Investigating the Specificity of Pre-Speech Auditory Modulation - From Global Gating to Selective Silence?

Note

While this repository might be subject to further changes and optimizations, the repository was further published as a time-stamped, immutable, and permanent version under the DOI above which can be used for exact replication attemps.

This Repository

This repository contains all code related to the research project Investigating the Specificity of Pre-Speech Auditory Modulation – From Global Gating to Selective Silence?, conducted by Tim Dressler at the University of Oldenburg, under the supervision of Prof. Dr. Stefan Debener and Prof. Dr. Andrea Hildebrandt.

The study was preregistered on OSF. Any deviations from the preregistration are documented here.

The repository includes:

• Analysis code used for data evaluation
• Experimental code used for stimulus presentation and data collection
• Supporting documents: participant instructions, questionnaires, etc.

Note: No data is included in this repository but may be made available upon request.

Structure

psam\
│
├── analysis_script\
│   │
│   ├── MATLAB\
│   │   ├── tid_psam_beh_analysis.m
│   │   ├── tid_psam_beh_preprocessing_2.m
│   │   ├── tid_psam_check_filters_erp.m
│   │   ├── tid_psam_check_filters_svm.m
│   │   ├── tid_psam_erp_analysis.m
│   │   ├── tid_psam_erp_pilot.m
│   │   ├── tid_psam_erp_preprocessing.m
│   │   ├── tid_psam_exclude_trials.m
│   │   ├── tid_psam_feature_analysis.m
│   │   ├── tid_psam_helper.m
│   │   ├── tid_psam_hilbert_preparation.m
│   │   ├── tid_psam_ica_preprocessing.m
│   │   ├── tid_psam_questionnaire_input.m
│   │   ├── tid_psam_set_markers.m
│   │   ├── tid_psam_svm_preparation.m
│   │   └── tid_psam_svm_preprocessing.m
│   │
│   ├── R\
│   │   ├── tid_psam_beh_analysis.R
│   │   ├── tid_psam_erp_analysis.R
│   │   ├── tid_psam_get_package_versions.R
│   │   ├── tid_psam_install_requirements_R.R
│   │   ├── tid_psam_questionnaire_analysis.R
│   │   └── tid_psam_svm_analysis.R
│   │
│   ├── praat\
│   │   │
│   │   ├── plugin_VocalToolkit\
│   │   │
│   │   ├── Praat.exe
│   │   ├── tid_psam_beh_preprocessing_1.praat
│   │   └── tid_psam_prepare_stimuli.praat
│   │
│   ├── python\
│   │   └── tid_psam_svm_analysis.py
│   │
│   └── tid_psam_run_pipeline.py
│
├── config\
│
├── data\ (NOT INCLUDED IN THIS REPOSITORY, CAN BE REQUESTED)
│   │
│   ├── BIDS\
│   │
│   └── questionnaire_data\
│
│
├── documents\
│
├── experiment_script\
│   ├── tid_psam_create_conditions_file.m
│   ├── tid_psam_determine_loudness.m
│   ├── tid_psam_main_experiment_ALTERNATIVE_NO_CIRCLE.psyexp
│   ├── tid_psam_main_experiment_ALTERNATIVE_NO_CIRCLE.py
│   ├── tid_psam_select_stimuli.m
│   └── tid_psam_stimuli_recording_ALTERNATIVE_NO_CIRCLE_adapted.py
│
├── functions\
│   ├── bemobil_avref.m
│   ├── bemobil_detect_bad_channels.m
│   ├── shadedErrorBar.m
│   ├── tid_psam_archive_subj_TD.m
│   ├── tid_psam_check_folder_TD.R
│   ├── tid_psam_check_folder_TD.m
│   ├── tid_psam_check_folder_clean_up_folder_TD.py
│   ├── tid_psam_check_id_TD.m
│   ├── tid_psam_clean_up_folder_TD.R
│   ├── tid_psam_clean_up_folder_TD.m
│   ├── tid_psam_copy_files_from_subfolders_TD.m
│   ├── tid_psam_get_transition_bandwidth_TD.m
│   ├── tid_psam_hjorth_activity_TD.m
│   ├── tid_psam_hjorth_complexity_TD.m
│   ├── tid_psam_hjorth_mobility_TD.m
│   ├── tid_psam_plot_flagged_ICs_TD.m
│   └── tid_psam_plot_rms_bins_TD.m
│
├── testing\
│
├── .gitattributes
├── .gitignore
├── LICENSE
├── README.md
└── requirements.txt

• analysis_script contains all code relating to the analysis. Individual scripts can be found in the respective subfolders. To run the entire pipeline (which (only) the raw data is needed for), run tid_psam_run_pipeline.py.
• config contains files related to the EEG system. Needed for the analysis.
• data contains the data. It is not included here be can be requested. If the data is available, it has to be placed in the path. Note that the raw data (BIDS/) and the questionnaire data (questionnaire_data/) is needed for running the pipeline. Processed data will be saved automatically in further subfolders under data/.
• documents contains documents used during the data collection such as the participant information, instructions and the used questionnaires. Not needed to run any of the code.
• experiment_script contains all code related to running the experiment (mainly PsychoPy-based).
• functions contains all code related to any self-created and fetched functions. Some can be used independently of this project. Check them out.
• testing contains mutiple files related to testing. Not needed to run any of the code.
• requirements.txt contains all the libraries used for the python-based analysis scripts. Use pip install -r requirements.txt to install all needed python dependencies.

