {{MNE}}-{{Python}}},
  author = {Gramfort, Alexandre and Luessi, Martin and Larson, Eric and Engemann, Denis A. and Strohmeier, Daniel and Brodbeck, Christian and Goj, Roman and Jas, Mainak and Brooks, Teon and Parkkonen, Lauri and H{\"a}m{\"a}l{\"a}inen, Matti S.},
  year = {2013},
  volume = {7},
  pages = {1--13},
  doi = {10.3389/fnins.2013.00267},
  journal = {Frontiers in Neuroscience},
  number = {267}
}
% everything else
@article{AblinEtAl2018,
  author = {Ablin, Pierre and Cardoso, Jean-Francois and Gramfort, Alexandre},
  doi = {10.1109/TSP.2018.2844203},
  journal = {IEEE Transactions on Signal Processing},
  number = {15},
  pages = {4040-4049},
  title = {Faster {{Independent Component Analysis}} by Preconditioning with Hessian Approximations},
  volume = {66},
  year = {2018}
}

@article{AcunzoEtAl2012,
  author = {Acunzo, David J. and MacKenzie, Graham and {van Rossum}, Mark C.W.},
  doi = {10.1016/j.jneumeth.2012.06.011},
  journal = {Journal of Neuroscience Methods},
  number = {1},
  pages = {212-218},
  title = {Systematic Biases in Early {{ERP}} and {{ERF}} Components as a Result of High-Pass Filtering},
  volume = {209},
  year = {2012}
}

@article{Alday2019,
  title = {How much baseline correction do we need in {ERP} research? Extended {GLM} model can replace baseline correction while lifting its limits},
  author = {Alday, Phillip M.},
  year = {2019},
  volume = {56},
  doi = {10.1111/psyp.13451},
  journal = {Psychophysiology},
  number = {12}
}

@article{ArtoniEtAl2018,
  author = {Artoni, Fiorenzo and Delorme, Arnaud and Makeig, Scott},
  doi = {10.1016/j.neuroimage.2018.03.016},
  journal = {NeuroImage},
  pages = {176-187},
  title = {Applying Dimension Reduction to {{EEG}} Data by {{Principal Component Analysis}} Reduces the Quality of Its Subsequent {{Independent Component}} Decomposition},
  volume = {175},
  year = {2018}
}

@article{AvantsEtAl2008,
  author = {Avants, Brian B. and Epstein, Charles L. and Grossman, Murray C. and Gee, James C.},
  doi = {10.1016/j.media.2007.06.004},
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  number = {1},
  pages = {26-41},
  shorttitle = {Symmetric Diffeomorphic Image Registration with Cross-Correlation},
  title = {Symmetric Diffeomorphic Image Registration with Cross-Correlation: Evaluating Automated Labeling of Elderly and Neurodegenerative Brain},
  volume = {12},
  year = {2008}
}

@article{BailletEtAl2001,
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  pages = {14-30},
  title = {Electromagnetic Brain Mapping},
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  year = {2001}
}

@inproceedings{BarachantEtAl2010,
  author = {Barachant, Alexandre and Bonnet, Stephane and Congedo, Marco and Jutten, Christian},
  booktitle = {2010 IEEE International Workshop on Multimedia Signal Processing},
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  year = {2010},
  pages={472-476},
  doi = {10.1109/MMSP.2010.5662067}
}

@book{Barber2012,
  address = {{Cambridge}},
  author = {Barber, David},
  isbn = {978-0-521-51814-7},
  publisher = {{Cambridge University Press}},
  title = {Bayesian Reasoning and Machine Learning},
  url = {http://www.cs.ucl.ac.uk/staff/d.barber/brml/},
  year = {2012}
}

