Extended Data Fig. 9: Functional connectivity analysis.
From: DeepCor: denoising fMRI data with contrastive autoencoders
(a) Overview of the functional connectivity evaluation pipeline, incorporating a Yeo et al.-defined 51-region brain mask. The pipeline processes whole-brain fMRI data, applies denoising methods, extracts regional mean signals, and computes interregional Pearson correlations to generate functional connectivity matrices. (b) Functional connectivity matrices from a single participant, derived from raw data, as well as CompCor-, DeNN-, and DeepCor-denoised fMRI signals. (c) Bar plot comparing within-network and between-network correlation strengths (n=200) across the four methods (raw data, CompCor, DeNN, and DeepCor). Error bars represent standard errors. Statistical significance was assessed using a one-sided Wilcoxon signed-rank test, comparing each denoising method (CompCor, DeNN, and DeepCor) with Raw data for Within-Network and Between-Network correlations, and comparing DeepCor with Raw, CompCor, and DeNN for the Difference (Within - Between) measure, with significance levels denoted as p < 0.001 (***). Exact p-values: Within-Network (vs Raw) - CompCor p = 2.8 × 10−33, DeNN p = 7.2 × 10−35, DeepCor p = 9.0 × 10−32; Between-Network (vs Raw) - CompCor p = 4.5 × 10−34, DeNN p = 7.2 × 10−35, DeepCor p = 7.2 × 10−35; Difference (Within-Between; DeepCor vs others) - vs Raw p = 1.0 × 10−34, vs CompCor p = 2.9 × 10−34, vs DeNN p = 9.6 × 10−34. (d) Mean correlation +/- SEM between the FEF and PCC, two regions exhibiting anticorrelated activity, across denoising methods. Background shading indicates the correlation values, scaled consistently with the connectivity matrices. FEF: Frontal Eye Field, PCC: Posterior Cingulate Cortex.