Note

While the requirements.txt contains all needed dependencies for running the python-based analysis and tid_psam_install_requirements_R.R installs all the requirements needed for the R-based analysis, MATLAB dependencies have to be installed manually (see below). Praat.exe as well as the Praat Vocal Processing Toolbox are included in the repository.

Usage

It is recommended to use a dedicated Python environment (e.g., through Conda) to mitigate the risk of potential version conflicts.

conda create -n psam python==3.13.4
conda activate psam

To install Python dependencies run the following line.

pip install -r requirements.txt

To install R dependencies, run tid_psam_install_requirements_R.R in RStudio.

It is assumed that Conda, R and MATLAB (and the MATLAB dependecies, see below) are installed! It is recommended that the pipeline is run using VSCode.

Warning

As all scripts are called from tid_psam_run_pipeline.py, the path the RScript.exe needs to be adapted manually in the script! Also, paths in the Praat scripts need to be adapted manually!

After requesting the data copy it into the folder as specified above and run tid_psam_run_pipeline.py in VSCode.

Dependecies

This table includes all needed software to run the analysis pipeline.

Type	Software/Package	Version	Status
Software	MATLAB	R2024a	Manual Installation needed
Software	R	4.5.0	Manual Installation needed
Software	Python	3.13.4	Manual Installation needed
Software	Praat	6.4.27	Included in the repository, no installation needed
MATLAB Toolbox	EEGLAB	v2023.0	Manual Installation needed
MATLAB Toolbox	ICLabel	v1.4	Manual Installation needed
MATLAB Toolbox	Audio Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Control System Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Curve Fitting Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Data Acquisition Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	DSP System Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Image Acquisition Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Image Processing Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Instrument Control Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Mapping Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Parallel Computing Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Signal Processing Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	Statistics and ML Toolbox	24.1	Manual Installation needed
MATLAB Toolbox	System Identification Toolbox	24.1	Manual Installation needed
R Package	tidyr	1.3.1	Automatically installed
R Package	afex	1.4.1	Automatically installed
R Package	emmeans	1.11.1	Automatically installed
R Package	readxl	1.4.5	Automatically installed
R Package	car	3.1.3	Automatically installed
R Package	corrplot	0.95	Automatically installed
R Package	dplyr	1.1.4	Automatically installed
R Package	ez	4.4.0	Automatically installed
R Package	ggplot2	3.5.2	Automatically installed
R Package	ggstatsplot	0.13.1	Automatically installed
R Package	DescTools	0.99.60	Automatically installed
R Package	ggpubr	0.6.0	Automatically installed
R Package	ggeffects	2.2.1	Automatically installed
R Package	cowplot	1.1.3	Automatically installed
R Package	tidyverse	2.0.0	Automatically installed
R Package	psych	2.5.3	Automatically installed
R Package	rstatix	0.7.2	Automatically installed
R Package	rstudioapi	0.17.1	Automatically installed
R Package	stringr	1.5.1	Automatically installed
R Package	lme4	1.1.37	Automatically installed
R Package	performance	0.14.0	Automatically installed
R Package	Rmisc	1.5.1	Automatically installed
R Package	nparLD	2.2	Automatically installed
R Package	RVAideMemoire	0.9.83.11	Automatically installed
R Package	effectsize	1.0.1	Automatically installed
R Package	lmerTest	3.1.3	Automatically installed
R Package	smplot2	0.2.5	Automatically installed
R Package	devtools	2.4.5	Automatically installed
R Package	renv	1.1.4	Automatically installed
Python Package	colorama	0.4.6	Automatically installed
Python Package	contourpy	1.3.2	Automatically installed
Python Package	cycler	0.12.1	Automatically installed
Python Package	et_xmlfile	2.0.0	Automatically installed
Python Package	fonttools	4.58.2	Automatically installed
Python Package	joblib	1.5.1	Automatically installed
Python Package	kiwisolver	1.4.8	Automatically installed
Python Package	matplotlib	3.10.3	Automatically installed
Python Package	numpy	2.3.0	Automatically installed
Python Package	openpyxl	3.1.5	Automatically installed
Python Package	packaging	25.0	Automatically installed
Python Package	pandas	2.3.0	Automatically installed
Python Package	pillow	11.2.1	Automatically installed
Python Package	pip	25.1	Automatically installed
Python Package	pyparsing	3.2.3	Automatically installed
Python Package	python-dateutil	2.9.0.post0	Automatically installed
Python Package	pytz	2025.2	Automatically installed
Python Package	scikit-learn	1.7.0	Automatically installed
Python Package	scipy	1.15.3	Automatically installed
Python Package	seaborn	0.13.2	Automatically installed
Python Package	setuptools	78.1.1	Automatically installed
Python Package	six	1.17.0	Automatically installed
Python Package	threadpoolctl	3.6.0	Automatically installed
Python Package	tqdm	4.67.1	Automatically installed
Python Package	tzdata	2025.2	Automatically installed
Python Package	wheel	0.45.1	Automatically installed
Praat Tool	Praat Vocal Toolkit	2012–2024	Included in the repository, no installation needed