@inproceedings{BekhtiEtAl2016,
  address = {{Trento}},
  author = {Bekhti, Yousra and Strohmeier, Daniel and Jas, Mainak and Badeau, Roland and Gramfort, Alexandre},
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  doi = {10.1109/PRNI.2016.7552337},
  isbn = {978-1-4673-6530-7},
  pages = {1-4},
  publisher = {{IEEE}},
  title = {M/{{EEG}} Source Localization with Multi-Scale Time-Frequency Dictionaries},
  year = {2016}
}

@article{BellSejnowski1995,
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}

@article{BergScherg1994,
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}

@inproceedings{BigdelyShamloEtAl2013,
  author = {Bigdely-Shamlo, Nima and Kreutz-Delgado, Kenneth and Robbins, Kay and Miyakoshi, Makoto and Westerfield, Marissa and Bel-Bahar, Tarik and Kothe, Christian and Hsi, Jessica and Makeig, Scott},
  doi = {10.1109/GlobalSIP.2013.6736796},
  booktitle = {2013 IEEE Global Conference on Signal and Information Processing},
  pages = {1--4},
  title = {Hierarchical event descriptor {(HED)} tags for analysis of event-related {EEG} studies},
  organization = {IEEE},
  year = {2013},
}

@article{BlankertzEtAl2008,
  author = {Blankertz, Benjamin and Tomioka, Ryota and Lemm, Steven and Kawanabe, Motoaki and Müller, Klaus-Robert},
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  journal = {IEEE Signal Processing Magazine},
  number = {1},
  pages = {41-56},
  title = {Optimizing Spatial Filters for Robust {{EEG}} Single-Trial Analysis},
  volume = {25},
  year = {2008}
}

@article{Bookstein1989,
  author = {Bookstein, Fred L.},
  doi = {10.1109/34.24792},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  number = {6},
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}

@article{BrookesEtAl2008,
  author = {Brookes, Matthew J. and Vrba, Jiri and Robinson, Stephen E. and Stevenson, Claire M. and Peters, Andrew M. and Barnes, Gareth R. and Hillebrand, Arjan and Morris, Peter G.},
  doi = {10.1016/j.neuroimage.2007.09.050},
  journal = {NeuroImage},
  number = {4},
  pages = {1788-1802},
  title = {Optimising Experimental Design for {{MEG}} Beamformer Imaging},
  volume = {39},
  year = {2008}
}

@article{BrunaEtAl2018,
  doi = {10.1088/1741-2552/aacfe4},
  year = {2018},
  publisher = {{IOP} Publishing},
  volume = {15},
  number = {5},
  pages = {056011},
  author = {Ricardo Bru{\~{n}}a, Fernando Maest{\'{u}}, Ernesto Pereda},
  title = {Phase locking value revisited: teaching new tricks to an old dog},
  journal = {Journal of Neural Engineering},
}

@techreport{BurdakovMerkulov2001,
  title={On a new norm for data fitting and optimization problems},
  author={Burdakov, Oleg and Merkulov, Boris},
  number={LiTH-MAT-R-2001-29},
  address={Link{\"o}ping},
  institution={Link{\"o}ping University},
  type = {Technical {{Report}}},
  year={2001}
}

@article{CamposViolaEtAl2009,
  author = {Campos Viola, Filipa and Thorne, Jeremy and Edmonds, Barrie and Schneider, Till and Eichele, Tom and Debener, Stefan},
  doi = {10.1016/j.clinph.2009.01.015},
  journal = {Clinical Neurophysiology},
  number = {5},
  pages = {868-877},
  title = {Semi-Automatic Identification of Independent Components Representing {{EEG}} Artifact},
  volume = {120},
  year = {2009}
}

@article{ChambonEtAl2018,
  author = {Chambon, Stanislas and Galtier, Mathieu N. and Arnal, Pierrick J. and Wainrib, Gilles and Gramfort, Alexandre},
  doi = {10.1109/TNSRE.2018.2813138},
  journal = {IEEE Transactions on Neural Systems and Rehabilitation Engineering},
  number = {4},
  pages = {758-769},
  title = {A Deep Learning Architecture for Temporal Sleep Stage Classification Using Multivariate and Multimodal Time Series},
  volume = {26},
  year = {2018}
}

