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Course Material for COGNESTIC 2022

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

Below you will find documents, videos and web links that will be used for the course or can be used for preparation.

Introduction and Open Science Rik Henson & Olaf Hauk
Websites	OSF UKRN BIDS
Suggested 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
Suggested viewing	Statistical power in neuroimaging PayWall: open access Comedian's Perspective on science and media

Structural MRI Marta Correia
Software	FSL Freesurfer
Datasets	Freesurfer tutorial data
Suggested reading	Good et al, 2001, A VBM study of ageing Smith et al, 2004, Structural MRI analysis in FSL Dale et al, 1999, Cortical surface-based analysis I Fischl et al, 1999, Cortical surface-based analysis II
Suggested viewing	Using the command line Introduction to MRI Physics talk coming soon.

Diffusion MRI I Marta Correia
Software	FSL
Datasets	BTC_preop
Suggested reading	FSL Diffusion Toolbox Wiki Smith et al, 2006, Tract-based spatial statistics (TBSS)
Suggested viewing	Introduction to Diffusion MRI talk coming soon.

Diffusion MRI II Marta Correia
Software	MRtrix3
Datasets	BTC_preop
Suggested reading
Suggested viewing	Introduction to Diffusion MRI talk coming soon.

fMRI I - Data management, content, manipulation Dace Apšvalka
Software
Datasets	Wakeman Multimodal
Suggested reading
Suggested viewing

fMRI II - Quality control & Pre-processing Dace Apšvalka
Software
Datasets	Wakeman Multimodal
Suggested reading
Suggested viewing

fMRI III - Statistical Analysis Dace Apšvalka
Software
Datasets	Wakeman Multimodal
Suggested reading
Suggested viewing

fMRI IV - Reporting Dace Apšvalka
Software
Datasets	Wakeman Multimodal
Suggested reading
Suggested viewing

Connectivity for fMRI Rik Henson
Software	SPM12
Datasets	Wakeman Multimodal
Suggested reading	Resting-state functional Connectivity Simple Intro to DCM fMRI preprocessing in SPM12 (for demo) SPM12 manual (Chapter 36)
Suggested viewing	fMRI Functional Connectivity, including DCM Talk on Bayesian Model Comparison coming soon

Eye-tracking Edwin Dalmijer
Software
Datasets
Suggested reading
Suggested viewing

EEG/MEG I – Pre-processing Olaf Hauk
Software	MNE-Pythonneuro
Datasets	Sample dataset in MNE-Python. Tutorials
Suggested reading	Digitial Filtering Filtering How To Maxwell Filtering
Suggested viewing	Preprocessing What are we measuring with M/EEG?

EEG/MEG II – Source Estimation Olaf Hauk
Software	MNE-Python
Datasets	Sample dataset in MNE-Python. Tutorials
Suggested reading	Linear source estimation and spatial resolution
Suggested viewing	M/EEG Source Analysis in SPM

EEG/MEG III – Time-Frequency and Functional Connectivity Olaf Hauk
Software	MNE-Python
Datasets	Sample dataset in MNE-Python. Tutorials
Suggested reading	Tutorial on Functional Connectivity Analyzing Neural Time Series Data
Suggested viewing	Time-frequency and functional connectivity analysis Time-Frequency Analysis of EEG Time Series

Graph Theory Caroline Nettekoven
Software	Brain Connectivity Toolbox in Matlab
Datasets	Coding exercises Exercise solutions
Suggested reading	Complex brain networks: graph theoretical analysis of structural and functional systems
Suggested viewing	Slides

MVPA/RSA I Daniel Mitchell
Software	The Decoding Toolbox in Matlab
Datasets	The Decoding Toolbox example dataset (See toolbox webpage for a lower resolution alternative)
Suggested reading	Mur et al. (2009) Revealing representational content with pattern-information fMRI--an introductory guide Hebart et al. (2014) The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data
Suggested viewing	Excellent presentations from Martin Hebart's MVPA course, on: Introduction to MVPA Introduction to classification

MVPA/RSA II Daniel Mitchell
Software	The RSA toolbox in Matlab (Alternatively, https://git.fmrib.ox.ac.uk/hnili/rsa)
Datasets
Suggested 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
Suggested viewing	Martin Hebart's lecture on RSA

Statistics in R Peter Watson
Software	R
Datasets	Data&Code Readme
Suggested reading	Statistical Methods for Psychology (Howell) Introduction to R
Suggested viewing	CBU Statistics Lectures

Brain Stimulation Ajay Halai
Software
Datasets
Suggested reading
Suggested viewing

DCM for M/EEG Rik Henson
Software	SPM12
Datasets	Wakeman Multimodal
Suggested reading	Preprocessing M/EEG in SPM12 Simple Intro to DCM
Suggested viewing	Talk on DCM for M/EEG coming soon MEEG connectivity other than DCM (not demo'ed, and related to Hauk talks above)

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Course Material for COGNESTIC 2022