Newer
Older
The code provides the scripts used to perform the preprocessing and analyses reported in Kosciessa, J.Q., Lindenberger, U. & Garrett, D.D. Thalamocortical excitability modulation guides human perception under uncertainty. Nature Communications 12, 2430 (2021). https://doi.org/10.1038/s41467-021-22511-7
Primary EEG, fMRI, and behavioral data are available from https://osf.io/ug4b8/ (https://doi.org/10.17605/OSF.IO/UG4B8).
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
## 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