研究发现,脑部MRI预处理并非越多越好,适度即可。
How Much MRI Preprocessing Is Enough? A Cost-Utility Study for Brain MRI Foundation Models

- 固定模型与评估任务,测试7级预处理对3D MRI自监督训练的影响。
- 最高级预处理(P7)仅在少数任务中提升效果,整体增益不足4%。
- 部分任务可在下游阶段补强预处理,无需全程高成本处理。
MRI预处理定义了脑部MRI基础模型的输入分布,但常被视为常规数据清洗而非建模选择。本文探究自监督3D MRI预训练中,预处理的成本效益:在保持数据集(20,000个异构脑部MRI体积)、3D ViT骨干网络、掩码策略和下游评估一致的前提下,对比从P0到P7共7级预处理方案在掩码自编码(MAE)与联合嵌入预测学习(JEPA)中的表现。结果表明,不存在简单的‘越多越好’规律。P0/P1数值不稳定,故P2为最低可行级别;从P2以上进一步优化,仅使MAE和JEPA的综合效用分别提升3.4和1.8个百分点,多数对比差异不显著。强化预处理仅在特定场景有效:IDH预测略有改善,年龄回归与肿瘤分割多数在P2已达最优,而MCI分类在P7有最明显提升。跨层级迁移实验显示,部分P7优势可通过下游阶段增强预处理恢复,无需全程使用高成本预处理。研究建议将预处理视为面向下游任务的权衡决策,而非默认升级流程。代码已开源:https://github.com/PangJiangShuan/PreBrain。
原文摘要 · Abstract (English)
MRI preprocessing defines the input distribution seen by brain MRI foundation models, yet it is usually treated as routine data cleaning rather than a modeling choice. We ask how much preprocessing is worth its computational cost for self-supervised 3D MRI pretraining. Keeping the corpus, 3D ViT backbone, masking protocol, and downstream evaluations fixed, we compare a graded P0-P7 preprocessing spectrum for masked autoencoding (MAE) and joint-embedding predictive learning (JEPA) on 20,000 heterogeneous brain MRI volumes, then transfer the encoders to IDH prediction, MCI classification, brain age regression, and GLI/PED tumor segmentation. The results do not support a simple "more is better" rule. P0/P1 are numerically unstable, making P2 the lowest-cost feasible level; beyond P2, choosing the best feasible preprocessing level improves aggregate utility by only 3.4 percentage points for MAE and 1.8 percentage points for JEPA, with most paired gains statistically unresolved. Stronger preprocessing is beneficial only in selected regimes: IDH improves modestly, AGE and GLI/PED are often near or best at P2, and MCI shows the clearest empirical P7 gain. Cross-level MCI transfer further shows that much of the P7 advantage can be recovered by applying stronger preprocessing downstream, without requiring P7 throughout pretraining. These findings recast MRI preprocessing as a downstream-aware cost-utility decision rather than a default escalation pipeline. Code is available at https://github.com/PangJiangShuan/PreBrain.
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