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Course Material for COGNESTIC 2024

The Cognitive Neuroimaging Skills Training In Cambridge (COGNESTIC) is a 2-week course that provides researchers with training in state-of-the-art methods for reproducible and open neuroimaging analysis and related methods. You can find more information on the COGNESTIC webpage.

Software Installation Instructions

Attendees must read and follow these pre-course preparations.

Essential Preparation Materials

You will find the course easier if you can study as much of the material below in advance (e.g, many of the videos below give the theory to the examples we will work through in the course). This section contains essential viewing; a second section contains less critical background, but which you might nonetheless find useful.

Background to Open Science Rik Henson
Viewing	Open Cognitive Neuroscience

Primer on Python Kshipra Gurunandan
Viewing	Introduction to Python and notebooks

Structural MRI I and II - VBM and surface-based analysis Marta Correia
Viewing	Introduction to MRI Physics and image contrast Slides

Diffusion MRI I - Preprocessing, model fitting and group analysis Marta Correia
Viewing	Introduction to Diffusion MRI - Part I Slides

Diffusion MRI II - Tractography and the anatomical connectome Marta Correia
Viewing	Introduction to Diffusion MRI - Part II Slides

fMRI I - Data Organisation Dace Apšvalka
Viewing	fMRI Data Structure & Terminology (6:47) Brain imaging data structure (11:07)

fMRI II - Preprocessing Dace Apšvalka
Viewing	fMRI Artifacts and Noise (11:57) Pre-processing I (10:17) Pre-processing II (7:42)

fMRI III - Analysis Dace Apšvalka
Viewing	GLM applied to fMRI (11:21) Model Building – conditions and contrasts (11:48) Model Building - nuisance variables (13:58) Multiple Comparisons (9:03) Group-level Analysis I (7:05)

fMRI Connectivity Petar Raykov
Viewing	Functional Connectivity in fMRI

Network Analysis Rik Henson
Viewing	Introduction to Network Neuroscience

EEG/MEG I – Measurement and Pre-processing Olaf Hauk
Viewing	1. Overview of EEG/MEG data processing from raw data to source estimates Event-related paradigm, sample dataset, power spectrum, pre-processing, artefact correction, epoching and averaging, visualization, source estimation. 2. The generation of EEG/MEG signals Dipole sources, volume currents, sensor types (EEG, magnetometers, gradiometers) and their leadfields. 3.Frequency and temporal filtering of EEG/MEG data Frequency spectrum, temporal smoothing, relationship between frequency and time domain, filters (low-/high-/band-pass, Notch), aliasing, decibels. 4. Differential sensitivity of EEG and MEG Volume conduction, sensor types and their leadfields, sensitivity maps, dipoles vs spatially extended sources. 5.Event-related potentials and fields Averaging, evoked and induced activity, number of trials, artefact rejection, parametric designs, regression. Fore more on this topic see here.

EEG/MEG II – Head Modelling and Source Estimation Olaf Hauk
Viewing	1. The EEG/MEG forward model Basic formulation of the EEG/MEG forward problem, linear equation, basics of head modelling, examples of sensory evoked responses. 2. The EEG/MEG inverse problem Non-uniqueness, under-determinedness, examples of non-uniqueness, source estimates for sensorily evoked activity. 3. The spatial resolution of linear EEG/MEG source estimation Leakage and blurring, resolution matrix, point-spread functions (PSFs), cross-talk functions (CTFs), examples of PSFs and CTFs, regions-of-interest for source estimation. 4. Noise and regularisation in EEG/MEG source estimates Over- and under-fitting, smoothing, regularisation parameter, data whitening, noise covariance matrix. Fore more on this topic see here.

EEG/MEG III – Time-Frequency and Functional Connectivity Analysis Olaf Hauk
Viewing	1. Frequency spectra and the Fourier analysis Periodic basis functions, Fourier Decomposition, frequency spectrum, Nyquist Theorem, steady state response. 2. Time-frequency analysis and wavelets Fourier analysis, wavelets, trade-off between time and frequency resolution, wavelets, number of cycles, evoked and induced activity, beta bursts. 3.The basics of functional connectivity methods Types of connectivity, amplitude envelope correlation, resting state analysis, Hilbert envelope, phase-locking, coherence, SNR bias, time-resolved connectivity. Fore more on this topic see here.

