# Do 3D Medical Foundation Models See Through MRI Artifacts? A Controlled Study of Representation Robustness

arXiv: https://arxiv.org/abs/2608.06613 · HTML: https://mlsanity.com/paper/2608.06613/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 27 references that are in the map.
- First posted on arXiv 6 Aug 2026.

## Builds on (most cited first, 12 of 12)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Shortcut Learning in Deep Neural Networks](https://mlsanity.com/paper/2004.07780/) (2020)
- [Similarity of Neural Network Representations Revisited](https://mlsanity.com/paper/1905.00414/) (2019)
- [TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning](https://mlsanity.com/paper/2003.04696/) (2020)
- [RankMe: Assessing the downstream performance of pretrained self-supervised representations by their rank](https://mlsanity.com/paper/2210.02885/) (2022)
- [Machine Learning with Multi-Site Imaging Data: An Empirical Study on the Impact of Scanner Effects](https://mlsanity.com/paper/1910.04597/) (2019)
- [A generalizable 3D framework and model for self-supervised learning in medical imaging](https://mlsanity.com/paper/2501.11755/) (2025)
- [Gibbs-Ringing Artifact Removal Based on Local Subvoxel-shifts](https://mlsanity.com/paper/1501.07758/) (2015)
- [FAST-AID Brain: Fast and Accurate Segmentation Tool using Artificial Intelligence Developed for Brain](https://mlsanity.com/paper/2208.14360/) (2022)
- [Building a General SimCLR Self-Supervised Foundation Model Across Neurological Diseases to Advance 3D Brain MRI Diagnoses](https://mlsanity.com/paper/2509.10620/) (2025)
- [A Modality-agnostic Multi-task Foundation Model for Human Brain Imaging](https://mlsanity.com/paper/2509.00549/) (2025)
- [Non-Reference Quality Assessment for Medical Imaging: Application to Synthetic Brain MRIs](https://mlsanity.com/paper/2407.14994/) (2024)

## Built on by (most cited first, 1 of 1)

- [Dataset-Specific Encoding of Image Content Underlies Cross-Dataset Failure in Brain MRI Foundation Models](https://mlsanity.com/paper/2610.13027/) (2026)

## Abstract (arXiv)

Self-supervised 3D medical foundation models are increasingly used as general-purpose feature extractors, yet their sensitivity to MRI artifacts remains poorly understood. We present a controlled evaluation of representation robustness across five pretrained 3D encoders spanning different architectures, objectives, pretraining domains, and dataset scales. Using BraTS-Africa cases with four MRI sequences, we generate seven frequency- and image-domain artifacts at five predefined corruption settings. Robustness is assessed using linear centered kernel alignment (CKA), RankMe, and UMAP, complemented by an independent segmentation-consistency analysis. We find that robustness is strongly model- and artifact-dependent. 3DINO exhibits the most consistently stable representations, while BrainIAC is highly sensitive to several corruptions; NeuroVFM, BrainFM, and Neuro-SimCLR show intermediate but distinct artifact-specific profiles. Across many conditions, CKA decreases substantially while RankMe remains comparatively stable, indicating that artifacts often distort representation geometry without causing dimensional collapse. Segmentation consistency also degrades under corruption, particularly for ghosting and Rician noise, but aligns only partially with representation-level robustness. These findings show that larger-scale or domain-specific pretraining alone does not guarantee artifact invariance and motivate explicit robustness evaluation before deploying 3D foundation models in heterogeneous MRI settings.