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references_to_implemented_methods [2012/08/08 12:09]
robert added 2001 review by Baillet
references_to_implemented_methods [2017/06/20 14:08] (current)
robert fixed broken link
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 {{tag>​eeg meg source headmodel freq statistics coherence}} {{tag>​eeg meg source headmodel freq statistics coherence}}
  
-====== References ======= +====== References to implemented methods ======
-===== References to implemented methods ======+
  
-This list is far from complete, many more algorithms that have been published in papers are implemented in FieldTrip. If you want to know which paper describes a method in detail and it is not given here, you can ask on the email [[discussion list]].+This list is far from complete, many more algorithms that have been published in papers are implemented in FieldTrip. If you want to know which paper describes a method in detail and the information ​is not given here, you can ask on the email [[discussion list]].
  
 +If possible, please provide a link to the online version of the manuscript. A link to [[http://​www.ncbi.nlm.nih.gov/​pubmed|pubmed]] or [[http://​www.sciencedirect.com|sciencedirect]] is in general nice, as it allows quick cross-referencing.
 +
 +If allowed, you can also upload a pdf version to the wiki and provide a link here. Please check [[http://​www.sherpa.ac.uk/​romeo/​|Sherpa Romeo]] for the copyright conditions and whether you are allowed to
 +  - release the publisher version, i.e. the final online pdf version from Elsevier or so
 +  - release a [[http://​www.eprints.org/​openaccess/​self-faq/#​self-archiving|self-archived]] version, i.e. your own pdf (or word) document as it has been accepted for publication
 +  - not release a copy of the manuscript that is freely available to everyone
 ==== EEG and MEG forward modeling ==== ==== EEG and MEG forward modeling ====
  
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 Biomed Eng. 1991 May;​38(5):​409-17. ​ Biomed Eng. 1991 May;​38(5):​409-17. ​
  
 +== Forward model solution for EEG, using FEM ==
 +Vorwerk, J., Magyari, L., Ludewig, J., Oostenveld, R., & Wolters, C. H. (2013). //​[[http://​journals.sagepub.com/​doi/​pdf/​10.1177/​1550059413507209|The FieldTrip-SimBio pipeline for finite element EEG forward computations in MATLAB: Validation and application.]]//​ In Abstracts of Presentations at the International Conference on Basic and Clinical Multimodal Imaging (BaCI), Geneva, Switzerland,​ September 5-8, 2013. Clin EEG Neurosci. 2013. PMID: 24368763 DOI: 10.1177/​1550059413507209.
 +
 +Vorwerk, J., Cho, J.-H., Rampp, S., Hamer, H., Knosche, T.R., Wolters, C.H., //​[[https://​www.ncbi.nlm.nih.gov/​pubmed/​24971512|A Guideline for Head Volume Conductor Modeling in EEG and MEG.]]// NeuroImage, 100, pp.590-607, (2014).
 +
 +Vorwerk, J., Clerc, M., Burger, M. and Wolters, C.H., //​[[https://​www.ncbi.nlm.nih.gov/​pubmed/​23096316|Comparison of Boundary Element and Finite Element Approaches to the EEG Forward Problem.]]//​ Biomedical Engineering,​ 57(Suppl.1),​ pp.795-798, doi:​10.1515/​bmt-2012-4152,​ (2012).
 ==== EEG and MEG source estimation ==== ==== EEG and MEG source estimation ====
  
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 == Source localization by fitting an equivalent current dipole model == == Source localization by fitting an equivalent current dipole model ==
 Scherg M. Scherg M.
-Fundamentals of dipole source potential analysis.+[[http://​apsychoserver.psych.arizona.edu/​jjbareprints/​psyc501a/​readings/​Scherg_Fundamentals%20of%20Dipole%20Source%20Potentials_Auditory%20Evoked%20Agnetic%20Fileds_1990.pdf|Fundamentals of dipole source potential analysis.]]
 In: //Auditory evoked magnetic fields and electric potentials.//​ eds. F. Grandori, M. Hoke and G.L. Romani. ​ In: //Auditory evoked magnetic fields and electric potentials.//​ eds. F. Grandori, M. Hoke and G.L. Romani. ​
 Advances in Audiology, vol. 6. Karger, Basel, pp 40-69, 1990. Advances in Audiology, vol. 6. Karger, Basel, pp 40-69, 1990.
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 == Distributed source reconstruction using linear estimation ​ == == Distributed source reconstruction using linear estimation ​ ==
  