EEG/MEG IV – Further Topics and BIDS Olaf Hauk & Máté Aller
Viewing	1. Primer on group statistics for EEG/MEG data Regions-of-interest (ROI) analysis, multiple comparison problem, cluster-based permutation tests, problems estimating cluster extent, MNE-Python tutorial. 2. Primer on decoding and RSA with EEG/MEG data Basics of linear decoding, temporal generalisation, interpreting decoding weights, back-projection, representational similarity analysis (RSA). 3. Primer on multimodal integration Types of neural “activity”, differential sensitivity of EEG/MEG vs fMRI, source weighting and priors, estimating deep sources with EEG/MEG. Fore more on this topic see here.

MVPA/RSA I and II Daniel Mitchell & Máté Aller
Viewing	Excellent presentations from Martin Hebart's MVPA course, on: Introduction to MVPA Introduction to classification. If the links don't work, download from here and here. Martin Hebart's lecture on RSA. If the link fails, download from here. Primer on decoding and RSA with EEG/MEG data

Additional Extra

If you want additional background, consider some of the below:

Background to Open Science Rik Henson
Websites	OSF UKRN BIDS
Reading	Munafo et al, 2017, problems in science Button et al, 2013, power in neuroscience Poldrack et al, 2017, reproducible neuroimaging Marek et al, 2022, power in neuroimaging association studies
Viewing	Statistical power in neuroimaging PayWall: open access Comedian's Perspective on science and media
Slides	Open Science Talk Slides

Primer on Python Kshipra Gurunandan
Software	Python, Pandas, NumPy, Matplotlib, Seaborn
Datasets	Wakeman Multimodal
Useful references	Python concepts with examples, Quick reference, Cheatsheets
Slides and scripts	Slides Notebooks and HTMLs

Structural MRI I - Voxel-based morphometry Marta Correia
Software	FSL
Suggested reading	Introduction to GLM for structural MRI analysis Good et al, 2001, A VBM study of ageing Smith et al, 2004, Structural MRI analysis in FSL

Structural MRI II - Surface-based analyses Marta Correia
Software	Freesurfer
Suggested reading	Dale et al, 1999, Cortical surface-based analysis I Fischl et al, 1999, Cortical surface-based analysis II
Suggested viewing	Using the command line

Diffusion MRI I - Preprocessing, Model Fitting and Group Analysis Marta Correia
Software	dipy, FSL
Suggested reading	FSL Diffusion Toolbox Wiki Le Bihan et al, 2015, What water tells us about biological tissues Soares et al, 2013, A short guide to Diffusion Tensor Imaging Smith et al, 2006, Tract-based spatial statistics (TBSS)

Diffusion MRI II - Tractography and the Anatomical Connectome Marta Correia
Software	dipy
Suggested reading	MR Diffusion Tractography

fMRI I - Data Organisation Dace Apšvalka
Software	HeudiConv, PyBIDS, NiBabel, Nilearn
Websites	Brain Imaging Data Structure BIDS Starter Kit BIDS Specification v1.9.0
Suggested reading	The brain imaging data structure (BIDS), Gorgolewski et al., 2016 The past, present, and future of the brain imaging data structure (BIDS), Poldrack et al., 2024

fMRI II - Pre-processing Dace Apšvalka
Software	MRIQC, fMRIprep, NiPype
Suggested reading	Functional Magnetic Resonance Imaging Methods, Chen & Glover, 2015 Quality control in functional MRI studies with MRIQC and fMRIPrep, Provins et al., 2023 fMRIPrep: a robust preprocessing pipeline for functional MRI, Esteban et al., 2018 Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python, Gorgolewski et al., 2011

fMRI III - Analysis Dace Apšvalka
Software	Nilearn
Suggested reading	The Statistical Analysis of fMRI Data, Lindquist, 2008 Controlling the familywise error rate in functional neuroimaging: a comparative review, Nichols & Hayasaka, 2003 Analysis of task-based functional MRI data preprocessed with fMRIPrep, Esteban et al., 2020 Guidelines for reporting an fMRI study, Poldrack et al., 2008
Suggested viewing	Model Building - temporal basis sets (11:08) GLM Estimation (9:11) Noise Models- AR models (9:57) Inference- Contrasts and t-tests (11:05) Multiple Comparisons by Martin Lindquist and Tor Wager (9:03) FWER Correction (16:11) FDR Correction (5:25) More about multiple comparisons (14:39)

fMRI Connectivity Petar Raykov
Software	Nilearn
Datasets	movie dataset
Reading	Resting-state functional Connectivity Learning and comparing functional connectomes across subjects
Viewing	fMRI Functional Connectivity in fMRI Overview of Effective Connectivity (not covered in person)
Tutorial slides and scripts	Functional Connectivity Nilearn Practical DCM tutorial in SPM (not covered in-person)

