ECoG_alphaPRF

Analysis tools and MATLAB scripts for Yuasa et al., 2023, "Spatial tuning of alpha oscillations in human visual cortex" (eLife reviewed preprint: https://elifesciences.org/reviewed-preprints/90387). This repository contains all necessary code to reproduce the analyses and figures from the paper.

Initial Setup

Option 1: Using ToolboxToolbox (Recommended)

1. Install ToolboxToolbox

2. Set up the configuration files using either method:

   Method A: Using Winawerlab Registry

   1. Download the Winawerlab toolbox registry:

      # For MacOS
      rm -rf ~/MATLAB/toolboxes/ToolboxRegistry
      git clone https://github.com/WinawerLab/ToolboxRegistry ~/MATLAB/toolboxes/ToolboxRegistry

      See also: https://wikis.nyu.edu/display/winawerlab/ToolboxToolbox

   Method B: Direct Configuration

   1. Download and copy configuration files:

      # For MacOS
      git clone https://github.com/KenYMB/ECoG_alphaPRF ~/MATLAB/toolboxes/ECoG_alphaPRF
      cp ECoG_alphaPRF/ToolboxToolbox/*.json ~/MATLAB/toolboxes/ToolboxRegistry/configurations/

3. Install dependencies:

   tbUse ECoG_alphaPRF

Option 2: Manual Setup

1. Download and set path to the following toolboxes:
   • ECoG_alphaPRF (This toolbox: https://github.com/KenYMB/ECoG_alphaPRF)
   • ECoG_utils (https://github.com/WinawerLab/ECoG_utils)
   • analyzePRF (https://github.com/cvnlab/analyzePRF)
   • Fieldtrip (https://github.com/fieldtrip/fieldtrip)

Analysis Setup

1. Set Working Directory

You have three options to set the working directory for saving data and figures:

A. Edit the file analysisRootPath.m in the 'Environment' folder:

rootPath = 'YOUR/ANALYSIS/DIRECTORY';  % Edit this line in the file

B. Set the analysis directory by running this command in MATLAB:

analysisRootPath = 'YOUR/ANALYSIS/DIRECTORY';  % The toolbox will use this directory for analysis

Note: This sets a MATLAB variable that the toolbox uses to determine where to save data and figures.

C. Copy analysisRootPath.m to your current working directory (the toolbox will use this location)

Note: If no working directory is specified through any of these methods, the toolbox defaults to its installation location.

2. Download Data

The BIDS-formatted dataset is available on OpenNeuro: Visual ECoG dataset

To automatically download the data (only available if 'openneuro' is already installed on Mac/Linux; new installations are no longer supported).:

s0_downloadData

Getting Started

• Example scripts are available in the 'SampleScripts' directory
• To reproduce the paper's main figures, run s7_makeFigures
• For supplementary figures, run s8_makeSupplementaryFigures