BSc-Thesis: Effect of stimulus duration on event-related potentials during a rapid serial visual presentation task
Author: Jan Sauter
Supervisor(s): René Skukies, Martin Geiger
Year: 2025
The main goal was to assess the effect of stimulus durations (100-15000 ms) in a rapid serial presentation (RSVP) task with faces as visual stimuli and no inter-stimulus intervals (ISIs). Further the applicability of deconvolution-based overlap correction in combination with duration modelling was assessed. Also linear and non-linear modelling approaches for the duration effect were compared and the effect of ISIs was analyzed with a control task condition where ISIs varied (800-2500 ms). An additional analysis on a habituation effect during a stimulus sequence was conducted as well.
The Preprocessing script Preprocessing_final.m was ran on the raw data from Martin Geigers study /store/dat/MSc_EventDuration.
Script requirements: function/ccs_runamica15.m script running the amica algorithm (provided by the CCS group)
Preprocessed EEG data and corresponding event files were saved to derivative folder /store/dat/MSc_EventDuration/derivatives/25_Jan_BSc_preprocessing/preprocessed_final in BIDS conform format.
Due to issues with the preprocessing script the VEOGU EOG channel subjects 13, 38 were not preprocessed.
The script contains boolean values which indicate wether output should be genrated for several steps of the preprocessing, which would then be saved in the derivative folder. Final results of these outputs can be found in the following directories/files:
- Channels removed (
bad_channels/bad_channels_overview_final.csv) - ICA components and overview (overview:
ica/amica/ica_rejection_overview_final.csv, individual components:ica/amica/components_final/ica_rejection_overview_final.csv) - Sections marked by ASR rejection (
ASR_cleaning_final)
The filter_50Hz folder also contains the output from two suspicious subjects which were saved manually
For the individual inspection of the ERPs from each subject, the anaylsis_singleSubjects.jl must be ran.
The script offers interaction feautures which allow to select a subject and channel (P7, PO7, P8, PO8, O1, O2) for inspection of the ERPs.
Analysis accross all subjects was conducted in the analysis_group_blank.jl for the ISI effect and analysis_group_duration.jl for the stimulus duration effect.
The scripts also contain interaction features which allow to choose the channel which should be visualized and toggle between task conditions regarding the cluster-depth permutation test outputs for the ISI effect analysis.
Plots used in figures were usually generated at the end of a section and then used in Affinity Designer to generate complex plots.
These complex plots are saved in the plots folder of this git repository.
The notebooks produce plots in the outputs from which the complex plots are generated from or can at least be retraced to.
The notebook visualizations.jl contains which generates visualizations for the stimulus duration and ISI duration distributions, which were also used in the task.png figure.
visualizations.ipynb contains code in order to generate visualizations of removed channels.
│projectdir <- Project's main folder. It is initialized as a Git
│ repository with a reasonable .gitignore file.
│
├── report <- **Immutable and add-only!**
│ ├── proposal <- Proposal PDF
│ ├── thesis <- Final Thesis PDF
│ ├── talks <- PDFs (and optionally pptx etc) of the Intro,
| | Midterm & Final-Talk
|
├── _research <- WIP scripts, code, notes, comments,
│ | to-dos and anything in an alpha state.
│
├── plots <- All exported plots go here, best in date folders.
| | Note that to ensure reproducibility it is required that all plots can be
| | recreated using the plotting scripts in the scripts folder.
|
├── notebooks <- Pluto, Jupyter, Weave or any other mixed media notebooks.*
│
├── scripts <- Various scripts, e.g. simulations, plotting, analysis,
│ │ The scripts use the `src` folder for their base code.
│
├── src <- Source code for use in this project. Contains functions,
│ structures and modules that are used throughout
│ the project and in multiple scripts.
│
├── test <- Folder containing tests for `src`.
│ └── runtests.jl <- Main test file
│ └── setup.jl <- Setup test environment
│
├── README.md <- Top-level README. A fellow student needs to be able to
| | continue your project. Think about her!!
|
├── .gitignore <- focused on Julia, but some Matlab things as well
│
├── (Manifest.toml) <- Contains full list of exact package versions used currently.
|── (Project.toml) <- Main project file, allows activation and installation.
└── (Requirements.txt)<- in case of python project - can also be an anaconda file, MakeFile etc.
*Instead of having a separate notebooks folder, you can also delete it and integrate your notebooks in the scripts folder. However, notebooks should always be marked by adding nb_ in front of the file name.