README.md

Brain-behaviour relationship in scene categorization

This code was used for the project "Empirically identifying and computationally modelling the brain-behavior relationship for human scene categorization" by Karapetian et al. (2023). The code was written in Matlab 2021a, Python 3.6 and Tensorflow 2.7.

To clone this repository, use

git clone https://github.com/Agnessa14/Perceptual-decision-making.git

1. Preprocessing of EEG data

• Preprocess the EEG data according to the standard steps, as described in the manuscript: Preprocessing_PDM_full_experiment.m.

This script relies on functions from the Fieldtrip toolbox.

The output is a Matlab structure timelock.mat which is used in subsequent analyses.

2. Decoding (MVPA)

Decoding and distance-to-hyperplane analyses were performed with the SVM from the libsvm toolbox:.

1. Scene decoding

• Decode individual scene identity from subject-level EEG data: SVM_object_decoding_full_experiment.m

• Average the decoding results across individuals and plot the results: plot_decoding_both_tasks.m

2. Category decoding

• Decode scene category from subject-level EEG date: dth_pseudotrials_SVM_full_experiment_cross_validated.m

• Average the decoding results across individuals and plot the results: plot_decoding_both_tasks.m

3. Searchlight analysis

• Perform decoding in channel space:
  • subject-level:
    • scene identity: SVM_object_decoding_full_experiment_searchlight.m
    • scene category: dth_pseudotrials_SVM_full_experiment_cross_validated_sl.m
  • average: all_subjects_decoding_sl.m
  • plot: plot_topography_searchlight_decoding.m

4. Multidimensional scaling (MDS)

• Visualize peak decoding results using MDS: mds_peak_decoding.m

• Visualize peak distance-to-hyperplane results: mds_peak_dth_correlation.m

3. Distance-to-hyperplane analysis

1. Obtain the subject-level distances to the natural/man-made hyperplane

• Using the same script as for category decoding, calculate the distances: dth_pseudotrials_SVM_full_experiment_cross_validated.m

2. Correlate distances and reaction times

• Correlate the subject-level distances with median RTs, average over subjects, and plot: dth_all_distances_median_RT.m

• Plot results from both tasks together: plot_dth_both_tasks.m

3. Searchlight analysis

• Perform distance-to-hyperplane analysis in channel space:
  • subject-level: dth_pseudotrials_SVM_full_experiment_cross_validated_sl.m
  • average: dth_all_distances_median_RT_searchlight.m
  • plot: plot_topography_searchlight_dth_ak.m

4. Modelling with RCNN

1. Fine-tuning RCNN

• Fine-tune the BLNet (from Spoerer et al., original repo here) - initially trained on ecoset (Mehrer et al., 2017): rnn_dth_finetune_rnn_larger_dataset.ipynb

• Load the weights from the fine-tuned model:

import urllib
_, msg = urllib.request.urlretrieve(
    'https://osf.io/4fdky/download', 'model_02.11_2_weights.h5')
print(msg)

2. Feature and RT extraction

• Extract features from hidden layers and RTs from the prediction layer: rnn_dth_collect_activations.ipynb

3. Representational similarity analysis (RSA) with EEG

1. EEG representational dissimilarity matrix (RDM) construction

• Create subject-level RDMs at every time point using 1-Pearson's r: pearson_object_decoding_full_experiment.m

• Calculate the noise ceiling: noise_ceiling_rsa.m

2. RCNN RDM construction

• Create RDMs using 1-Pearson's r at the selected layers and time steps: RNN_test_Input_RDM_Correlations.ipynb

3. Correlation between RDMs

• Correlate (Spearman's) subject-level EEG and RCNN RDMs at every time point, selected layer and network time step: rsa_rnn_eeg_subject_by_subject_averaged_timesteps.m

4. Correlation between RTs

• Correlate (Pearson's) every subject's RTs with RCNN RTs and plot: plot_RT_rnn_vs_human.m

• Calculate the noise ceiling: noise_ceiling_RT.m

5. Distance-to-hyperplane analysis between EEG and RCNN RTs

• Correlate subject-level EEG distances with RCNN RTs: rnn_dth_all_distances_median_RT.m

5. Statistics examples

• Permutation test and FDR correction: fdr_permutation_stats.m

• Bootstrapping: bootstrap_peak_latency.m