将SAM2 adapted用于3D MRI分割,显著提升边界识别能力。
SAMRI-3D: Adapting SAM2 for 3D MRI Segmentation with Global Volume Tokens

- 用全局体积令牌增强模型对低对比度边界的感知能力
- 在34个数据集上平均Dice达0.78,优于现有医学模型
- 零额外计算成本,适合临床影像分析与研究者使用
以分割一切模型2(SAM2)为代表的基座模型已变革自然图像与视频分割,近期工作开始将其应用于医学影像。然而这些适配多为通用模型,将MRI视为众多模态之一;大规模、专用于MRI的建模与基准测试仍有限,尽管MRI软组织对比度低,单切片中许多边界难以分辨。本文提出SAMRI-3D,一个基于SAM2的3D MRI分割方法与基准。该基准是迄今最大的纯MRI评估:涵盖34个数据集(27个公开,7个内部),共10,392个体积,覆盖12个解剖域和10+序列,并设明确的训练/未见划分。冻结图像编码器,仅微调轻量解码器与记忆模块,使平均Dice从零样本SAM2的0.58提升至0.76,显著优于近期基于SAM的医学模型(SAMed-2: 0.69,Medical-SAM2: 0.49,SAM-Med3D: 0.37)。为应对不可见边界,引入全局体积令牌(GVT):通过截断符号距离场(TSDF)重建目标训练的持久记忆令牌,推理时丢弃(无额外开销)。完整模型SAMRI-3D在全部34个数据集上达到最高精度(0.78)且方差最低,独特地在8个保留数据集上无性能下降(未见0.79,已见0.78);按序列分析显示,TSDF目标在单切片对比度最弱时提升最大。论文将发布基准、代码与模型。
原文摘要 · Abstract (English)
Foundation models such as Segment Anything Model 2 (SAM2) have transformed natural-image and video segmentation, and recent work has begun adapting them to medical imaging. These adaptations, however, are largely general-purpose models that treat MRI as one modality among many; large-scale, MRI-specific modelling and benchmarking remain limited, even though MRI's low soft-tissue contrast leaves many boundaries effectively invisible on individual slices. We present SAMRI-3D, a benchmark and method for 3D MRI segmentation with SAM2. The SAMRI-3D benchmark is the largest MRI-only evaluation to date - 10,392 volumes from 34 datasets (27 public, 7 in-house) spanning 12 anatomical domains and 10+ sequences, with explicit seen/unseen splits. Freezing the image encoder and fine-tuning only the lightweight decoder and memory modules raises mean Dice from 0.58 (zero-shot SAM2) to 0.76, surpassing recent SAM-based medical models (SAMed-2 0.69, Medical-SAM2 0.49, SAM-Med3D 0.37) with strong statistical significance. To target invisible boundaries, we introduce Global Volume Tokens (GVT): persistent memory tokens trained with a Truncated Signed Distance Field (TSDF) reconstruction objective that is discarded at inference (zero added cost). This full model, SAMRI-3D, attains the best accuracy (0.78) and lowest variance across all 34 datasets and, uniquely, shows no drop on 8 held-out datasets (0.79 unseen vs. 0.78 seen); per-sequence analysis confirms the TSDF objective helps most where per-slice contrast is weakest. We will release the benchmark, code, and models in this paper.
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