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references_to_review_papers_and_teaching_material [2018/06/12 12:49]
robert [Programming]
references_to_review_papers_and_teaching_material [2018/10/21 15:15] (current)
42.49.180.224 [References to review papers and teaching material]
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 ====== References to review papers and teaching material ======= ====== References to review papers and teaching material =======
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 MEG: An Introduction to Methods. by Peter Hansen, Morten Kringelbach,​ Riitta Salmelin. [[http://​brainmaster.com/​software/​pubs/​brain/​MEG%20-%20An%20Intro.pdf|Pdf]],​ [[http://​www.amazon.com/​MEG-Introduction-Methods-Peter-Hansen/​dp/​0195307232/​ref=sr_1_2?​s=books&​ie=UTF8&​qid=1375859237&​sr=1-2&​keywords=magnetoencephalography|Amazon]]. MEG: An Introduction to Methods. by Peter Hansen, Morten Kringelbach,​ Riitta Salmelin. [[http://​brainmaster.com/​software/​pubs/​brain/​MEG%20-%20An%20Intro.pdf|Pdf]],​ [[http://​www.amazon.com/​MEG-Introduction-Methods-Peter-Hansen/​dp/​0195307232/​ref=sr_1_2?​s=books&​ie=UTF8&​qid=1375859237&​sr=1-2&​keywords=magnetoencephalography|Amazon]].
 +
 ===== Guidelines for acquisition,​ analysis and publication ===== ===== Guidelines for acquisition,​ analysis and publication =====
- 
- 
 Specifically for MEG we recommend the[[http://​www.sciencedirect.com/​science/​article/​pii/​S1053811912009895|Good practice for conducting and reporting MEG research]] paper by Joachim Gross et al. that was published in 2012 in NeuroImage. ​ Specifically for MEG we recommend the[[http://​www.sciencedirect.com/​science/​article/​pii/​S1053811912009895|Good practice for conducting and reporting MEG research]] paper by Joachim Gross et al. that was published in 2012 in NeuroImage. ​
  
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 Nature has a [[http://​www.nature.com/​authors/​policies/​checklist.pdf|Reporting Checklist For Life Sciences Articles]] that is helpful to consider when you write your manuscript, also when you don't plan to submit it to Nature. Nature has a [[http://​www.nature.com/​authors/​policies/​checklist.pdf|Reporting Checklist For Life Sciences Articles]] that is helpful to consider when you write your manuscript, also when you don't plan to submit it to Nature.
-===== Data Sharing ===== 
  
-For data sharing we recommend that you consider organizing your data along the lines of the [[http://​bids.neuroimaging.io|BIDS standard]]. See [[http://​www.nature.com/​articles/​sdata201644|The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments]] for an introduction. Although not final yet, there is a proposed extension to BIDS that details how to organize ​[[https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM/​edit#​heading=h.qdzsf8lh4for|MEG data in BIDS]].+===== Programming ===== 
 +MathWorks provides [[https://​www.mathworks.com/​help/​matlab/​getting-started-with-matlab.html|online tutorials]] to help you get started with the desktop and programming environment. 
 + 
 +For an introduction to MATLAB have a look at the excellent tutorial and exercises in [[http://​www.antoniahamilton.com/​matlab.html|MATLAB for Psychologists]]. 
 + 
 +Mike X. Cohen, [[https://​www.amazon.com/​MATLAB-Brain-Cognitive-Scientists-Press/​dp/​0262035820/​ref=la_B00EWB0HO2_1_1?​s=books&​ie=UTF8&​qid=1496819058&​sr=1-1|MATLAB for Brain and Cognitive Scientists]],​ MIT Press, 2017. 
 + 
 +Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, et al. (2014) [[http://​journals.plos.org/​plosbiology/​article?​id=10.1371/​journal.pbio.1001745|Best Practices for Scientific Computing]]. PLoS Biol 12(1): e1001745. https://​doi.org/​10.1371/​journal.pbio.1001745 
 + 
 +===== Data Sharing ===== 
 +For data sharing we recommend that you consider organizing your data along the lines of the [[http://​bids.neuroimaging.io|BIDS standard]]. See [[http://​www.nature.com/​articles/​sdata201644|The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments]] for an introduction ​and [[https://www.nature.com/articles/sdata2018110|MEG-BIDS, the brain imaging data structure extended to magnetoencephalography]]. The **[[:​reference:​data2bids]]** function helps to organize your data in the BIDS structure.
  
