Region-Aware Reconstruction Strategy for Pre-training fMRI Foundation Model

Ruthwik Reddy Doodipala, Pankaj Pandey, Carolina Torres Rojas, Manob Jyoti Saikia, Ranganatha Sitaram

Keywords: foundation models, self-supervised learning, fMRI, masked autoencoder, neuroimaging

TL;DR: We introduce an ROI-guided masking strategy for fMRI foundation model pre-training that improves interpretability and classification performance by integrating anatomical region masking into self-supervised masked autoencoding.

Abstract: The emergence of foundation models in neuroimaging is driven by the increasing availability of large-scale and heterogeneous brain imaging datasets. Recent advances in self-supervised learning, particularly reconstruction-based objectives, have demonstrated strong potential for pretraining models that generalize effectively across diverse downstream functional MRI (fMRI) tasks. In this study, we explore region-aware reconstruction strategies for a foundation model in resting-state fMRI, moving beyond approaches that rely on random region masking. Specifically, we introduce an ROI-guided masking strategy using the Automated Anatomical Labelling Atlas (AAL3), applied directly to full 4D fMRI volumes to selectively mask semantically coherent brain regions during self-supervised pretraining. Using the ADHD-200 dataset comprising 973 subjects with resting-state fMRI scans, we show that our method achieves a 4.23% improvement in classification accuracy for distinguishing healthy controls from individuals diagnosed with ADHD, compared to conventional random masking. Region-level attribution analysis reveals that brain volumes within the limbic region and cerebellum contribute most significantly to reconstruction fidelity and model representation. Our results demonstrate that masking anatomical regions during model pretraining not only enhances interpretability but also yields more robust and discriminative representations. In future work, we plan to extend this approach by evaluating it on additional neuroimaging datasets, and developing new loss functions explicitly derived from region-aware reconstruction objectives. These directions aim to further improve the robustness and interpretability of foundation models for functional neuroimaging.

Submission Number: 25