# Deep Learning-Based Cross-Anatomy CT Synthesis Using Adapted nnResU-Net with Anatomical Feature Prioritized Loss

arXiv: https://arxiv.org/abs/2509.22394 · HTML: https://mlsanity.com/paper/2509.22394/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 13 references that are in the map.
- First posted on arXiv 26 Sep 2025.

## Builds on (most cited first, 8 of 8)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Perceptual Losses for Real-Time Style Transfer and Super-Resolution](https://mlsanity.com/paper/1603.08155/) (2016)
- [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)
- [EnhanceNet: Single Image Super-Resolution Through Automated Texture Synthesis](https://mlsanity.com/paper/1612.07919/) (2016)
- [SynthRAD2025 Grand Challenge dataset: generating synthetic CTs for radiotherapy](https://mlsanity.com/paper/2502.17609/) (2025)
- [Anatomical feature-prioritized loss for enhanced MR to CT translation](https://mlsanity.com/paper/2410.10328/) (2024)

## Abstract (arXiv)

We present a patch-based 3D nnUNet adaptation for MR to CT and CBCT to CT image translation using the multicenter SynthRAD2025 dataset, covering head and neck (HN), thorax (TH), and abdomen (AB) regions. Our approach leverages two main network configurations: a standard UNet and a residual UNet, both adapted from nnUNet for image synthesis. The Anatomical Feature-Prioritized (AFP) loss was introduced, which compares multilayer features extracted from a compact segmentation network trained on TotalSegmentator labels, enhancing reconstruction of clinically relevant structures. Input volumes were normalized per-case using zscore normalization for MRIs, and clipping plus dataset level zscore normalization for CBCT and CT. Training used 3D patches tailored to each anatomical region without additional data augmentation. Models were trained for 1000 and 1500 epochs, with AFP fine-tuning performed for 500 epochs using a combined L1+AFP objective. During inference, overlapping patches were aggregated via mean averaging with step size of 0.3, and postprocessing included reverse zscore normalization. Both network configurations were applied across all regions, allowing consistent model design while capturing local adaptations through residual learning and AFP loss. Qualitative and quantitative evaluation revealed that residual networks combined with AFP yielded sharper reconstructions and improved anatomical fidelity, particularly for bone structures in MR to CT and lesions in CBCT to CT, while L1only networks achieved slightly better intensity-based metrics. This methodology provides a stable solution for cross modality medical image synthesis, demonstrating the effectiveness of combining the automatic nnUNet pipeline with residual learning and anatomically guided feature losses.