# Benchmarking CNN-based Models against Transformer-based Models for Abdominal Multi-Organ Segmentation on the RATIC Dataset

arXiv: https://arxiv.org/abs/2603.18616 · HTML: https://mlsanity.com/paper/2603.18616/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 22 references that are in the map.
- First posted on arXiv 19 Mar 2026.

## Builds on (most cited first, 16 of 16)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation](https://mlsanity.com/paper/1809.10486/) (2018)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)
- [HybridMIM: A Hybrid Masked Image Modeling Framework for 3D Medical Image Segmentation](https://mlsanity.com/paper/2303.10333/) (2023)
- [The RSNA Abdominal Traumatic Injury CT (RATIC) Dataset](https://mlsanity.com/paper/2405.19595/) (2024)
- [EM-Net: Efficient Channel and Frequency Learning with Mamba for 3D Medical Image Segmentation](https://mlsanity.com/paper/2409.17675/) (2024)
- [SegResMamba: An Efficient Architecture for 3D Medical Image Segmentation](https://mlsanity.com/paper/2503.07766/) (2025)

## Abstract (arXiv)

Accurate multi-organ segmentation in abdominal CT scans is essential for computer-aided diagnosis and treatment. While convolutional neural networks (CNNs) have long been the standard approach in medical image segmentation, transformer-based architectures have recently gained attention due to their ability to model long-range dependencies. In this study, we systematically benchmark the three hybrid transformer-based models UNETR, SwinUNETR, and UNETR++ against a strong CNN baseline, SegResNet, for volumetric multi-organ segmentation on the heterogeneous RATIC dataset. The dataset comprises 206 annotated CT scans from 23 institutions worldwide, covering five abdominal organs. All models were trained and evaluated under identical preprocessing and training conditions using the Dice Similarity Coefficient (DSC) as the primary metric. The results show that the CNN-based SegResNet achieves the highest overall performance, outperforming all hybrid transformer-based models across all organs. Among the transformer-based approaches, UNETR++ delivers the most competitive results, while UNETR demonstrates notably faster convergence with fewer training iterations. These findings suggest that, for small- to medium-sized heterogeneous datasets, well-optimized CNN architectures remain highly competitive and may outperform hybrid transformer-based designs.