# Pre- and Post-Treatment Brain Metastases Segmentation Using nnU-Net with Post-Processing for BraTS 2026

arXiv: https://arxiv.org/abs/2609.11477 · HTML: https://mlsanity.com/paper/2609.11477/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 28 references that are in the map.
- First posted on arXiv 10 Sep 2026.

## Builds on (most cited first, 13 of 13)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [Metrics reloaded: Recommendations for image analysis validation](https://mlsanity.com/paper/2206.01653/) (2022)
- [MedPerf: Open Benchmarking Platform for Medical Artificial Intelligence using Federated Evaluation](https://mlsanity.com/paper/2110.01406/) (2021)
- [The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI](https://mlsanity.com/paper/2405.18368/) (2024)
- [Understanding metric-related pitfalls in image analysis validation](https://mlsanity.com/paper/2302.01790/) (2023)
- [Analysis of the MICCAI Brain Tumor Segmentation -- Metastases (BraTS-METS) 2025 Lighthouse Challenge: Brain Metastasis Segmentation on Pre- and Post-treatment MRI](https://mlsanity.com/paper/2504.12527/) (2025)

## Abstract (arXiv)

Brain metastases exhibit high inter-lesion variability in size, enhancement pattern, and post-treatment appearance, making volumetric segmentation of both pre- and post-treatment cases the central challenge of the BraTS 2026 Task 1 (Brain Metastases). We build a pragmatic pipeline on a 5-fold nnU-Net ResEnc-L ensemble, in which each fold is trained independently for 1,000 epochs with the standard Dice + cross-entropy loss on 1,296 four-modality training cases. This ensemble is followed by a rule-based post-processing cascade tuned for the lesion-wise Dice similarity coefficient (LW-DSC), a detection-oriented metric that behaves very differently from the traditional global Dice. The final pipeline reaches an LW-DSC of 0.733 / 0.751 / 0.713 / 0.549 on the enhancing tumour (ET), tumour core (TC), whole tumour (WT), and resection cavity (RC) sub-regions on the official validation leaderboard. Rather than trusting these leaderboard gains, we audit every post-processing stage with a five-fold out-of-fold (OOF) analysis with no model-training leakage over all 1,296 training cases, scored with the official BraTS evaluation code (BraTS_evaluation): it confirms two stages as robust, per-fold-consistent improvements while the third improves only the leaderboard and does not reproduce out-of-fold. We further provide a mechanistic analysis of the LW-DSC metric that explains why recall-recovering post-processing carries low risk whereas component deletion does not, and we report thirteen negative results spanning loss engineering, alternative backbones, and inference-time settings, several of which run counter to widely held intuitions. Source code is released under Apache-2.0 at https://github.com/hornbeamliu/brats2026-met.