smathot/pupillometry_erg_and_eeg

Analysis scripts for a study using pupillometry, ERG, and EEG to study low-level visual perception

Spontaneous Fluctuations in Pupil Size Shape Retinal Responses to Visual Stimuli

Experimental resources for the following manuscript:

• Mathôt, S., Weiden, D., Dimigen, O. (in preparation). Spontaneous Fluctuations in Pupil Size Shape Retinal Responses to Visual Stimuli.

Analysis code is stored on GitHub:

• https://github.com/smathot/pupillometry_erg_and_eeg

Everything else (experiment file, data, checkpoints, and output) is stored on the OSF:

• https://osf.io/g5utq/

Dependencies

The main dependencies are eeg_eyetracking_parser and datamatrix (>= 1.0) which can be installed as follows:

pip install eeg_eyetracking_parser datamatrix

See environment.yaml for a complete description of the Python environment used for the analysis.

The experiment file requires OpenSesame 4.0. The experiment requires the Pulse_EVT2 plug-in, which needs to be installed separately.

System requirements

Most of the analyses require 16GB of memory. To run the memoization script for multiple participants in parallel, 64 GB is recommended. To speed up the decoding analyses, a cuda-enabled graphics card is recommended.

Running the analysis

Explanation of files and folders on the OSF

The analysis scripts are hosted on GitHub. However, the data files, intermediate files, and output files are hosted on the OSF. You need both in order to reproduce the analyses.

• data\ contains .zip archives with the raw data organized in BIDS format. There is one archive per participant, which needs to be extracted. Eye tracking data is in EyeLink .edf format. EEG data is in Brain Vision format (.vhdr, .vmrk, .eeg).
• checkpoints\ contains processed data named by the date on which they were generated.

Analysis scripts

The analysis scripts are named by the type of analysis they perform. In addition, analysis_utils.py is a module with helper functions that are used by the other analysis scripts. This file is not intended to be executed directly.

Data logbook

• In the .vmrk file for session 82, line 263 contained an extraneous trigger that was manually removed.
• In the .vmrk file for session 111, line 184 contained an extraneous trigger that was manually removed.
• Sessions 101, 102 were excluded due to excessive blinking and reduced data quality.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.