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

parents
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
--------
*preproc*
- preprocess EEG data (see Wiki page in preproc repo)
*ERP*
- calculate ERPs
- assess CPP, peri-response potential
*tfr_periresponse*
- time-frequency analysis on pre-response beta power (contra vs. ipsilateral)
*tfr*
- time-frequency wavelet transform for lower frequency range
- multivariate PLS (requires external toolbox) of load effect (requires gamma data, see below)
*gamma*
- multitaper analysis for gamma range, pre-stim normalization
*ssvep*
- supplementary analysis of 30 Hz SSVEP (based on single-trial MTM with spectral normalization)
*rhythmdetection*
- eBOSC analysis of rhythms during stimulus presentation
- extraction of posterior alpha and frontal theta, linear effects analysis
*cfc*
- cross-frequency coupling between alpha phase and broadband gamma power, using eBOSC's indicated rhythm onsets
*entropy*
- calculate time-resolved sample entropy (1st scale of mMSE toolbox)
- assess linear load effect
*aperiodic*
- calculate linear background spectrum, assess linear load effect
## eye
--------
*preproc*
- read in of ocular edfs to matrices
*pupil*
- 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.
*behavMerge*
- read in raw data and build summary matrix across subjects
- plot main effects, and perform linear mixed effects modeling of RTs and Accs
*HDDM*
- run hierarchical drift-diffusion models, separately for EEG & MRI session
- assess main effects and inter-individual reliability across sessions
- control analysis: target agreement
*multimodal*
- 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.
*preproc*
- perform fMRI preprocessing (see Methods section)
*preproc_extended*
- DVARS interpolation, CSF + WM regression
- (creates separate output structures used in thalNuclei for plotting)
*spm*
- creates the first level analysis using SPM
*pls*
- 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
*thalNuclei*
- visualize thalamic loadings and dynamics
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