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An OpenMind for 3D Medical Vision Self-supervised Learning

Conference: ICCV 2025 arXiv: 2412.17041 Code: https://github.com/MIC-DKFZ/nnssl Area: Medical Imaging Keywords: Self-supervised learning, 3D medical imaging, pretraining dataset, brain MRI, benchmark

TL;DR

This work releases OpenMind, the largest publicly available 3D medical imaging pretraining dataset (114k brain MRI volumes), and conducts a systematic benchmark of existing 3D SSL methods on this dataset using state-of-the-art CNN (ResEnc-L) and Transformer (Primus-M) architectures, establishing the current SOTA for 3D medical image SSL.

Background & Motivation

The 3D medical imaging SSL field lacks consistency and standardization, making fair comparison among existing methods impossible due to three key issues: 1. Absence of large-scale public pretraining datasets: Large datasets (e.g., UK-BioBank >100k, ABCD >40k) are restricted by data use agreements (DUAs) requiring institutional review and mandatory authorship, impeding reproducible research. Most SSL methods are developed on small-scale or private data. 2. Inconsistent architectural choices: Different methods adopt CNNs, ViTs, Swin Transformers, or hybrid architectures, precluding direct comparison of the methods themselves. 3. Inconsistent downstream evaluation: Varying choices of evaluation datasets and small evaluation set sizes undermine result reliability.

Core Problem

How to establish a standardized benchmark for 3D medical image SSL—with unified pretraining data, architecture choices, and evaluation protocols—so as to determine the true value of SSL pretraining and identify the current SOTA?

Method

Overall Architecture

Rather than proposing a new SSL method, this paper makes three key contributions:

a) OpenMind Dataset - Source: 800 public studies from the OpenNeuro platform following the BIDS format - Scale: 114k 3D brain MRI volumes (34,191 subjects), covering 23 MRI modalities - Includes 71k direct 3D MRI scans + 15k 4D DWI preprocessed into 43k 3D images (MD maps, FA maps, T2-weighted images) - CC-BY-4.0 license with no access restrictions - Accompanied by anonymization masks, anatomical masks, unified metadata, and image quality scores (IQS, 1–5) - Released on HuggingFace

b) SSL Benchmark - Two SOTA architectures: ResEnc-L (CNN) and Primus-M (Transformer) - Seven SSL methods: VoCo, SwinUNETR pretraining, SimCLR, VolumeFusion (VF), ModelsGenesis (MG), MAE, S3D/SimMIM - 15 downstream datasets: 12 segmentation + 3 classification - Split into 4 development sets (for hyperparameter tuning) + 8 segmentation test sets + 3 classification test sets

c) Open-source Release - Pretraining and fine-tuning framework code - All pretrained model checkpoints - Integration into the nnU-Net framework

Key Designs

Pretraining Configuration: - All methods uniformly pretrained on OpenMind for 1000 epochs × 250 steps/epoch - Trained with 4×40GB A100 GPUs using DDP - Unified spacing: 1mm³ isotropic; z-score normalization

Five Fine-tuning Strategies (one of the core contributions): 1. Default: Polynomial lr decay, initial lr decreasing from 1e-2 to 1e-3 (transfer learning setting) 2. Frozen: Encoder frozen; only the decoder is trained 3. Warm-Up: Linear lr increase followed by transition to the default schedule 4. Valley: Decreasing lr for decoder training → linear warm-up for the full network → default 5. Sawtooth: Two-stage warm-up: frozen encoder with increasing lr for decoder → increasing lr warm-up for the full network → default

Optimal for CNN: Sawtooth; Optimal for Transformer: Warm-Up

Data Filtering Experiments (data-centric): - Filtering low-quality images by IQS (three thresholds) - Modality filtering (retaining only T1w, T2w, FLAIR) - Whether anonymized regions are included in the reconstruction loss

Loss & Training

Each SSL method uses its standard loss (no new method is proposed in this paper): - MAE/S3D/SimMIM: L2 reconstruction loss (applied only to masked regions) - SimCLR: NT-Xent contrastive loss - VoCo: Cosine similarity + regularization - VF: Cross-entropy segmentation loss (pseudo-segmentation task) - MG: Denoising + masked reconstruction - SwinUNETR: Inpainting + rotation prediction + contrastive learning (equal-weight aggregation)

Fine-tuning is performed for 150 or 1000 epochs, batch size=2, using nnU-Net's polynomial lr schedule.

Key Experimental Results

Segmentation Results (DSC %, 150-epoch fine-tuning, averaged over 12 datasets)

Method Architecture All Mean ID Mean OOD Mean vs. Scratch 150ep
Scratch 1k ResEnc-L 70.47 64.15 89.43 -
Scratch ResEnc-L 68.44 62.23 87.08 -
MAE ResEnc-L 70.91 65.11 88.30 +2.47
S3D ResEnc-L 70.36 64.46 88.06 +1.92
MG ResEnc-L 70.30 64.37 88.09 +1.86
SimCLR ResEnc-L 69.44 63.40 87.56 +1.00
VoCo ResEnc-L 68.50 62.14 87.58 +0.06
Scratch 1k Primus-M 67.01 60.05 87.90 -
Scratch Primus-M 63.62 57.29 82.61 -
MAE Primus-M 70.42 64.34 88.69 +6.80
SimMIM Primus-M 69.18 62.85 88.16 +5.56
VF Primus-M 68.19 61.75 87.51 +4.57

