21855
Comment:
|
23377
|
Deletions are marked like this. | Additions are marked like this. |
Line 9: | Line 9: |
||__Tutorial slides and scripts__ ||[[attachment:COGNESTIC_OpenCogNeuro.pdf|FSL DTI and TBSS slides]] || | |
Line 19: | Line 19: |
||__Tutorial slides and scripts__ ||[[attachment:COGNESTIC_FSLVBM.pdf|FSLVBM slides]] <<BR>> [[attachment:FSLVBM_tutorials.docx|FSLVBM tutorial]] <<BR>> [[attachment:FSLVBM_cognestic_all.sh|FSLVBM bash script]] <<BR>> <<BR>> [[attachment:COGNESTIC_FS_CorticalThickness.pdf|FreeSurfer Cortical Thickness slides]] <<BR>> [[attachment:FreeSurfer_tutorials.docx|Freesurfer tutorials]] <<BR>> [[attachment:FS_check_location.sh|FS check location script]] <<BR>> [[attachment:FS_visualising_output.sh|FS visualising the output script]]<<BR>> [[attachment:FS_group_analysis.sh|FS group analysis script]] <<BR>> [[attachment:FS_ROI_analysis.sh|FS ROI analysis script]] || | |
Line 29: | Line 30: |
||__Tutorial slides and scripts__ ||[[attachment:COGNESTIC_FSL_DTI&TBSS.pdf|FSL DTI and TBSS slides]] || | |
Line 39: | Line 41: |
||__Tutorial slides and scripts__ ||[[attachment:COGNESTIC_MRtrix_tractography.pdf|MRtrix Tractography slides]] || | |
Line 49: | Line 52: |
||Slides and scripts__ || || | |
Line 59: | Line 62: |
||Slides and scripts__ || || | |
Line 69: | Line 72: |
||Slides and scripts__ || || | |
Line 79: | Line 82: |
||Slides and scripts__ || || | |
Line 89: | Line 92: |
||Slides and scripts__ || || | |
Line 99: | Line 102: |
||Slides and scripts__ || || | |
Line 109: | Line 112: |
||Slides and scripts__ || || | |
Line 119: | Line 122: |
||Slides and scripts__ || || | |
Line 129: | Line 131: |
||Slides and scripts__ || || | |
Line 139: | Line 141: |
||Slides and scripts__ || || | |
Line 148: | Line 150: |
||__Suggested viewing__ ||Excellent presentations from Martin Hebart's MVPA course, on:<<BR>>[[https://fmrif.nimh.nih.gov/course/mvpa_course/2017/02_lecture1|Introduction to MVPA]]<<BR>>[[https://fmrif.nimh.nih.gov/course/mvpa_course/2017/03_lecture2|Introduction to classification]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/27779910/%20|Tutorial on EEG/MEG decoding]] || | ||__Suggested viewing__ ||Excellent presentations from Martin Hebart's MVPA course, on:<<BR>>[[https://fmrif.nimh.nih.gov/course/mvpa_course/2017/02_lecture1|Introduction to MVPA]]<<BR>>[[https://fmrif.nimh.nih.gov/course/mvpa_course/2017/03_lecture2|Introduction to classification]] || ||Slides and scripts__ || || |
Line 157: | Line 159: |
||__Suggested reading__ ||[[https://www.frontiersin.org/articles/10.3389/neuro.06.004.2008/full|Kriegeskorte et al. (2008) Representational similarity analysis - connecting the branches of systems neuroscience]]<<BR>>[[https://www.cell.com/trends/cognitive-sciences/fulltext/S1364-6613(13)00127-7|Kriegeskorte & Kievit (2013) Representational geometry: integrating cognition, computation, and the brain]] <<BR>>[[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003553|Nili et al. (2014) A toolbox for representational similarity analysis]] || | ||__Suggested reading__ ||[[https://www.frontiersin.org/articles/10.3389/neuro.06.004.2008/full|Kriegeskorte et al. (2008) Representational similarity analysis - connecting the branches of systems neuroscience]]<<BR>>[[https://www.cell.com/trends/cognitive-sciences/fulltext/S1364-6613(13)00127-7|Kriegeskorte & Kievit (2013) Representational geometry: integrating cognition, computation, and the brain]] <<BR>>[[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003553|Nili et al. (2014) A toolbox for representational similarity analysis]]<<BR>> <<BR>>EEG/MEG: <<BR>> [[https://pubmed.ncbi.nlm.nih.gov/27779910/%20|Tutorial on EEG/MEG decoding]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/27779910|Temporal Generalization]] || |
Line 159: | Line 161: |
||Slides and scripts__ || || | |
Line 169: | Line 171: |
||Slides and scripts__ || || | |
Line 179: | Line 181: |
||Slides and scripts__ || || | |
Line 189: | Line 191: |
||Slides and scripts__ || || |
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 |
||
Websites |
||
Suggested reading |
Munafo et al, 2017, problems in science |
|
Suggested viewing |
Open Cognitive Neuroscience (will give this talk live on day) |
|
Tutorial slides and scripts |
Structural MRI - VBM and Surface-based Analysis |
||
Software |
||
Datasets |