-Dale AM, Liu AK, Fischl B, Buckner RL, Belliveau JW, Lewine JD, Halgren E (2000): //[[http://http://​www.ncbi.nlm.nih.gov/​pubmed?​term=Dynamic%20statistical%20parametric%20mapping%3A%20combining%20fMRI%20and%20MEG%20to%20produce%20high-resolution%20spatiotemporal%20maps%20of%20cortical%20activity|Dynamic statistical parametric mapping: combining fMRI and MEG to produce high-resolution spatiotemporal maps of cortical activity.]]//​ Neuron 26:55-67.+Dale AM, Liu AK, Fischl B, Buckner RL, Belliveau JW, Lewine JD, Halgren E (2000): //​[[http://​www.ncbi.nlm.nih.gov/​pubmed?​term=Dynamic%20statistical%20parametric%20mapping%3A%20combining%20fMRI%20and%20MEG%20to%20produce%20high-resolution%20spatiotemporal%20maps%20of%20cortical%20activity|Dynamic statistical parametric mapping: combining fMRI and MEG to produce high-resolution spatiotemporal maps of cortical activity.]]//​ Neuron 26:55-67.
  
 Arthur K. Liu, Anders M. Dale, and John W. Belliveau (2002): //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​11870926|Monte Carlo Simulation Studies of EEG and MEG Localization Accuracy.]]//​ Human Brain Mapping 16:47-62. Arthur K. Liu, Anders M. Dale, and John W. Belliveau (2002): //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​11870926|Monte Carlo Simulation Studies of EEG and MEG Localization Accuracy.]]//​ Human Brain Mapping 16:47-62.
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 Fa-Hsuan Lin, Thomas Witzel, Matti S. Hamalainen, Anders M. Dale, John W. Belliveau, and Steven M. Stufflebeam (2004): //​[[http://​www.ncbi.nlm.nih.gov/​pmc/​articles/​PMC2884198/​|Spectral spatiotemporal imaging of cortical oscillations and interactions in the human brain.]]// NeuroImage 23:582-595. Fa-Hsuan Lin, Thomas Witzel, Matti S. Hamalainen, Anders M. Dale, John W. Belliveau, and Steven M. Stufflebeam (2004): //​[[http://​www.ncbi.nlm.nih.gov/​pmc/​articles/​PMC2884198/​|Spectral spatiotemporal imaging of cortical oscillations and interactions in the human brain.]]// NeuroImage 23:582-595.
  
 +== Using multiple signal classification (MUSIC) to scan the source space ==
 +
 +Mosher JC, Lewis PS, Leahy RM. //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​1601435|Multiple dipole modeling and localization from spatio-temporal MEG data.]]// IEEE Trans Biomed Eng. 1992 Jun;​39(6):​541-57.
 +
 +Mosher JC, Baillet S, Leahy RM. //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​10426406|EEG source localization and imaging using multiple signal classification approaches.]]//​ J Clin Neurophysiol. 1999 May;​16(3):​225-38.
 ==== Frequency analysis ==== ==== Frequency analysis ====
  
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 J Neurosci. 1997 Jan 15;​17(2):​722-34. J Neurosci. 1997 Jan 15;​17(2):​722-34.
  
-==== Spatial realignment of channel-level MEG data ====+==== Dealing with different head positions and with movements ​====
  
 Knosche TR. Knosche TR.
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 Biomed Tech (Berl). 2002 Mar;​47(3):​59-62. Biomed Tech (Berl). 2002 Mar;​47(3):​59-62.
  
