Adapting 2D Multi-Modal Large Language Model for 3D CT Image Analysis

3D CT analysis spans a continuum from low-level perception to high-level clinical understanding. Existing 3D-oriented analysis methods adopt either isolated task-specific modeling or task-agnostic end-to-end paradigms to produce one-hop outputs, impeding the systematic accumulation of perceptual evidence for downstream reasoning. In parallel, recent multimodal large language models (MLLMs) exhibit improved visual perception and can integrate visual and textual information effectively, yet their predominantly 2D-oriented designs fundamentally limit their ability to perceive and analyze volumetric medical data. To bridge this gap, we propose 3DMedAgent, a unified agent that enables 2D MLLMs to perform general 3D CT analysis without 3D-specific fine-tuning. 3DMedAgent coordinates heterogeneous visual and textual tools through a flexible MLLM agent, progressively decomposing complex 3D analysis into tractable subtasks that transition from global to regional views, from 3D volumes to informative 2D slices, and from visual evidence to structured textual representations. Central to this design, 3DMedAgent maintains a long-term structured memory that aggregates intermediate tool outputs and supports query-adaptive, evidence-driven multi-step reasoning. We further introduce the DeepChestVQA benchmark for evaluating unified perception-to-understanding capabilities in 3D thoracic imaging. Experiments across over 40 tasks demonstrate that 3DMedAgent consistently outperforms general, medical, and 3D-specific MLLMs, highlighting a scalable path toward general-purpose 3D clinical assistants.Code and data are available at https://github.com/jinlab-imvr/3DMedAgent.

Recent progress in medical vision-language models (VLMs) has achieved strong performance on image-level text-centric tasks such as report generation and visual question answering (VQA). However, achieving fine-grained visual grounding and volumetric spatial reasoning in 3D medical VLMs remains challenging, particularly when aiming to unify these capabilities within a single, generalizable framework. To address this challenge, we proposed MedVL-SAM2, a unified 3D medical multimodal model that concurrently supports report generation, VQA, and multi-paradigm segmentation, including semantic, referring, and interactive segmentation. MedVL-SAM2 integrates image-level reasoning and pixel-level perception through a cohesive architecture tailored for 3D medical imaging, and incorporates a SAM2-based volumetric segmentation module to enable precise multi-granular spatial reasoning. The model is trained in a multi-stage pipeline: it is first pre-trained on a large-scale corpus of 3D CT image-text pairs to align volumetric visual features with radiology-language embeddings. It is then jointly optimized with both language-understanding and segmentation objectives using a comprehensive 3D CT segmentation dataset. This joint training enables flexible interaction via language, point, or box prompts, thereby unifying high-level visual reasoning with spatially precise localization. Our unified architecture delivers state-of-the-art performance across report generation, VQA, and multiple 3D segmentation tasks. Extensive analyses further show that the model provides reliable 3D visual grounding, controllable interactive segmentation, and robust cross-modal reasoning, demonstrating that high-level semantic reasoning and precise 3D localization can be jointly achieved within a unified 3D medical VLM.

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable success in 2D medical image understanding, their extension to 3D volumetric imaging remains hindered by prohibitive annotation costs and dataset opacity. Current data formats, predominantly consisting of rigid Visual Question Answering (VQA) pairs or unstructured final clinical reports, typically fail to capture explicit clinical reasoning. To address this limitation, we introduce a large-scale structured reasoning dataset constructed via a novel slice-wise data synthesis paradigm. Inspired by the genuine diagnostic workflow of radiologists, this paradigm models visual cognition by decomposing the complex 3D reading process, translating global clinical priors into fine-grained, per-slice observations that are subsequently synthesized into an interpretable Chain-of-Thought (CoT). Crucially, this synthesized reasoning framework enforces essential clinical principles: sequential spatial tracking, multi-slice spatial awareness for artifact mitigation, and differential exclusion. To validate this approach, we instruction-tune a standard 2D-pretrained MLLM baseline using the synthesized data to enhance its volumetric comprehension. Comprehensive evaluations across multiple 3D medical benchmarks demonstrate that our method yields significant performance improvements over the 2D baseline. Furthermore, the resulting model exhibits robust spatial reasoning capabilities and rivals resource-intensive native 3D architectures, effectively bridging the performance gap. Ultimately, this data-centric strategy unlocks deep volumetric understanding and highly interpretable clinical logic without requiring computationally expensive 3D-specific pre-training. The complete repository, including datasets and training workflows, is publicly available at https://github.com/2020420145009/hounsfield.