Key Findings: - MAE-pretrained ResEnc-L with 150-epoch fine-tuning surpasses the 1000-epoch from-scratch baseline (70.91 vs. 70.47) - Transformers (Primus-M) benefit substantially more from pretraining than CNNs (+6.80 vs. +2.47) - MAE-pretrained Primus-M nearly matches ResEnc-L (70.42 vs. 70.91), and even surpasses it on several datasets (ATL, COS, ACD)

Classification Results

  • Contrastive learning methods (VoCo, SwinUNETR, SimCLR) perform best on classification
  • MAE performs worst on classification
  • This indicates that global features (contrastive learning) suit classification, while local features (reconstruction) suit segmentation
  • No single SSL method achieves top performance on both segmentation and classification simultaneously

Ablation Study

  1. Fine-tuning strategy: Sawtooth (CNN) and Warm-Up (Transformer) are optimal; the Frozen strategy degrades performance significantly, suggesting that current SSL representations have insufficient generalizability
  2. Data filtering: Removing the lowest-quality images (retaining ~57%) yields a slight improvement (+0.15 DSC); however, reducing modality diversity (retaining only T1w/T2w/FLAIR, 62% of data) hurts performance (−0.43 DSC)
  3. Anonymization awareness: Excluding anonymized regions from the reconstruction loss improves MAE and S3D performance (MAE All Mean: 70.91→71.29)
  4. Extended fine-tuning: 1000-epoch fine-tuning benefits OOD datasets but may cause degradation (overfitting) on datasets where pretraining is already effective

Highlights & Insights

  1. Major dataset contribution: 114k 3D brain MRIs constitute the largest publicly available 3D medical imaging dataset under a CC-BY license, substantially lowering the barrier to SSL research
  2. First large-scale evidence that pretrained Transformers can match CNNs in 3D medical segmentation: MAE-pretrained Primus-M surpasses the strongest ResEnc-L on several datasets
  3. Systematic benchmark: Unified data, architecture, and evaluation across 7 methods × 2 architectures × 15 downstream tasks yield reliable conclusions
  4. Critical role of fine-tuning strategies: Fine-tuning strategy is found to have a major impact on pretraining efficacy; Sawtooth/Warm-Up substantially outperform naive fine-tuning
  5. Complete open-source ecosystem: Dataset, code framework, all checkpoints, and nnU-Net integration provide strong practical value
  6. Image quality metadata (IQS): First exploration of data-centric approaches in 3D medical SSL

Limitations & Future Work

  1. Restricted to brain MRI: All pretraining data are head-and-neck MRI; transferability to CT, chest, or abdominal imaging remains to be validated
  2. Classification experiments are less reliable: The classification pipeline is less mature than nnU-Net; some datasets approach chance performance (ABI ~50% balanced accuracy)
  3. Limited gains from data filtering: Simple IQS-based filtering yields only marginal improvements; the potential of data-centric methods remains underexplored
  4. Only 1000 pretraining epochs: Computational constraints preclude longer pretraining, which may reveal different trends
  5. PEFT methods not explored: Although freezing the encoder yields poor results, parameter-efficient fine-tuning approaches such as LoRA may mitigate this
  6. Metadata-aware SSL not explored: The dataset provides rich metadata that is not leveraged during pretraining
Aspect Ours Prior Work
Pretraining data 114k public 3D MRI Small-scale or private data (e.g., ABCD requires institutional approval)
Architecture comparison Unified comparison of CNN + Transformer Each method uses its own architecture
Downstream evaluation 15 datasets, development/test split Few datasets, unstable results
Reproducibility Fully open-source (data + code + weights) Mostly non-reproducible

OpenMind is complementary to CT-Rate (50k CT): OpenMind focuses on MRI, is larger in scale (114k), and has a more permissive license (CC-BY vs. CC-BY-NC).

Broader implications: - Evidence for Transformers in medical imaging: First large-scale demonstration that pretraining can close the performance gap between Transformers and CNNs - Fine-tuning strategy as a research direction: Fine-tuning strategy selection deserves greater attention in other SSL + medical imaging tasks - Data-centric SSL: Although simple filtering has limited effect, the dataset is large enough to support more sophisticated data curation approaches (e.g., semantic deduplication, curriculum learning) - Cross-modality pretraining: Future work can combine CT datasets (e.g., CT-Rate) for multi-modal SSL - Urgent need for PEFT methods: Given that frozen encoder underperforms and extended fine-tuning causes overfitting, LoRA/Adapter-style methods hold great promise for 3D SSL fine-tuning

Rating

  • Novelty: ⭐⭐⭐⭐ [Not a methodological contribution, but the systematic dataset + benchmark contribution is highly valuable and establishes the first standard for 3D medical SSL]
  • Experimental Thoroughness: ⭐⭐⭐⭐⭐ [7 methods × 2 architectures × 15 datasets × 5 fine-tuning strategies + data filtering + anonymization ablations — extremely comprehensive]
  • Writing Quality: ⭐⭐⭐⭐⭐ [Clear structure, rigorous experimental design, well-summarized findings]
  • Value: ⭐⭐⭐⭐⭐ [Dataset + benchmark + open-source framework are of tremendous community value; this will serve as the standard reference for 3D medical SSL]