-== Scalp current density mapping ==+Stolk A, Todorovic A, Schoffelen J-M, Oostenveld R. 
 +// {{:​faq:​stolkneuroimage2013.pdf|Online and offline tools for head movement compensation in MEG.}}  
 +// NeuroImage. 2013. 
 + 
 +==== Scalp current density mapping ​====
  
 TF Oostendorp, A van Oosterom. TF Oostendorp, A van Oosterom.
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 mapping applied to Event-Related Desynchronization (ERD) research.]]//​ Clinical Neurophysiology,​ 111, 1300-1305. mapping applied to Event-Related Desynchronization (ERD) research.]]//​ Clinical Neurophysiology,​ 111, 1300-1305.
  
-==== Statistics for EEG- and MEG-data ​====+==== Connectivity analysis ​====
  
-== Statistical inference by means of permutation ​==+== General tutorial + some things to think about ==
  
-Maris E., Oostenveld R. //[[http://www.ncbi.nlm.nih.gov/sites/entrez?​Db=pubmed&​Cmd=ShowDetailView&​TermToSearch=17517438|Nonparametric statistical testing of EEG- and MEG-data.]]//​ J Neurosci Methods. 2007 Apr 10+Bastos and Schoffelen ​//[[http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full|A Tutorial Review ​of Functional Connectivity Analysis Methods and Their Interpretational Pitfalls]]// 
- +
-Maris E., Schoffelen J.M., Fries P. //[[http://www.ncbi.nlm.nih.gov/​sites/entrez?​Db=pubmed&​Cmd=ShowDetailView&​TermToSearch=17395267|Nonparametric statistical testing ​of coherence differences.]]// +
-J Neurosci Methods. 2007 Jun 15;​163(1):​161-75. +
- +
-==== Connectivity analysis ====+
  
 == Coherence == == Coherence ==
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 Vinck M, Oostenveld R, van Wingerden M, Battaglia F, Pennartz CM. //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​21276857|An improved index of phase-synchronization for electrophysiological data in the presence of volume-conduction,​ noise and sample-size bias.]]// Neuroimage. 2011 Apr 15;​55(4):​1548-65. Epub 2011 Jan 27. PMID: 21276857 Vinck M, Oostenveld R, van Wingerden M, Battaglia F, Pennartz CM. //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​21276857|An improved index of phase-synchronization for electrophysiological data in the presence of volume-conduction,​ noise and sample-size bias.]]// Neuroimage. 2011 Apr 15;​55(4):​1548-65. Epub 2011 Jan 27. PMID: 21276857
  
-==== Brain-computer interfacing ====+== Spike-LFP phase-coupling measures ​==
  
-Van Gerven, M.A.J.JensenO. //​[[http://​www.sciencedirect.com/science?​_ob=ArticleURL&​_udi=B6T04-4VGPJNH-1&​_user=10&​_rdoc=1&​_fmt=&​_orig=search&​_sort=d&​view=c&​_acct=C000050221&​_version=1&​_urlVersion=0&​_userid=10&​md5=09def4bc21af5427ef3f82d069c45c1d|Attention Modulations ​of Posterior Alpha as a Control Signal for Two-Dimensional Brain-Computer Interfaces.]]// J Neurosci Methods. 2009179:78-84.+Vinck, M, Battaglia FP, Womelsdorf TPennartz CM. //​[[http://​www.ncbi.nlm.nih.gov/pubmed/​22187161|Improved measures ​of phase-coupling between spikes and the Local Field Potential.]]// 2011DOI10.1007/​s10827-011-0374-4
  
-==== Machine learning ​==== +==== Statistics for EEG- and MEG-data ​====
-Van Gerven, M.A.J., Hesse, C., Jensen, O., Heskes, T. // [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19285139|Interpreting Single Trial Data using Groupwise Regularisation.]]//​ +
-Neuroimage. 2009; 46(3):​665-76.+
  
-==== Spike-LFP phase-coupling measures ====+Maris E. //​[[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1469-8986.2011.01320.x/​pdf|Statistical Testing in Electrophysiological Studies]]// Psychophysiology (2012) Vol  49 No 4, pp. 549-65. 
  