Brain Network Analysis Rik Henson
Software	Python 3.7+, nxviz, python-louvain
Datasets
Reading	- (Review article) Bullmore, E., Sporns, O. Complex brain networks: graph theoretical analysis of structural and functional systems. Nat Rev Neurosci 10, 186–198 (2009). https://doi.org/10.1038/nrn2575 - (Textbook reference for more information) Alex Fornito, Andrew Zalesky, and Edward Bullmore. Fundamentals of brain network analysis. Academic press, 2016.
Viewing	Understanding your brain as a network and as art by Prof. Dani Bassett.
Slides	https://github.com/isebenius/COGNESTIC_network_analysis/ Slides

EEG/MEG I – Measurement and Pre-processing Olaf Hauk
Software and datasets	This will be part of a download that will become available later. MNE-Python software homepage MNE stand-alone installation instructions for COGNESTIC Jupyter script to download sample datasets in MNE-Python
Essential and suggested viewing	0. Overview of EEG/MEG data processing from raw data to source estimates Event-related paradigm, sample dataset, power spectrum, pre-processing, artefact correction, epoching and averaging, visualization, source estimation. 1. A brief history of timing A brief overview of the history of bioelectromagnetism, EEG and MEG. 2. The generation of EEG/MEG signals Dipole sources, volume currents, sensor types (EEG, magnetometers, gradiometers) and their leadfields. 3. Basics of EEG/MEG artefact correction Physiological and non-physiological artefacts, data decompositions, frequency/temporal/spatial filtering. 4. Frequency and temporal filtering of EEG/MEG data Frequency spectrum, temporal smoothing, relationship between frequency and time domain, filters (low-/high-/band-pass, Notch), aliasing, decibels. 5. Topographical artefact correction of EEG/MEG data Independent Component Analysis (ICA), Signal Space Projection (SSP), eye movement and heart beat artefacts. 6. Maxfiltering of MEG data Signal Space Separation, options of Maxfilter software (e.g. movement compensation). 7. Differential sensitivity of EEG and MEG Volume conduction, sensor types and their leadfields, sensitivity maps, dipoles vs spatially extended sources. 8. Event-related potentials and fields Averaging, evoked and induced activity, number of trials, artefact rejection, parametric designs, regression. + Origin, significance, and interpretation of EEG (Michael X Cohen) + Analysing MEG data with MNE-Python and its ecosystem (Alex Gramfort) + List of EEG/MEG lectures MNE-Python tutorials: Overview of MNE-Python processing pipeline from preprocessing to source estimation Preprocessing
Suggested reading	Digitial Filtering Filtering How To Maxwell Filtering General EEG/MEG Literature
Slides and scripts	Slides: 1 2 3 Scripts