@article{ChenEtAl2010,
  author = {Chen, Yilun and Wiesel, Ami and Eldar, Yonina C. and Hero, Alfred O.},
  doi = {10.1109/TSP.2010.2053029},
  journal = {IEEE Transactions on Signal Processing},
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  year = {2010}
}

@article{CichyEtAl2014,
  author = {Cichy, Radoslaw Martin and Pantazis, Dimitrios and Oliva, Aude},
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}

@book{Cohen2014,
  place={Cambridge, MA},
  title={Analyzing Neural Time Series Data: Theory and Practice},
  publisher={MIT Press},
  author={Cohen, Mike X.},
  year={2014}
}

@article{Cohen2019,
  author={Cohen, Michael X},
  doi = {10.1016/j.neuroimage.2019.05.048},
  journal = {NeuroImage},
  pages = {81-86},
  title = {A better way to define and describe {Morlet} wavelets for time-frequency analysis},
  volume = {199},
  year = {2019}
}

@article{CohenHosaka1976,
  author = {Cohen, David and Hosaka, Hidehiro},
  doi = {10.1016/S0022-0736(76)80041-6},
  journal = {Journal of Electrocardiology},
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}

@article{CrosseEtAl2016,
  author = {Crosse, Michael J. and Di Liberto, Giovanni M. and Bednar, Adam and Lalor, Edmund C.},
  doi = {10.3389/fnhum.2016.00604},
  journal = {Frontiers in Human Neuroscience},
  shorttitle = {The Multivariate Temporal Response Function ({{mTRF}}) Toolbox},
  title = {The Multivariate Temporal Response Function ({{mTRF}}) Toolbox: A {{MATLAB}} Toolbox for Relating Neural Signals to Continuous Stimuli},
  volume = {10},
  year = {2016}
}

@article{DahneEtAl2014,
  author = {Dähne, Sven and Meinecke, Frank C. and Haufe, Stefan and Höhne, Johannes and Tangermann, Michael and Müller, Klaus-Robert and Nikulin, Vadim V.},
  doi = {10.1016/j.neuroimage.2013.07.079},
  journal = {NeuroImage},
  pages = {111-122},
  shorttitle = {{{SPoC}}},
  title = {{{SPoC}}: A Novel Framework for Relating the Amplitude of Neuronal Oscillations to Behaviorally Relevant Parameters},
  volume = {86},
  year = {2014}
}

@article{DalalEtAl2008,
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  doi = {10.1016/j.neuroimage.2008.01.023},
  journal = {NeuroImage},
  number = {4},
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  shorttitle = {Five-Dimensional Neuroimaging},
  title = {Five-Dimensional Neuroimaging: Localization of the Time–Frequency Dynamics of Cortical Activity},
  volume = {40},
  year = {2008}
}

@article{DaleEtAl1999,
  author = {Dale, Anders M. and Fischl, Bruce and Sereno, Martin I.},
  doi = {10.1006/nimg.1998.0395},
  journal = {NeuroImage},
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  year = {1999}
}

@article{DaleEtAl2000,
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}

@article{DaleSereno1993,
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  shorttitle = {Improved Localization of Cortical Activity by Combining {{EEG}} and {{MEG}} with {{MRI}} Cortical Surface Reconstruction},
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@article{DammersEtAl2008,
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  doi = {10.1109/TBME.2008.926677},
  journal = {IEEE Transactions on Biomedical Engineering},
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  year = {2008}
}

@article{DarvasEtAl2006,
  author = {Darvas, Felix and Ermer, John J. and Mosher, John C. and Leahy, Richard M.},
  doi = {10.1002/hbm.20171},
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  title = {Generic Head Models for Atlas-Based {{EEG}} Source Analysis},
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  year = {2006}
}

