Segmentation of Gray Matters and White Matters from Brain MRI data

Foundation models pretrained using self-supervised learning have transformed computer vision by learning transferable representations from large-scale unlabeled data. However, existing foundation models for neuroimaging remain limited by task-specific training, slice-based learning strategies, or relatively small pretraining datasets, restricting their generalizability across diverse brain MRI applications. In this work, we present BrainNext, a general-purpose self-supervised foundation model for volumetric brain MRI analysis. BrainNext combines masked autoencoder (MAE) pretraining with a native three-dimensional Bi-Directional xLSTM-UNet architecture to learn rich anatomical representations from 60,551 unlabeled brain MRI examinations spanning multiple MRI modalities. The pretrained model is subsequently adapted to downstream tasks through lightweight task-specific fine-tuning. We evaluate BrainNext on the Foundation Models for Medical Imaging (FOMO) 2025 Method Track, encompassing classification, segmentation, and brain-age estimation, where it achieved second place overall and ranked first in the meningioma segmentation task on the official FOMO 2025 challenge leaderboard, demonstrating strong transferability across heterogeneous neuroimaging tasks. These results highlight the potential of large-scale self-supervised pretraining to learn robust and transferable volumetric representations, establishing BrainNext as a scalable foundation model for diverse brain MRI applications.

A key challenge in medical image analysis is the scarcity of large annotated datasets for specific populations and diseases. As deep learning models rely heavily on labeled data, effective transfer learning strategies are needed to reduce the dependence on manual annotations. Self-supervised learning has emerged as a promising approach for developing foundation models by enabling the learning of transferable feature representations from large-scale unlabeled medical imaging datasets. In this study, we investigate voxel-level brain age prediction as a domain-specific self-supervised pretext task and compare it with image inpainting, a widely used non-domain-specific alternative. We further propose a multitask self-supervised pretraining framework that jointly optimizes both objectives to learn complementary neuroimaging representations. The pretrained models are evaluated on three downstream magnetic resonance image segmentation tasks: multiple sclerosis lesion segmentation, ischemic stroke lesion segmentation, and cortical brain structure segmentation. Overall, the proposed multitask pretraining framework consistently outperformed the single-task pretrained models and training from scratch across most experimental settings, demonstrating the benefit of combining domain-specific and general self-supervised learning pretext tasks for the development of generalizable neuroimaging foundation models.\ Code Availability: The source code used in this study is publicly available at https://github.com/TasneemN/Combining-General-and-Domain-Specific-Pretext-Tasks-for-Brain-MR-Image-Segmentation/

Precise localization and delineation of brain tumors using magnetic resonance imaging (MRI) are essential for planning therapy and guiding surgical decisions. To address this, we propose LoGSAM, a parameter-efficient, detection-driven framework that transforms radiologist dictation into text prompts for foundation-model-based localization and segmentation. Radiologist speech is first transcribed and translated using a pretrained Whisper ASR model, followed by negation-aware clinical NLP to extract tumor-specific textual prompts. These prompts guide text-conditioned tumor localization via a LoRA-adapted vision-language detection model, Grounding DINO (GDINO). The predicted bounding boxes are used as prompts for MedSAM to generate pixel-level tumor masks without any additional fine-tuning. On BRISC 2025, LoGSAM attains a Dice score of 80.32%, reaching 98.6% of a fully fine-tuned GDINO + MedSAM baseline while training fewer than 5% of its parameters, indicating a favorable accuracy/parameter trade-off. In addition, we evaluate the full pipeline using German dictations from a board-certified radiologist on unseen MRI scans, achieving 91.7% case-level class-extraction accuracy. These results highlight the feasibility of constructing a modular speech-to-segmentation pipeline from pretrained foundation models with minimal parameter updates.