EEG/MEG II – Head Modelling and Source Estimation Olaf Hauk
Software and datasets	This will be part of a download that will become available later. MNE-Python software homepage MNE stand-alone installation instructions for COGNESTIC Jupyter script to download sample datasets in MNE-Python
Essential and suggested viewing	0. Overview of EEG/MEG data processing from raw data to source estimates Event-related paradigm, sample dataset, power spectrum, pre-processing, artefact correction, epoching and averaging, visualization, source estimation. 1. The EEG/MEG forward model Basic formulation of the EEG/MEG forward problem, linear equation, basics of head modelling, examples of sensory evoked responses. 2. Source spaces for EEG/MEG source estimation Cortical surface, volumetric source space, spatial sampling, spatial normalisation, subcortical areas, source orientation. 3. Head models for EEG/MEG source estimation <<BR>>Volume conduction, Boundary Element Method (BEM), Finite Element Method (FEM), head model accuracy. 4. The EEG/MEG inverse problem Non-uniqueness, under-determinedness, examples of non-uniqueness, source estimates for sensorily evoked activity. 5. The spatial resolution of linear EEG/MEG source estimation Leakage and blurring, resolution matrix, point-spread functions (PSFs), cross-talk functions (CTFs), examples of PSFs and CTFs, regions-of-interest for source estimation. 6. Comparison of spatial resolution for linear EEG/MEG source estimation methods Point-spread functions (PSFs), cross-talk functions (CTFs), resolution metrics (localisation error, spatial deviation), combination of EEG and MEG, PSFs and CTFs for minimum-norm type methods and beamformers, comparison of resolution metrics for minimum-norm type methods and beamformers. 7. Noise and regularisation in EEG/MEG source estimates Over- and under-fitting, smoothing, regularisation parameter, data whitening, noise covariance matrix. + List of EEG/MEG lectures MNE-Python Tutorials: Forward Models and Source Spaces Source Estimation
Suggested reading	Linear source estimation and spatial resolution Comparison of common head models (e.g. BEM) Guidelines for head modelling (incl. FEM) General EEG/MEG Literature
Slides and scripts	Slides: 1 2 3 Scripts

EEG/MEG III – Time-Frequency and Functional Connectivity Analysis Olaf Hauk
Software and datasets	This will be part of a download that will become available later. MNE-Python software homepage MNE stand-alone installation instructions for COGNESTIC Jupyter script to download sample datasets in MNE-Python
Essential and suggested viewing	1. The basics of signals in the frequency domain Oscillations, periodic signals, sine and cosine, polar representation, complex numbers. 2. Frequency spectra and the Fourier analysis Periodic basis functions, Fourier Decomposition, frequency spectrum, Nyquist Theorem, steady state response. 3. Time-frequency analysis and wavelets Fourier analysis, wavelets, trade-off between time and frequency resolution, wavelets, number of cycles, evoked and induced activity, beta bursts. 4. The basics of functional connectivity methods Types of connectivity, amplitude envelope correlation, resting state analysis, Hilbert envelope, phase-locking, coherence, SNR bias, time-resolved connectivity. 5. Spatial resolution (leakage) and connectivity Connectivity in sensor and source space, point-spread and cross-talk, (non-)zero-lag signals, orthogonalisation, imaginary part of coherency, source space parcellations.
Suggested reading	Tutorial on Functional Connectivity Analyzing Neural Time Series Data General EEG/MEG Literature
Slides and scripts	Slides: 1 2 3 Scripts

EEG/MEG IV – Statistics and BIDS Olaf Hauk & Máté Aller
Software	MNE-Python MNE Installation for Cognestic
Datasets	Sample dataset in MNE-Python. Tutorials MNE Installation for Cognestic M/EEG combined dataset Download Datasets
Suggested reading	Estimating subcortical sources from EEG/MEG Tutorial on converting MEG data to BIDS format Example using MNE-BIDS-Pipeline for processing combined M/EEG data
Suggested viewing	Talk on Multimodal Integration
Slides and scripts	Notebooks Exercises Slides1 Slides2 Notebooks mne-bids-pipeline Slides mne-bids-pipeline

MVPA/RSA I Daniel Mitchell
Software	Python 3.7+, including numpy, matplotlib, nilearn & scikit-learn. (To visualise MRI data, you can use your software of choice, although for nifti format data you might like to consider MRIcroN or MRIcroGL.)
Datasets	"NI-edu-data-minimal" faces dataset
Reading	Mur et al. (2009) Revealing representational content with pattern-information fMRI--an introductory guide
Slides and scripts	Notebooks and slides are on the COGNESTIC github

MVPA/RSA II Daniel Mitchell & Máté Aller
Software	Python implementation of the RSA Toolbox: Version 3.0
Datasets	Example data included with RSA toolbox
Reading	Kriegeskorte et al. (2008) Representational similarity analysis - connecting the branches of systems neuroscience Kriegeskorte & Kievit (2013) Representational geometry: integrating cognition, computation, and the brain Nili et al. (2014) A toolbox for representational similarity analysis Schutt et al. (2023) Statistical inference on representational geometries EEG/MEG: Tutorial on EEG/MEG decoding Temporal Generalization Interpretation of Weight Vectors
Slides and scripts	We will demo the RSA toolbox using the jupyter notebooks in the "demos" folder of the toolbox, also available, along with the slides, on the COGNESTICgithub. EEGMEG Notebooks EEG/MEG Slides