@article{DelormeMakeig2004,
  title = {{EEGLAB}: an open source toolbox for analysis of single-trial {EEG} dynamics including independent component analysis},
  volume = {134},
  issn = {0165-0270},
  shorttitle = {{EEGLAB}},
  doi = {10.1016/j.jneumeth.2003.10.009},
  language = {eng},
  number = {1},
  journal = {Journal of Neuroscience Methods},
  author = {Delorme, Arnaud and Makeig, Scott},
  month = mar,
  year = {2004},
  pmid = {15102499},
  keywords = {Computer Simulation, Electroencephalography, Evoked Potentials, Software},
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}

@article{DestrieuxEtAl2010,
  author = {Destrieux, Christophe and Fischl, Bruce and Dale, Anders and Halgren, Eric},
  doi = {10.1016/j.neuroimage.2010.06.010},
  journal = {NeuroImage},
  number = {1},
  pages = {1-15},
  title = {Automatic Parcellation of Human Cortical Gyri and Sulci Using Standard Anatomical Nomenclature},
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  year = {2010}
}

@inproceedings{DharmapraniEtAl2016,
  address = {Orlando, FL, USA},
  title = {A comparison of independent component analysis algorithms and measures to discriminate between {EEG} and artifact components},
  isbn = {978-1-4577-0220-4},
  doi = {10.1109/EMBC.2016.7590828},
  booktitle = {2016 38th {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} and {Biology} {Society} ({EMBC})},
  publisher = {IEEE},
  author = {Dharmaprani, Dhani and Nguyen, Hoang K. and Lewis, Trent W. and DeLosAngeles, Dylan and Willoughby, John O. and Pope, Kenneth J.},
  year = {2016},
  pages = {825--828},
}


@article{DufauEtAl2015,
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  year = {2015}
}

@book{EfronHastie2016,
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  author = {Efron, Bradley and Hastie, Trevor},
  isbn = {978-1-107-14989-2},
  number = {5},
  publisher = {{Cambridge University Press}},
  series = {Institute of {{Mathematical Statistics}} Monographs},
  shorttitle = {Computer Age Statistical Inference},
  title = {Computer Age Statistical Inference: Algorithms, Evidence, and Data Science},
  url = {https://hastie.su.domains/CASI/},
  year = {2016}
}

@article{EngemannGramfort2015,
  author = {Engemann, Denis A. and Gramfort, Alexandre},
  doi = {10.1016/j.neuroimage.2014.12.040},
  journal = {NeuroImage},
  pages = {328-342},
  title = {Automated Model Selection in Covariance Estimation and Spatial Whitening of {{MEG}} and {{EEG}} Signals},
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}

@article{FischlEtAl1999,
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@article{FischlEtAl2004,
  author = {Fischl, Bruce and Salat, David H. and {van der Kouwe}, André J.W. and Makris, Nikos and Ségonne, Florent and Quinn, Brian T. and Dale, Anders M.},
  doi = {10.1016/j.neuroimage.2004.07.016},
  journal = {NeuroImage},
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  title = {Sequence-Independent Segmentation of Magnetic Resonance Images},
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  year = {2004}
}

@article{FishburnEtAl2019,
  title={Temporal derivative distribution repair (TDDR): a motion correction method for {fNIRS}},
  doi = {10.1016/j.neuroimage.2018.09.025},
  author={Fishburn, Frank A and Ludlum, Ruth S and Vaidya, Chandan J and Medvedev, Andrei V},
  journal={NeuroImage},
  volume={184},
  pages={171--179},
  year={2019},
  publisher={Elsevier}
}

