Multimodal magnetic resonance imaging (MRI) provides complementary information for sub-region analysis of brain tumors. Plenty of methods have been proposed for automatic brain tumor segmentation using four common MRI modalities and achieved remarkable performance. In practice, however, it is common to have one or more modalities missing due to image corruption, artifacts, acquisition protocols, allergy to contrast agents, or simply cost. In this work, we propose a novel two-stage framework for brain tumor segmentation with missing modalities. In the first stage, a multimodal masked autoencoder (M3AE) is proposed, where both random modalities (i.e., modality dropout) and random patches of the remaining modalities are masked for a reconstruction task, for self-supervised learning of robust multimodal representations against missing modalities. To this end, we name our framework M3AE. Meanwhile, we employ model inversion to optimize a representative full-modal image at marginal extra cost, which will be used to substitute for the missing modalities and boost performance during inference. Then in the second stage, a memory-efficient self distillation is proposed to distill knowledge between heterogenous missing-modal situations while fine-tuning the model for supervised segmentation. Our M3AE belongs to the ‘catch-all’ genre where a single model can be applied to all possible subsets of modalities, thus is economic for both training and deployment. Extensive experiments on BraTS 2018 and 2020 datasets demonstrate its superior performance to existing state-of-the-art methods with missing modalities, as well as the efficacy of its components. Our code is available at: https://github.com/ccarliu/m3ae.

Most existing federated learning (FL) methods for medical image analysis only considered intramodal heterogeneity, limiting their applicability to multimodal imaging applications. In practice, it is not uncommon that some FL participants only possess a subset of the complete imaging modalities, posing inter-modal heterogeneity as a challenge to effectively training a global model on all participants’ data. In addition, each participant would expect to obtain a personalized model tailored for its local data characteristics from the FL in such a scenario. In this work, we propose a new FL framework with federated modality-specific encoders and multimodal anchors (FedMEMA) to simultaneously address the two concurrent issues. Above all, FedMEMA employs an exclusive encoder for each modality to account for the inter-modal heterogeneity in the first place. In the meantime, while the encoders are shared by the participants, the decoders are personalized to meet individual needs. Specifically, a server with full-modal data employs a fusion decoder to aggregate and fuse representations from all modality-specific encoders, thus bridging the modalities to optimize the encoders via backpropagation reversely. Meanwhile, multiple anchors are extracted from the fused multimodal representations and distributed to the clients in addition to the encoder parameters. On the other end, the clients with incomplete modalities calibrate their missing-modal representations toward the global full-modal anchors via scaled dot-product cross-attention, making up the information loss due to absent modalities while adapting the representations of present ones. FedMEMA is validated on the BraTS 2020 benchmark for multimodal brain tumor segmentation. Results show that it outperforms various up-to-date methods for multimodal and personalized FL and that its novel designs are effective. Our code is available.