 A good example for a data publication is given in [[http://​dx.doi.org/​10.1038/​sdata.2015.1|A multi-subject,​ multi-modal human neuroimaging dataset]], which includes MEG, EEG and fMRI. The dataset itself is available from [[https://​openfmri.org/​dataset/​ds000117|OpenfMRI]]. A good example for a data publication is given in [[http://​dx.doi.org/​10.1038/​sdata.2015.1|A multi-subject,​ multi-modal human neuroimaging dataset]], which includes MEG, EEG and fMRI. The dataset itself is available from [[https://​openfmri.org/​dataset/​ds000117|OpenfMRI]].
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 The Human Connectome Project (HCP) also provides good examples for data sharing and documentation. In [[https://​dx.doi.org/​10.1016/​j.neuroimage.2013.05.056|Adding dynamics to the Human Connectome Project with MEG]] the MEG component of the HCP is described, which is available for download from the [[https://​www.humanconnectome.org|HCP website]]. ​ The Human Connectome Project (HCP) also provides good examples for data sharing and documentation. In [[https://​dx.doi.org/​10.1016/​j.neuroimage.2013.05.056|Adding dynamics to the Human Connectome Project with MEG]] the MEG component of the HCP is described, which is available for download from the [[https://​www.humanconnectome.org|HCP website]]. ​
  
-===== Statistics ​=====+====== References to review papers and teaching material =======
  
 +Here we try to compile a list of background reading/​studying material. If you know of good papers or other material, please add it by clicking on the edit button.===== Statistics =====
 The following paper illustrates several problems associated with the lack of robustness and gives recommendations:​ Rousselet, G.A. & Pernet, C.R. (2012) [[https://​www.frontiersin.org/​articles/​10.3389/​fnhum.2012.00119/​full|Improving standards in brain-behavior correlation analyses]]. Frontiers in human neuroscience,​ 6, 119. The following paper illustrates several problems associated with the lack of robustness and gives recommendations:​ Rousselet, G.A. & Pernet, C.R. (2012) [[https://​www.frontiersin.org/​articles/​10.3389/​fnhum.2012.00119/​full|Improving standards in brain-behavior correlation analyses]]. Frontiers in human neuroscience,​ 6, 119.
  
 The blog post [[https://​garstats.wordpress.com/​2018/​06/​11/​ejn2017|Correlations in neuroscience:​ are small n, interaction fallacies, lack of illustrations and confidence intervals the norm?]] by Guillaume Rousselet has some interesting observations and recommendations. The blog post [[https://​garstats.wordpress.com/​2018/​06/​11/​ejn2017|Correlations in neuroscience:​ are small n, interaction fallacies, lack of illustrations and confidence intervals the norm?]] by Guillaume Rousselet has some interesting observations and recommendations.
- 
-===== Signal processing ===== 
-[[http://​www.amazon.com/​Analyzing-Neural-Time-Data-Neuropsychology/​dp/​0262019876/​ref=la_B00EWB0HO2_1_1?​s=books&​ie=UTF8&​qid=1436709055&​sr=1-1|Analyzing Neural Time Series Data: Theory and Practice]]. by Mike X. Cohen. ​ 
- 
-[[http://​faculty.washington.edu/​dbp/​sapabook.html|Spectral Analysis for Physical Applications:​ Multitaper and Conventional Univariate Techniques]] Donald B. Percival and Andrew T. Walden, 1993.  
- 
-Bruns A. [[http://​www.sciencedirect.com/​science/​article/​pii/​S0165027004001098|Fourier-,​ Hilbert- and wavelet-based signal analysis: are they really different approaches?​]] J Neurosci Methods. 2004 Aug 30;​137(2):​321-32. 
- 
-The [[http://​ssltool.sourceforge.net/​history.html|Brief History of the EEG Surface Laplacian]] by Paul L. Nunez explains how the surface Laplacian and SCD relate. The surface laplacian is further explained on the [[ftp://​ftp.egi.com/​pub/​documentation/​technotes/​SurfaceLaplacian.pdf|EGI website]]. 
  