@article{GlasserEtAl2016,
  author = {Glasser, Matthew F. and Coalson, Timothy S. and Robinson, Emma C. and Hacker, Carl D. and Harwell, John and Yacoub, Essa and Ugurbil, Kamil and Andersson, Jesper and Beckmann, Christian F. and Jenkinson, Mark and Smith, Stephen M. and Van Essen, David C.},
  doi = {10.1038/nature18933},
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  number = {7615},
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  title = {A multi-modal parcellation of human cerebral cortex},
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@article{GlasserEtAl2016supp,
  author = {Glasser, Matthew F. and Coalson, Timothy S. and Robinson, Emma C. and Hacker, Carl D. and Harwell, John and Yacoub, Essa and Ugurbil, Kamil and Andersson, Jesper and Beckmann, Christian F. and Jenkinson, Mark and Smith, Stephen M. and Van Essen, David C.},
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@article{GoldbergerEtAl2000,
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  shorttitle = {{{PhysioBank}}, {{PhysioToolkit}}, and {{PhysioNet}}},
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@article{GoldenholzEtAl2009,
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  doi = {10.1002/hbm.20571},
  journal = {Human Brain Mapping},
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}

@article{GoncalvesEtAl2003,
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  doi = {10.1109/TBME.2003.812164},
  journal = {IEEE Transactions on Biomedical Engineering},
  number = {6},
  pages = {754-767},
  title = {In Vivo Measurement of the Brain and Skull Resistivities Using an {{EIT}}-Based Method and Realistic Models for the Head},
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@article{GraimannEtAl2002,
  author = {Graimann, Bernhard and Huggins, Jane E. and Levine, Simon P. and Pfurtscheller, Gert},
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  number = {1},
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@article{GramfortEtAl2010,
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  doi = {10.1109/tbme.2009.2037139},
  year = {2010},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  volume = {57},
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}

@incollection{GramfortEtAl2011,
  address = {{Berlin; Heidelberg}},
  author = {Gramfort, Alexandre and Strohmeier, Daniel and Haueisen, Jens and Hämäläinen, Matti S. and Kowalski, Matthieu},
  booktitle = {Information {{Processing}} in {{Medical Imaging}}},
  doi = {10.1007/978-3-642-22092-0_49},
  editor = {Székely, Gábor and Hahn, Horst K.},
  isbn = {978-3-642-22091-3 978-3-642-22092-0},
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	issn = {1053-8119},
	doi = {10.1016/j.neuroimage.2013.04.086},
	abstract = {The conductivity profile of the head has a major effect on EEG signals, but unfortunately the conductivity for the most important compartment, skull, is only poorly known. In dipole modeling studies, errors in modeled skull conductivity have been considered to have a detrimental effect on EEG source estimation. However, as dipole models are very restrictive, those results cannot be generalized to other source estimation methods. In this work, we studied the sensitivity of EEG and combined MEG+EEG source estimation to errors in skull conductivity using a distributed source model and minimum-norm (MN) estimation. We used a MEG/EEG modeling set-up that reflected state-of-the-art practices of experimental research. Cortical surfaces were segmented and realistically-shaped three-layer anatomical head models were constructed, and forward models were built with Galerkin boundary element method while varying the skull conductivity. Lead-field topographies and MN spatial filter vectors were compared across conductivities, and the localization and spatial spread of the MN estimators were assessed using intuitive resolution metrics. The results showed that the MN estimator is robust against errors in skull conductivity: the conductivity had a moderate effect on amplitudes of lead fields and spatial filter vectors, but the effect on corresponding morphologies was small. The localization performance of the EEG or combined MEG+EEG MN estimator was only minimally affected by the conductivity error, while the spread of the estimate varied slightly. Thus, the uncertainty with respect to skull conductivity should not prevent researchers from applying minimum norm estimation to EEG or combined MEG+EEG data. Comparing our results to those obtained earlier with dipole models shows that general judgment on the performance of an imaging modality should not be based on analysis with one source estimation method only.},
	language = {en},
	journal = {NeuroImage},
	author = {Stenroos, Matti and Hauk, Olaf},
	month = nov,
	year = {2013},
	keywords = {Electroencephalography, Inverse problem, Magnetoencephalography, Minimum-norm estimation, Skull conductivity},
	pages = {265--272}
}

