This repository contains Matlab code to reproduce analyses and figures reported in Piantoni G, Montenegro S, Flinker A, Devore S, Devinsky O, Doyle W, Dugan P, Friedman D, Ramsey N, Petridou N, Winawer JA (2022) Temporal dynamics of neural responses in human visual cortex. The Journal of Neuroscience 42(40):7562-7580 (https://doi.org/10.1523/JNEUROSCI.1812-21.2022).
Paper figures can be reproduced by running the scripts located in mkFigures/.
The full pipeline, to extract and process the data for the analyses reported in the paper, can be run using the script tde_run.m
First, it is necessary to download the BIDS-formatted data from OpenNeuro: Visual ECoG dataset https://openneuro.org/datasets/ds004194
The files located in the derivatives/Groen2022TemporalDynamics/ folder on OpenNeuro should be placed in a directory inside this Github repository named 'analysis' (see function help for analysisRootPath.m).
The script tde_run.m contains demo code showing how to extract and preprocess the data from the main BIDS directory and how to fit temporal models to the resulting neural time courses.
The code has dependencies to the following toolboxes:
- https://github.com/WinawerLab/ECoG_utils
- https://github.com/fieldtrip/fieldtrip
- https://github.com/acerbilab/bads
When using the repository, it may be helpful to make use of the ToolboxToolbox which is a Matlab toolbox provided by provided by ToolboxHub to manage code/toolbox dependencies. See https://wikis.nyu.edu/display/winawerlab/ToolboxToolbox for more instructions on how to set it up. The relevant ToolboxToolbox config associated with this Github repository is located here: https://github.com/WinawerLab/ToolboxRegistry/blob/master/configurations/temporalECoG.json
Some of the data (e.g. retinotopic atlases) were computed using code located in: https://github.com/BAIRR01/BAIRanalysis
Please contact Iris Groen (i.i.a.groen@uva.nl, https://orcid.org/0000-0002-5536-6128) for questions.