Freesurfer tutorial data |
|
Suggested reading |
Introduction to GLM for structural MRI analysis |
|
Suggested viewing |
Using the command line |
|
Tutorial slides and scripts |
FSLVBM slides |
Diffusion MRI I - DTI Model Fitting and Group Analysis |
||
Software |
||
Datasets |
||
Suggested reading |
FSL Diffusion Toolbox Wiki |
|
Suggested viewing |
||
Tutorial slides and scripts |
Diffusion MRI II - Tractography and Structural Connectivity |
||
Software |
||
Datasets |
||
Suggested reading |
||
Suggested viewing |
||
Tutorial slides and scripts |
fMRI I - Data management, structure, manipulation |
||
Software |
||
Datasets |
||
Suggested reading |
Gorgolewski et al., 2016, The brain imaging data structure (BIDS) |
|
Suggested viewing |
BIDS for MRI: Structure and Conversion by Taylor Salo (13:39) |
|
Slides and scripts |
|
fMRI II - Quality control & Pre-processing |
||
Software |
||
Datasets |
||
Suggested reading |
Chen & Glover (2015), Functional Magnetic Resonance Imaging Methods |
|
Suggested viewing |
fMRI Artifacts and Noise by Martin Lindquist and Tor Wager (11:57) |
|
Slides and scripts |
|
fMRI IV - Group Level Analysis & Reporting |
||
Software |
||
Datasets |
||
Suggested reading |
Mumford & Nichols (2006), Modeling and inference of multisubject fMRI data |
|
Suggested viewing |
Group-level Analysis I by Martin Lindquist and Tor Wager (7:05) |
|
Slides and scripts |
|
Connectivity for fMRI |
||
Software |
||
Datasets |
||
Suggested reading |
Resting-state functional Connectivity |
|
Suggested viewing |
fMRI Functional Connectivity, including DCM |
|
Slides and scripts |
|
Eye-tracking |
||
Software |
Python NumPy, SciPy, Matplotlib |
|
Datasets |
EyeLink EDF examples (to be provided) |
|
Suggested reading |
https://doi.org/10.3758/s13428-021-01762-8 Paper on eye-tracking reporting standards (great for beginners and experts alike) |
|
Suggested viewing |
https://www.youtube.com/watch?v=F5eBln42VyM Talk at the MRC CBU on how to hack pupillometry studies |
|
Slides and scripts |
|
EEG/MEG I – Pre-processing |
||
Software |
||
Datasets |
Sample dataset in MNE-Python. Tutorials |
|
Suggested reading |
Digitial Filtering |
|
Suggested viewing |
||
Slides and scripts |
|
EEG/MEG II – Source Estimation |
||
Software |
||
Datasets |
Sample dataset in MNE-Python. Tutorials |
|
Suggested reading |
Linear source estimation and spatial resolution |
|
Suggested viewing |
||
Slides and scripts |
|
EEG/MEG III – Time-Frequency and Functional Connectivity |
||
Software |
||
Datasets |
Sample dataset in MNE-Python. Tutorials |
|
Suggested reading |
Tutorial on Functional Connectivity |
|
Suggested viewing |
Time-frequency and functional connectivity analysis |
|
Slides and scripts |
|
Graph Theory |
||
Software |
||
Datasets |
||
Suggested reading |
Complex brain networks: graph theoretical analysis of structural and functional systems |
|
Suggested viewing |
||
Slides and scripts |
|
MVPA/RSA I |
||
Software |
||
Datasets |
The Decoding Toolbox example dataset |
|
Suggested reading |
Mur et al. (2009) Revealing representational content with pattern-information fMRI--an introductory guide |
|
Suggested viewing |
Excellent presentations from Martin Hebart's MVPA course, on: |
|
Slides and scripts |
|
MVPA/RSA II |
||
Software |
The RSA toolbox in Matlab |
|
Datasets |
Group-averged example data from Mitchell & Cusack (2016) Semantic and emotional content of imagined representations in human occipitotemporal cortex |
|
Suggested reading |
Kriegeskorte et al. (2008) Representational similarity analysis - connecting the branches of systems neuroscience |
|
Suggested viewing |
||
Slides and scripts |
|
Statistics in R |
||
Software |
||
Datasets |
||
Suggested reading |
Statistical Methods for Psychology (Howell) |
|
Suggested viewing |
||
Slides and scripts |
|
Brain Stimulation |
||
Software |
SIMNIBS (also requires access to Matlab, FSL and Freesurfer to run certain functions, see SIMNIBS installation guide) and k-wave |
|
Datasets |
||
Suggested reading |
Approaches to brain stimulation ; what can we infer from brain stimulation; using NIBS clinically ; focused ultrasound 1 and 2 |
|
Suggested viewing |
||
Slides and scripts |
|
DCM for M/EEG |
||
Software |
||
Datasets |
||
Suggested reading |
||
Suggested viewing |
Talk on DCM for M/EEG |
|
Slides and scripts |
|