README.md

Description

This folder contains all the code necessary for processing and analyzing the data, computing statistics, and making individual figure panels for the toonCat project (Yao et al., 2025).

Table of Contents

• Dependencies
• Folder Structure
• Usage

Dependencies

Code should run on your local machine assuming the following dependencies

Processing Pipeline

• MATLAB 2023a
• Freesurfer v6.0
• vistasoft (https://github.com/vistalab/vistasoft)
• knkutils (https://github.com/kendrickkay/knkutils)
• alignvolumedata (https://github.com/kendrickkay/alignvolumedata)

Analysis Pipeline

• R >= 4.2.2
• tidyverse
• dplyr
• ggplot2
• lme4
• emmeans
• janitor
• extrafont
• kableExtra
• sjPlot
• broom
• rlang
• fs

Folder Structure

processing: Includes numbered MATLAB scripts used to process the structural and functional data.

• toonCat_step1 - toonCat_step3: pRF analysis; these scripts run the pRF model (step1), setup retinopic map drawing (step2), and extract retinotopic data from each individual and prepare it for analysis (step3). Also outputs center and coverage panels for Fig 3A and Fig 4A&B.
• toonCat_step4 - toonCat_step6: category-selectivity analysis; these scripts run fLoC analysis (step4), setup category ROI drawing (step5), and extract category data from each individual and prepare it for analysis (step6)
• utils: Contains functions for each of the steps, organized via subdirectories step#/

analysis: Includes code used to analyze data extracted from the processing code, perform LMMs, and generate output figures.

• code: Contains R and R markdown files used to generate main figures and supplementary figures.
• data: Contains processed data used for figure generation and statistics
• figures_tables: Contains main figure outputs and supplement figures outputes and tables. Tables contain full statistical outputs in .png and .csv formats.

Usage

To regenerate all data, install all processing dependencies, run code in processing,and then run code in analysis. To rerun statistics, use processed data and only run analysis code; setup/dependency installation is included in pipeline (toonCat_analysisSetup.R).