Brain Stimulation Elizabeth Michael & Ajay Halai
Reading	TMS-EEG: https://doi.org/10.1016/j.neuroimage.2016.10.031 https://doi.org/10.1016/j.xpro.2022.101435 https://pressrelease.brainproducts.com/tms-eeg/ TMS-fMRI: https://doi.org/10.31234/osf.io/9fyxb https://doi.org/10.1101/2021.05.28.446111
Slides	General TMS+EEG TMS+fMRI TMS+fMRI_Artefacts

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-Below you  will find documents, videos and web links that will be used for the course or can be used for preparation.
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+Attendees must read and follow these [[attachment:COGNESTIC Preparation.pdf|pre-course preparations]].
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-You will find the course easier if you can study as much of the material below in advance (e.g, many of the videos below give the theory to the examples we will work through in the course).
+You will find the course easier if you can study as much of the material below in advance (e.g, many of the videos below give the theory to the examples we will work through in the course). This section contains essential viewing; a second section contains less critical background, but which you might nonetheless find useful.
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+<<BR>> <<Anchor(pythonprimer )>>
||||||<tablewidth="100%" tablestyle="margin:0.5em 0px;border-collapse:collapse;border:1px dotted rgb(211, 211, 211);                        "style="padding:0.25em;border:1px dotted rgb(211, 211, 211);text-align:center;">~+'''Primer on Python'''+~ <<BR>> Kshipra Gurunandan ||
||<style="padding:0.25em;border:1px dotted rgb(211, 211, 211);">__Viewing__ ||<style="padding:0.25em;border:1px dotted rgb(211, 211, 211);">[[https://colab.research.google.com/github/cs231n/cs231n.github.io/blob/master/python-colab.ipynb|Introduction to Python and notebooks]] ||
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-||||||<tablewidth="100%"style="text-align:center">~+'''Structural MRI I and II'''+~''' - VBM and surface-based analysis '''<<BR>> Marta Correia ||
+||||||<tablewidth="100%"style="text-align:center">~+'''Structural MRI I and II - VBM and surface-based analysis'''+~<<BR>> Marta Correia ||
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-||||||<tablewidth="100%"style="text-align:center">~+'''fMRI I - Data Management'''+~ <<BR>> Dace Apšvalka ||
+||||||<tablewidth="100%"style="text-align:center">~+'''fMRI I - Data Organisation'''+~ <<BR>> Dace Apšvalka ||
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-||||||<tablewidth="100%" tablestyle="margin:0.5em 0px;border-collapse:collapse;border:1px dotted rgb(211, 211, 211);                 "style="padding:0.25em;border:1px dotted rgb(211, 211, 211);text-align:center;">~+'''MVPA/RSA I and II'''+~ <<BR>> Daniel Mitchell & Máté Aller ||
+||||||<tablewidth="100%" tablestyle="margin:0.5em 0px;border-collapse:collapse;border:1px dotted rgb(211, 211, 211);                                          "style="padding:0.25em;border:1px dotted rgb(211, 211, 211);text-align:center;">~+'''MVPA/RSA I and II'''+~ <<BR>> Daniel Mitchell & Máté Aller ||
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-||__Slides and scripts__ ||To be added ||
+||__Slides and scripts__ ||[[attachment:Primer on Python.pdf|Slides]] [[https://github.com/MRC-CBU/COGNESTIC/tree/main/01_Primer_on_Python|Notebooks and HTMLs]] ||
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-||||||<tablewidth="100%"style="text-align:center">~+'''fMRI I - Data Management'''+~ <<BR>> Dace Apšvalka ||
+||||||<tablewidth="100%"style="text-align:center">~+'''fMRI I - Data Organisation'''+~ <<BR>> Dace Apšvalka ||