@article{CroftBarry2000,
  title = {Removal of ocular artifact from the {EEG}: a review},
  author = {Croft, R. J. and Barry, R. J.},
  year = {2000},
  journal = {Clinical Neurophysiology},
  volume = {30},
  number = {1},
  pages = {5--19},
  doi = {10.1016/S0987-7053(00)00055-1}
}


@article{SeymourEtAl2022,
	title = {Interference suppression techniques for {OPM}-based {MEG}: {Opportunities} and challenges},
	volume = {247},
	issn = {1053-8119},
	shorttitle = {Interference suppression techniques for {OPM}-based {MEG}},
	doi = {10.1016/j.neuroimage.2021.118834},
	language = {en},
	journal = {NeuroImage},
	author = {Seymour, Robert A. and Alexander, Nicholas and Mellor, Stephanie and O'Neill, George C. and Tierney, Tim M. and Barnes, Gareth R. and Maguire, Eleanor A.},
	month = feb,
	year = {2022},
	pages = {118834}
}

@article{TierneyEtAl2021,
	title = {Modelling optically pumped magnetometer interference in MEG as a spatially homogeneous magnetic field},
	volume = {244},
	issn = {1053-8119},
	doi = {10.1016/j.neuroimage.2021.118484},
	language = {en},
	journal = {NeuroImage},
	author = {Tierney, Tim M. and Alexander, Nicholas and Mellor, Stephanie and Holmes, Niall and Seymour, Robert and O'Neill, George C. and Maguire, Eleanor A. and Barnes, Gareth R.},
	year = {2021},
}

@article{TierneyEtAl2022,
	title = {Spherical harmonic based noise rejection and neuronal sampling with multi-axis OPMs},
	journal = {NeuroImage},
	volume = {258},
	year = {2022},
	issn = {1053-8119},
	doi = {10.1016/j.neuroimage.2022.119338},
	author = {Tierney, Tim M. and Mellor, Stephanie nd O'Neill, George C. and Timms, Ryan C. and Barnes, Gareth R.},
}

@article{KumaravelEtAl2022,
	doi = {10.3390/s22197314},
	url = {https://doi.org/10.3390/s22197314},
	year = {2022},
	month = sep,
	publisher = {{MDPI} {AG}},
	volume = {22},
	number = {19},
	pages = {7314},
	author = {Velu Prabhakar Kumaravel and Marco Buiatti and Eugenio Parise and Elisabetta Farella},
	title = {Adaptable and Robust {EEG} Bad Channel Detection Using Local Outlier Factor ({LOF})},
	journal = {Sensors}
}

@article{BreunigEtAl2000,
	author = {Breunig, Markus M. and Kriegel, Hans-Peter and Ng, Raymond T. and Sander, J\"{o}rg},
	title = {LOF: Identifying Density-Based Local Outliers},
	year = {2000},
	issue_date = {June 2000},
	publisher = {Association for Computing Machinery},
	address = {New York, NY, USA},
	volume = {29},
	number = {2},
	url = {https://doi.org/10.1145/335191.335388},
	doi = {10.1145/335191.335388},
	journal = {SIGMOD Rec.},
	month = {may},
	pages = {93–104},
	numpages = {12},
	keywords = {outlier detection, database mining}
}

@article{OyamaEtAl2015,
	title = {Dry phantom for magnetoencephalography —{Configuration}, calibration, and contribution},
	volume = {251},
	issn = {0165-0270},
	doi = {10.1016/j.jneumeth.2015.05.004},
	journal = {Journal of Neuroscience Methods},
	author = {Oyama, Daisuke and Adachi, Yoshiaki and Yumoto, Masato and Hashimoto, Isao and Uehara, Gen},
	month = aug,
	year = {2015},
	pages = {24--36},
}
