# MRN: Harnessing 2D Vision Foundation Models for Diagnosing Parkinson's Disease with Limited 3D MR Data

arXiv: https://arxiv.org/abs/2509.17566 · HTML: https://mlsanity.com/paper/2509.17566/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 34 references that are in the map.
- First posted on arXiv 22 Sep 2025.

## Builds on (most cited first, 21 of 21)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [Vision Transformers for Dense Prediction](https://mlsanity.com/paper/2103.13413/) (2021)
- [VGGT: Visual Geometry Grounded Transformer](https://mlsanity.com/paper/2503.11651/) (2025)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [EVA: Exploring the Limits of Masked Visual Representation Learning at Scale](https://mlsanity.com/paper/2211.07636/) (2022)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Exploring Cross-Image Pixel Contrast for Semantic Segmentation](https://mlsanity.com/paper/2101.11939/) (2021)
- [M3D: Advancing 3D Medical Image Analysis with Multi-Modal Large Language Models](https://mlsanity.com/paper/2404.00578/) (2024)
- [SegVol: Universal and Interactive Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2311.13385/) (2023)
- [VoCo: A Simple-yet-Effective Volume Contrastive Learning Framework for 3D Medical Image Analysis](https://mlsanity.com/paper/2402.17300/) (2024)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (2024)
- [Domain Generalization for Medical Image Analysis: A Review](https://mlsanity.com/paper/2310.08598/) (2023)
- [Large-Scale 3D Medical Image Pre-training with Geometric Context Priors](https://mlsanity.com/paper/2410.09890/) (2024)
- [Multi-modal Vision Pre-training for Medical Image Analysis](https://mlsanity.com/paper/2410.10604/) (2024)

## Abstract (arXiv)

The automatic diagnosis of Parkinson's disease is in high clinical demand due to its prevalence and the importance of targeted treatment. Current clinical practice often relies on diagnostic biomarkers in QSM and NM-MRI images. However, the lack of large, high-quality datasets makes training diagnostic models from scratch prone to overfitting. Adapting pre-trained 3D medical models is also challenging, as the diversity of medical imaging leads to mismatches in voxel spacing and modality between pre-training and fine-tuning data. In this paper, we address these challenges by leveraging 2D vision foundation models (VFMs). Specifically, we crop multiple key ROIs from NM and QSM images, process each ROI through separate branches to compress the ROI into a token, and then combine these tokens into a unified patient representation for classification. Within each branch, we use 2D VFMs to encode axial slices of the 3D ROI volume and fuse them into the ROI token, guided by an auxiliary segmentation head that steers the feature extraction toward specific brain nuclei. Additionally, we introduce multi-ROI supervised contrastive learning, which improves diagnostic performance by pulling together representations of patients from the same class while pushing away those from different classes. Our approach achieved first place in the MICCAI 2025 PDCADxFoundation challenge, with an accuracy of 86.0% trained on a dataset of only 300 labeled QSM and NM-MRI scans, outperforming the second-place method by 5.5%.These results highlight the potential of 2D VFMs for clinical analysis of 3D MR images.