Commit c48693b0 authored by Julian Kosciessa's avatar Julian Kosciessa
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initialize readme, broad script overview

The code provides the scripts used to perform the preprocessing and analyses reported in Kosciessa, J. Q., Lindenberger, U., & Garrett, D. D. (2020). Thalamocortical excitability adjustments guide human perception under uncertainty.
Raw EEG and fMRI will be made available on OSF.
## eeg
- preprocess EEG data (see Wiki page in preproc repo)
- calculate ERPs
- assess CPP, peri-response potential
- time-frequency analysis on pre-response beta power (contra vs. ipsilateral)
- time-frequency wavelet transform for lower frequency range
- multivariate PLS (requires external toolbox) of load effect (requires gamma data, see below)
- multitaper analysis for gamma range, pre-stim normalization
- supplementary analysis of 30 Hz SSVEP (based on single-trial MTM with spectral normalization)
- eBOSC analysis of rhythms during stimulus presentation
- extraction of posterior alpha and frontal theta, linear effects analysis
- cross-frequency coupling between alpha phase and broadband gamma power, using eBOSC's indicated rhythm onsets
- calculate time-resolved sample entropy (1st scale of mMSE toolbox)
- assess linear load effect
- calculate linear background spectrum, assess linear load effect
## eye
- read in of ocular edfs to matrices
- preprocessing of pupil recordings, extract trial epochs
- calculate 1st derivative of pupil, assess linear effect & plot
## behavior
This group contains the scripts used for behavioral analyses, as well as multimodal LMMs.
- read in raw data and build summary matrix across subjects
- plot main effects, and perform linear mixed effects modeling of RTs and Accs
- run hierarchical drift-diffusion models, separately for EEG & MRI session
- assess main effects and inter-individual reliability across sessions
- control analysis: target agreement
- create matrix from individual measures of interest
- export to R
- R: partial repeated measures analyses, bivariate correlations
## fmri_task
This group contains the scripts used for the functional MRI analysis.
- perform fMRI preprocessing (see Methods section)
- DVARS interpolation, CSF + WM regression
- (creates separate output structures used in thalNuclei for plotting)
- creates the first level analysis using SPM
- performs the second level analysis using the SPM matrices as input
- this contains three main steps: 1) specify the task matrices according to design (2) preparing mean BOLD for PLS using the internal function (3) replace data in PLS-created datamats with 1st level SPM betas
- In addition, the scripts create a mask removing any voxels that have no values in any of the subjects
- visualize thalamic loadings and dynamics
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