-Vinck, M, Battaglia FP, Womelsdorf T, Pennartz CM. //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​22187161|Improved measures ​of phase-coupling between spikes and the Local Field Potential.]]//​ 2011; DOI: 10.1007/​s10827-011-0374-4+== Statistical inference by means of permutation ==
  
-===== References to review papers ====== +Maris E., Oostenveld R. //​[[http://​www.ncbi.nlm.nih.gov/​sites/​entrez?​Db=pubmed&​Cmd=ShowDetailView&​TermToSearch=17517438|Nonparametric statistical testing of EEGand MEG-data.]]// J Neurosci Methods. 2007 Apr 10;
-==== EEG and MEG source estimation ====+
  
-MichelC.M. et al. //​[[http://​www.ncbi.nlm.nih.gov/​pubmed/​15351361|EEG source imaging.]]// Clin Neurophysiol2004; 115(10):2195-222.+Maris E.Schoffelen J.M., Fries P. //​[[http://​www.ncbi.nlm.nih.gov/​sites/​entrez?​Db=pubmed&​Cmd=ShowDetailView&​TermToSearch=17395267|Nonparametric statistical testing of coherence differences.]]//​ 
 +J Neurosci Methods. 2007 Jun 15;​163(1):​161-75. 
 + 
 +== Multiple comparison corrections === 
 + 
 +Holm S. //​[[http://​www.jstor.org/​stable/4615733|A Simple Sequentially Rejective Multiple Test Procedure.]]// Scandinavian Journal of StatisticsVol. 6, No. 2 (1979), pp. 65-70. 
 + 
 +Hochberg Y. //​[[http://​www-stat.wharton.upenn.edu/​~steele/​Courses/​956/​Resource/​MultipleComparision/​Hochberg88.pdf|A Sharper Bonferroni Procedure for Multiple Tests of Significance]]//​ Biometrika Vol. 75 No. 4 (1988), pp. 800–802. 
 + 
 +Genovese C.R., Lazar N.A., Nichols T. //​[[http://​citeseerx.ist.psu.edu/​viewdoc/​download?​doi=10.1.1.208.9215&​rep=rep1&​type=pdf|Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate]]// Neuroimage Vol. 15 No. 4 (2002), pp. 870-8. 
 + 
 + 
 +== Machine learning == 
 + 
 +Van Gerven, M.A.J., Hesse, C., Jensen, O., Heskes, T. // [[http://​www.ncbi.nlm.nih.gov/​pubmed/​19285139|Interpreting Single Trial Data using Groupwise Regularisation.]]//​ 
 +Neuroimage. 2009; 46(3):​665-76. 
 + 
 +==== Brain-computer interfacing ==== 
 + 
 +Van Gerven, M.A.J., Jensen, O. //​[[http://​www.sciencedirect.com/​science?​_ob=ArticleURL&​_udi=B6T04-4VGPJNH-1&​_user=10&​_rdoc=1&​_fmt=&​_orig=search&​_sort=d&​view=c&​_acct=C000050221&​_version=1&​_urlVersion=0&​_userid=10&​md5=09def4bc21af5427ef3f82d069c45c1d|Attention Modulations of Posterior Alpha as a Control Signal for Two-Dimensional Brain-Computer Interfaces.]]//​ J Neurosci Methods. 2009; 179:78-84.
  
-Baillet, S and Mosher, J.C. //​[[http://​www.cubric.cf.ac.uk/​Documentation/​meg/​meg-background-reading/​baillet_IEEE_2001.pdf|Electomagnetic Brain Mapping]]// IEEE Signal Processing Magazine, 2001; November:​14-30.