Paper Hermes 2019 eLife

This repository contains functions and scripts that were used in developing the OV model and generate the results and figures from Hermes et al, 2019. If you use this code as a part of any publications, please please cite this work.

Code (c) Dora Hermes, Kendrick Kay and Jonathan Winawer

Please direct any comments about the code via the issues page associated with this GitHub repository, or via email to [email protected]

Download data

The data can be downloaded from https://osf.io/q4yad/. Unzip it and you should have all the data in the folder /data/. Move this directory to /root/directory/of/Paper_Hermes_2019_eLife/. The data can also be downloaded by running the code gammaModelDownloadData.m in /root/directory/of/Paper_Hermes_2019_eLife/.

Note on _events.tsv: in subject 3, we later found that there was a 73 ms additional delay in the connection between the stimulus onset and the moment the code arrived on the computer. Subtracting 73 ms from the stimulus onset will fix this error.

Software dependencies

Make sure that the following toolboxes are downloaded and in the path:

1. MATLAB utility functions written by Kendrick Kay (https://github.com/kendrickkay/knkutils)

   Put the root directory and all sub-directories in MATLAB path.

2. FileTrip (https://github.com/fieldtrip/fieldtrip)

   It is not recommended to put all sub-directories into MATLAB path, but rather put the /root/of/fieldtrip/ in the path, then run ft_defaults. Check this out.

3. VISTASOFT of VISTA lab at Stanford University (https://github.com/vistalab/vistasoft)

   Put the root directory and all sub-directories in MATLAB path.

4. JSONio (https://github.com/gllmflndn/JSONio)

   Put the root directory and all sub-directories in MATLAB path.

5. Chronux (http://chronux.org/)

   Put the root directory and all sub-directories in MATLAB path.

Matlab toolboxes:

1. curve_fitting_toolbox
2. optimization_toolbox
3. signal_toolbox
4. statistics_toolbox

Reproducing figures

The analyses data can be loaded and the figures can be reproduced with the functions in: /make_figures/

Reproducing analyses

Functions to analyses the data and fit the models can be found here: /processing/. Please note that the raw iEEG data are not included. Interested reader should refer to the reference Hermes, 2019 or script preprocess_ECoGDataBeforeShare.m for the detailed steps of pre-processing the raw data.

Acknowledgements

This code was made available with the support of the Netherlands Organization for Scientific Research www.nwo.nl under award number 016.VENI.178.048 to Dora Hermes and the National Institute Of Mental Health of the National Institutes of Health under Award Number R01MH111417 to Natalia Petridou and Jonathan Winawer. The ECoG data collection was facilitated by the Stanford Human Intracranial Cognitive Electrophysiology Program (SHICEP) and the Epilepsy Team at the UMC Utrecht Brain Center.

Reference

Hermes D, Petridou N, Kay K, Winawer J. 2019 An image-computable model for the stimulus selectivity of gamma oscillations. eLife 2019;8:e47035. DOI: https://doi.org/10.7554/eLife.47035