Agentic LLM Workflow for MR Spectroscopy Volume-of-Interest Placements in Brain Tumors

State-of-the-art large language models (LLMs) show high performance in general visual question answering. However, a fundamental limitation remains: current architectures lack the native 3D spatial reasoning required to directly analyze volumetric medical imaging, such as CT or MRI. Emerging agentic AI offers a new solution, eliminating the need for intrinsic 3D processing by enabling LLMs to orchestrate and leverage specialized external tools. Yet, the feasibility of such agentic frameworks in complex, multi-step radiological workflows remains underexplored. In this work, we present a training-free agentic pipeline for automated brain MRI analysis. Validating our methodology on several LLMs (GPT-5.4, Gemini 3.1 Pro, Claude Sonnet 4.6) with off-the-shelf domain-specific tools, our system autonomously executes complex end-to-end workflows, including preprocessing (skull stripping, registration), pathology segmentation (glioma, meningioma, metastases), and volumetric reasoning. We evaluate our framework across increasingly complex radiological tasks, from single-scan tumor and anatomy analysis to longitudinal response assessment requiring multi-timepoint comparisons. We analyze the impact of architectural design by comparing single-agent models against multi-agent "domain-expert" collaborations. To support rigorous evaluation of future agentic systems, we release a benchmark dataset of image-prompt-answer tuples derived from public data. Our results demonstrate that agentic AI can solve highly neuro-radiological image analysis tasks through tool use without the need for training or fine-tuning.

Accurate brain tumor segmentation from magnetic resonance imaging (MRI) is essential for diagnosis and treatment planning; however, manual delineation is labor-intensive and time-consuming. Existing approaches are either task-specific with limited generalization or rely on user-provided prompts during inference. We present BaT-SAM, a parameter-efficient adaptation framework that enables fully automatic brain tumor segmentation with the Segment Anything Model (SAM). BaT-SAM injects local inductive bias into SAM's frozen Vision Transformer (ViT) encoder via Conv-LoRA, where image features are processed by a sparsely gated mixture of multi-scale convolutional experts. This design compensates for the limited translation-equivariant inductive bias of vanilla ViTs while fine-tuning fewer than 5M parameters (less than 1% of the full model). To remove the need for user prompts, we further introduce a lightweight self-prompting box regressor that is jointly optimized with the adapter using scheduled sampling and predicts tumor locations directly from image embeddings. On the BRISC2025 benchmark, BaT-SAM achieves a weighted mean IoU of 0.832 while outperforming state-of-the-art benchmarks. It further demonstrates strong cross-dataset generalization, achieving Dice scores of 0.702 on Figshare and 0.784 on the LGG MRI Segmentation dataset.

Brain tumor MRI segmentation is essential for clinical diagnosis and treatment planning, enabling accurate lesion detection and radiotherapy target delineation. However, tumor lesions occupy only a small fraction of the volumetric space, resulting in severe spatial sparsity, while existing segmentation networks often overlook clinically observed spatial priors of tumor occurrence, leading to redundant feature computation over extensive background regions. To address this issue, we propose PGR-Net (Prior-Guided ROI Reasoning Network) - an explicit ROI-aware framework that incorporates a data-driven spatial prior set to capture the distribution and scale characteristics of tumor lesions, providing global guidance for more stable segmentation. Leveraging these priors, PGR-Net introduces a hierarchical Top-K ROI decision mechanism that progressively selects the most confident lesion candidate regions across encoder layers to improve localization precision. We further develop the WinGS-ROI (Windowed Gaussian-Spatial Decay ROI) module, which uses multi-window Gaussian templates with a spatial decay function to produce center-enhanced guidance maps, thus directing feature learning throughout the network. With these ROI features, a windowed RetNet backbone is adopted to enhance localization reliability. Experiments on BraTS-2019/2023 and MSD Task01 show that PGR-Net consistently outperforms existing approaches while using only 8.64M Params, achieving Dice scores of 89.02%, 91.82%, and 89.67% on the Whole Tumor region. Code is available at https://github.com/CNU-MedAI-Lab/PGR-Net.