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.
Below you will find documents, videos and web links that will be used for the course or can be used for preparation.
Software Installation Instructions
Access to much of the COGNESTIC-23 materials is available via Virtual Machine (VM). You will need at least 70GB of free space on your local hard drive, and at least 4GB of RAM. For instructions on how to install and set up the Cognestic23 VM see section ‘1 COGNESTIC Virtual Machine (full hands-on)’ for instructions. Data for the Structural MRI and Diffusion MRI are located inside the VM.
Full installation instructions can be found here. The installation can take some time (potentially more than an hour, depending on your download speed), so please reserve some time for this ahead of the event.
Essential
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).
(sessions below should be ordered as they will be in course, but just did my ones for an example)
Background to Open Science |
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Viewing |
Network Analysis |
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Viewing |
Additional Extra
If you want additional background, consider some of the below:
Background to Open Science |
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Websites |
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Reading |
Munafo et al, 2017, problems in science |
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Viewing |
Statistical power in neuroimaging |
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Slides |
Brain Network Analysis |
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Software |
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Datasets |
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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 |
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Viewing |
Understanding your brain as a network and as art by Prof. Dani Bassett. |
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Slides |
https://github.com/isebenius/COGNESTIC_network_analysis/ Slides |
***Below not updated yet
Primer on Python |
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Websites |
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Suggested reading |
None |
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Suggested viewing |
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Tutorial slides and scripts |
None |
Structural MRI I - Voxel-based morphometry |
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Software |
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Datasets |
Subset of the CamCAN dataset (~3GB) https://www.cam-can.org/, please sign data user agreement if using |
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Suggested reading |
Introduction to GLM for structural MRI analysis |
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Suggested viewing |
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Tutorial slides and scripts |
Intro to command line |
Structural MRI II - Surface-based analyses |
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Software |
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Datasets |
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Suggested reading |
Dale et al, 1999, Cortical surface-based analysis I |
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Suggested viewing |
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Tutorial slides and scripts |
Freesurfer slides |
Diffusion MRI I - The Diffusion Tensor Model |
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Software |
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Datasets |
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Suggested reading |
FSL Diffusion Toolbox Wiki |
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Suggested viewing |
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Tutorial slides and scripts |
FSL DTI and TBSS slides |
Diffusion MRI II - Tractography and the Anatomical Connectome |
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Software |
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Datasets |
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Suggested reading |
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Suggested viewing |
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Tutorial slides and scripts |
MRTrix tractography slides |
fMRI I - Data management, structure, manipulation |
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Software |
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Datasets |
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Suggested reading |
Gorgolewski et al., 2016 |
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Suggested viewing |
BIDS for MRI: Structure and Conversion by Taylor Salo (13:39) |
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Slides and scripts |
fMRI II - Quality control & Pre-processing |
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Software |
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Datasets |
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Suggested reading |
Chen & Glover (2015), Functional Magnetic Resonance Imaging Methods |
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Suggested viewing |
fMRI Artifacts and Noise by Martin Lindquist and Tor Wager (11:57) |
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Slides and scripts |
fMRI IV - Group Level Analysis & Reporting |
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Software |
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Datasets |
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Suggested reading |
Mumford & Nichols (2006), Modeling and inference of multisubject fMRI data |
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Suggested viewing |
Group-level Analysis I by Martin Lindquist and Tor Wager (7:05) |
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Slides and scripts |
fMRI Connectivity |
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Software |
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Datasets |
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Suggested reading |
Resting-state functional Connectivity |
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Suggested viewing |
fMRI Functional Connectivity in fMRI |
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Tutorial slides and scripts |
Functional Connectivity Nilearn Practical |
EEG/MEG I – Measurement and Pre-processing |
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Software and datasets |
This will be part of a download that will become available later. |
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Essential and suggested viewing |
0. Overview of EEG/MEG data processing from raw data to source estimates |
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Suggested reading |
Digitial Filtering |
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Slides and scripts |
TBA |
EEG/MEG II – Head Modelling and Source Estimation |
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Software and datasets |
This will be part of a download that will become available later. |
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Essential and suggested viewing |
0. Overview of EEG/MEG data processing from raw data to source estimates |
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Suggested reading |
Linear source estimation and spatial resolution |
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Slides and scripts |
TBA |
EEG/MEG III – Time-Frequency and Functional Connectivity Analysis |
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Software and datasets |
This will be part of a download that will become available later. |
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Essential and suggested viewing |
1. The basics of signals in the frequency domain |
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Suggested reading |
Tutorial on Functional Connectivity |
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Slides and scripts |
TBA |
EEG/MEG IV – Statistics and BIDS |
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Software |
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Datasets |
Sample dataset in MNE-Python. Tutorials |
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Suggested reading |
Estimating subcortical sources from EEG/MEG |
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Suggested viewing |
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Slides and scripts |
Notebooks Exercises Slides1 Slides2 |
MVPA/RSA I |
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Software |
CoSMoMVPA using Octave. (These are not included in the virtual machine; you will need to install them yourself. If you have Matlab, you are welcome to use it instead of Octave, but the demos will be in Octave because it is open source.) |
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Datasets |
Tutorial data from CoSMoMVPA toolbox |
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Suggested reading |
Mur et al. (2009) Revealing representational content with pattern-information fMRI--an introductory guide |
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Suggested viewing |
Excellent presentations from Martin Hebart's MVPA course, on: |
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Slides and scripts |
We will be using the demos from the "examples" folder of the CoSMoMVPA toolbox. |
MVPA/RSA II |
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Software |
Python implementation of the RSA Toolbox: Version 3.0 |
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Datasets |
Example data included with RSA toolbox |
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Suggested reading |
Kriegeskorte et al. (2008) Representational similarity analysis - connecting the branches of systems neuroscience |
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Suggested viewing |
Martin Hebart's lecture on RSA |
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Slides and scripts |
We will demo the RSA toolbox using the jupyter notebooks in the "demos" folder of the toolbox. |