# Benchmarking of Deep Learning Methods for Generic MRI Multi-Organ Abdominal Segmentation

arXiv: https://arxiv.org/abs/2507.17971 · HTML: https://mlsanity.com/paper/2507.17971/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 55 references that are in the map.
- First posted on arXiv 23 Jul 2025.

## Builds on (most cited first, 17 of 17)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Domain Randomization for Transferring Deep Neural Networks from Simulation to the Real World](https://mlsanity.com/paper/1703.06907/) (2017)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [Pseudo-Labeling and Confirmation Bias in Deep Semi-Supervised Learning](https://mlsanity.com/paper/1908.02983/) (2019)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://mlsanity.com/paper/2001.06535/) (2020)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [TotalSegmentator MRI: Robust Sequence-independent Segmentation of Multiple Anatomic Structures in MRI](https://mlsanity.com/paper/2405.19492/) (2024)
- [Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets](https://mlsanity.com/paper/2209.02032/) (2022)
- [MONAI Label: A framework for AI-assisted Interactive Labeling of 3D Medical Images](https://mlsanity.com/paper/2203.12362/) (2022)
- [A Learning Strategy for Contrast-agnostic MRI Segmentation](https://mlsanity.com/paper/2003.01995/) (2020)
- [Domain Shift in Computer Vision models for MRI data analysis: An Overview](https://mlsanity.com/paper/2010.07222/) (2020)
- [MRI-CORE: A Foundation Model for Magnetic Resonance Imaging](https://mlsanity.com/paper/2506.12186/) (2025)
- [Lymph Node Detection in T2 MRI with Transformers](https://mlsanity.com/paper/2111.04885/) (2021)
- [VIBESegmentator: Full Body MRI Segmentation for the NAKO and UK Biobank](https://mlsanity.com/paper/2406.00125/) (2024)
- [MRISegmentator-Abdomen: A Fully Automated Multi-Organ and Structure Segmentation Tool for T1-weighted Abdominal MRI](https://mlsanity.com/paper/2405.05944/) (2024)
- [Universal Lymph Node Detection in T2 MRI using Neural Networks](https://mlsanity.com/paper/2204.00622/) (2022)

## Abstract (arXiv)

Recent advances in deep learning have led to robust automated tools for segmentation of abdominal computed tomography (CT). Meanwhile, segmentation of magnetic resonance imaging (MRI) is substantially more challenging due to the inherent signal variability and the increased effort required for annotating training datasets. Hence, existing approaches are trained on limited sets of MRI sequences, which might limit their generalizability. To characterize the landscape of MRI abdominal segmentation tools, we present here a comprehensive benchmarking of the three state-of-the-art and open-source models: MRSegmentator, MRISegmentator-Abdomen, and TotalSegmentator MRI. Since these models are trained using labor-intensive manual annotation cycles, we also introduce and evaluate ABDSynth, a SynthSeg-based model purely trained on widely available CT segmentations (no real images). More generally, we assess accuracy and generalizability by leveraging three public datasets (not seen by any of the evaluated methods during their training), which span all major manufacturers, five MRI sequences, as well as a variety of subject conditions, voxel resolutions, and fields-of-view. Our results reveal that MRSegmentator achieves the best performance and is most generalizable. In contrast, ABDSynth yields slightly less accurate results, but its relaxed requirements in training data make it an alternative when the annotation budget is limited. The evaluation code and datasets are given for future benchmarking at https://github.com/deepakri201/AbdoBench, along with inference code and weights for ABDSynth.