 ===== Source estimation ===== ===== Source estimation =====
- 
 Michel, C.M. et al. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​15351361|EEG source imaging.]] Clin Neurophysiol,​ 2004; 115(10):​2195-222. Michel, C.M. et al. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​15351361|EEG source imaging.]] Clin Neurophysiol,​ 2004; 115(10):​2195-222.
  
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 The following paper is a review and gentle introduction into beamforming:​ The following paper is a review and gentle introduction into beamforming:​
 Hillebrand A, Singh KD, Holliday IE, Furlong PL, Barnes GR. Hillebrand A, Singh KD, Holliday IE, Furlong PL, Barnes GR.
-[[http://​dx.doi.org/​10.1002/​hbm.20102|A new approach to neuroimaging with magnetoencephalography.]] Hum Brain Mapp. 2005 Jun;​25(2):​199-211. ​+[[http://​dx.doi.org/​10.1002/​hbm.20102|A new approach to neuroimaging with magnetoencephalography.]] Hum Brain Mapp. 2005 Jun;​25(2):​199-211. 
 =====Connectivity===== =====Connectivity=====
  
 Schoffelen JM, Gross J. [[http://​onlinelibrary.wiley.com/​doi/​10.1002/​hbm.20745/​full|Source connectivity analysis with MEG and EEG.]] Hum Brain Mapp. 2009 Jun;​30(6):​1857-65. Schoffelen JM, Gross J. [[http://​onlinelibrary.wiley.com/​doi/​10.1002/​hbm.20745/​full|Source connectivity analysis with MEG and EEG.]] Hum Brain Mapp. 2009 Jun;​30(6):​1857-65.
  
-O’Neill GC, Barratt EL, Hunt BAE, Tewarie PK, Brookes, MJ. [[https://​doi.org/​10.1088/​0031-9155/​60/​21/​R271|Measuring electrophysiological connectivity by power envelope correlation:​ a technical review on MEG methods]]. Physics in Medicine and Biology, 2015 60(21), R271–R295. ​ +O’Neill GC, Barratt EL, Hunt BAE, Tewarie PK, Brookes, MJ. [[https://​doi.org/​10.1088/​0031-9155/​60/​21/​R271|Measuring electrophysiological connectivity by power envelope correlation:​ a technical review on MEG methods]]. Physics in Medicine and Biology, 2015 60(21), R271–R295.
-===== Programming ===== +
-MathWorks provides [[https://​www.mathworks.com/​help/​matlab/​getting-started-with-matlab.html|online tutorials]] to help you get started with the desktop and programming environment. +
- +
-For an introduction to MATLAB have a look at the excellent tutorial and exercises in [[http://​www.antoniahamilton.com/​matlab.html|MATLAB for Psychologists]]. +
- +
-Mike X. Cohen, [[https://​www.amazon.com/​MATLAB-Brain-Cognitive-Scientists-Press/​dp/​0262035820/​ref=la_B00EWB0HO2_1_1?​s=books&​ie=UTF8&​qid=1496819058&​sr=1-1|MATLAB for Brain and Cognitive Scientists]],​ MIT Press, 2017. +
- +
-Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, et al. (2014) [[http://​journals.plos.org/​plosbiology/​article?​id=10.1371/​journal.pbio.1001745|Best Practices for Scientific Computing]]. PLoS Biol 12(1): e1001745. https://​doi.org/​10.1371/​journal.pbio.1001745+