# How Much MRI Preprocessing Is Enough? A Cost-Utility Study for Brain MRI Foundation Models

arXiv: https://arxiv.org/abs/2606.08164 · HTML: https://mlsanity.com/paper/2606.08164/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 39 references that are in the map.
- First posted on arXiv 6 Jun 2026.

## Builds on (most cited first, 19 of 19)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis](https://mlsanity.com/paper/1908.06912/) (2019)
- [The University of California San Francisco Preoperative Diffuse Glioma MRI (UCSF-PDGM) Dataset](https://mlsanity.com/paper/2109.00356/) (2021)
- [BrainSegFounder: Towards 3D Foundation Models for Neuroimage Segmentation](https://mlsanity.com/paper/2406.10395/) (2024)
- [MRI-CORE: A Foundation Model for Magnetic Resonance Imaging](https://mlsanity.com/paper/2506.12186/) (2025)
- [Anatomical Foundation Models for Brain MRIs](https://mlsanity.com/paper/2408.07079/) (2024)
- [BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023](https://mlsanity.com/paper/2407.08855/) (2024)
- [A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning](https://mlsanity.com/paper/2506.14432/) (2025)
- [Domain Aware Multi-Task Pretraining of 3D Swin Transformer for T1-weighted Brain MRI](https://mlsanity.com/paper/2410.00410/) (2024)

## Abstract (arXiv)

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.