Multimodal Federated Learning (MFL) has emerged as a promising approach for collaboratively training multimodal models across distributed clients, particularly in healthcare domains. In the context of brain imaging analysis, modality incompleteness presents a significant challenge, where some institutions may lack specific imaging modalities (e.g., PET, MRI, or CT) due to privacy concerns, device limitations, or data availability issues. While existing work typically assumes modality completeness or oversimplifies missing-modality scenarios, we simulate a more realistic setting by considering both client-level and instance-level modality incompleteness in this study. Building on this realistic simulation, we propose ClusMFL, a novel MFL framework that leverages feature clustering for cross-institutional brain imaging analysis under modality incompleteness. Specifically, ClusMFL utilizes the FINCH algorithm to construct a pool of cluster centers for the feature embeddings of each modality-label pair, effectively capturing fine-grained data distributions. These cluster centers are then used for feature alignment within each modality through supervised contrastive learning, while also acting as proxies for missing modalities, allowing cross-modal knowledge transfer. Furthermore, ClusMFL employs a modality-aware aggregation strategy, further enhancing the model's performance in scenarios with severe modality incompleteness. We evaluate the proposed framework on the ADNI dataset, utilizing structural MRI and PET scans. Extensive experimental results demonstrate that ClusMFL achieves state-of-the-art performance compared to various baseline methods across varying levels of modality incompleteness, providing a scalable solution for cross-institutional brain imaging analysis.