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-||Slides and scripts__ __ ||TBA ||
+||Slides and scripts__ __ ||Slides: [[attachment:EMEG1_1_Measurement.pdf|1]] [[attachment:EMEG1_2_Preprocessing.pdf|2]] [[attachment:EMEG1_3_Averaging.pdf|3]] [[https://github.com/olafhauk/COGNESTIC2024scripts/|Scripts]] ||
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-||Slides and scripts__ __ ||TBA ||
+||Slides and scripts__ __ ||Slides: [[attachment:EMEG2_1_ForwardModelling.pdf|1]] [[attachment:EMEG2_2_MNE.pdf|2]] [[attachment:EMEG2_3_SpatialResolution.pdf|3]] [[https://github.com/olafhauk/COGNESTIC2024scripts/|Scripts]] ||
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-||Slides and scripts ||TBA ||
+||Slides and scripts ||Slides: [[attachment:EMEG3_1_TimeFrequency.pdf|1]] [[attachment:EMEG3_2_FunctionalConnectivity.pdf|2]] [[attachment:EMEG3_3_AdvancedFunctionalConnectivity.pdf|3]] [[https://github.com/olafhauk/COGNESTIC2024scripts/|Scripts]] ||
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-||<12%>__Software__ ||[[https://www.python.org/|Python 3.7+]], including numpy, matplotlib, & [[https://scikit-learn.org/stable/|scikit-learn]]. <<BR>> (To visualise MRI data, you can use your software of choice, although for nifti format data you might like to consider [[https://www.nitrc.org/projects/mricron|MRIcroN]] or [[https://www.nitrc.org/projects/mricrogl|MRIcroGL]].) ||
||__Datasets__ || ||
+||<12%>__Software__ ||[[https://www.python.org/|Python 3.7+]], including numpy, matplotlib, nilearn & [[https://scikit-learn.org/stable/|scikit-learn]]. <<BR>> (To visualise MRI data, you can use your software of choice, although for nifti format data you might like to consider [[https://www.nitrc.org/projects/mricron|MRIcroN]] or [[https://www.nitrc.org/projects/mricrogl|MRIcroGL]].) ||
||__Datasets__ ||[[https://openneuro.org/datasets/ds003965/versions/1.0.0|"NI-edu-data-minimal" faces dataset]] ||
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-||__Slides and scripts __ ||To be added nearer the time. ||
+||__Slides and scripts __ ||[[https://github.com/MRC-CBU/COGNESTIC/tree/main/09_MVPA_MRI|Notebooks and slides are on the COGNESTIC github]] ||
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-||__Slides and scripts__ ||We will demo the RSA toolbox using the jupyter notebooks in the "demos" folder of the toolbox. <<BR>>[[attachment:EEGMEG5-decoding.zip|EEGMEG Notebooks]] [[attachment:EMEG5_Decoding.pdf|EEG/MEG Slides]]<<BR>> ||
+||__Slides and scripts__ ||We will demo the RSA toolbox using the jupyter notebooks in the "demos" folder of the toolbox, also available, along with the slides, on the COGNESTIC[[https://github.com/MRC-CBU/COGNESTIC/tree/main/09_MVPA_MRI|github]]. <<BR>>[[attachment:EEGMEG5-decoding.zip|EEGMEG Notebooks]] [[attachment:EMEG5_Decoding.pdf|EEG/MEG Slides]]<<BR>> ||




<<BR>> <<Anchor(stimulation)>>
||||||<tablewidth="100%"style="text-align:center;">~+'''Brain Stimulation'''+~''' '''<<BR>> Elizabeth Michael & Ajay Halai ||
||__Reading__ ||TMS-EEG: <<BR>> https://doi.org/10.1016/j.neuroimage.2016.10.031 <<BR>> https://doi.org/10.1016/j.xpro.2022.101435 <<BR>> https://pressrelease.brainproducts.com/tms-eeg/ <<BR>>  <<BR>> TMS-fMRI: <<BR>> https://doi.org/10.31234/osf.io/9fyxb <<BR>> https://doi.org/10.1101/2021.05.28.446111 ||
||Slides||[[attachment:BrainStimSession2024_2.pdf|General]][[attachment:cognestic_TMSEEG.pdf|TMS+EEG]] [[attachment:TMS_FMRI_COGNESTIC_ASSEM.pdf|TMS+fMRI]] [[attachment:TMSfMRIArtifacts_V1_prt_nn.pdf|TMS+fMRI_Artefacts]]||

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Course Material for COGNESTIC 2024

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