# Learning to segment fetal brain tissue from noisy annotations

arXiv: https://arxiv.org/abs/2203.14962 · HTML: https://mlsanity.com/paper/2203.14962/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 61 references that are in the map.
- First posted on arXiv 25 Mar 2022.

## Builds on (most cited first, 27 of 27)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Rethinking the Inception Architecture for Computer Vision](https://mlsanity.com/paper/1512.00567/) (2015)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Generalized Cross Entropy Loss for Training Deep Neural Networks with Noisy Labels](https://mlsanity.com/paper/1805.07836/) (2018)
- [When Does Label Smoothing Help?](https://mlsanity.com/paper/1906.02629/) (2019)
- [Making Deep Neural Networks Robust to Label Noise: a Loss Correction Approach](https://mlsanity.com/paper/1609.03683/) (2016)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [Learning from Noisy Labels with Deep Neural Networks: A Survey](https://mlsanity.com/paper/2007.08199/) (2020)
- [Regularizing Neural Networks by Penalizing Confident Output Distributions](https://mlsanity.com/paper/1701.06548/) (2017)
- [Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation](https://mlsanity.com/paper/1908.10454/) (2019)
- [Convolutional Neural Networks for Medical Image Analysis: Full Training or Fine Tuning?](https://mlsanity.com/paper/1706.00712/) (2017)
- [Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis](https://mlsanity.com/paper/1804.06353/) (2018)
- [Deep learning with noisy labels: exploring techniques and remedies in medical image analysis](https://mlsanity.com/paper/1912.02911/) (2019)
- [Towards better decoding and language model integration in sequence to sequence models](https://mlsanity.com/paper/1612.02695/) (2016)
- [The Devil is in the Margin: Margin-based Label Smoothing for Network Calibration](https://mlsanity.com/paper/2111.15430/) (2021)
- [DeepCut: Object Segmentation from Bounding Box Annotations using Convolutional Neural Networks](https://mlsanity.com/paper/1605.07866/) (2016)
- [An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset](https://mlsanity.com/paper/2010.15526/) (2020)
- [Spatially Varying Label Smoothing: Capturing Uncertainty from Expert Annotations](https://mlsanity.com/paper/2104.05788/) (2021)
- [Robustness of Conditional GANs to Noisy Labels](https://mlsanity.com/paper/1811.03205/) (2018)
- [3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study](https://mlsanity.com/paper/1612.03925/) (2016)
- [Automatic brain tissue segmentation in fetal MRI using convolutional neural networks](https://mlsanity.com/paper/1906.04713/) (2019)
- [A Deep Attentive Convolutional Neural Network for Automatic Cortical Plate Segmentation in Fetal MRI](https://mlsanity.com/paper/2004.12847/) (2020)
- [Distributionally Robust Segmentation of Abnormal Fetal Brain 3D MRI](https://mlsanity.com/paper/2108.04175/) (2021)
- [Efficient multi-class fetal brain segmentation in high resolution MRI reconstructions with noisy labels](https://mlsanity.com/paper/2009.06275/) (2020)
- [Segmentation of the cortical plate in fetal brain MRI with a topological loss](https://mlsanity.com/paper/2010.12391/) (2020)

## Built on by (most cited first, 7 of 7)

- [Fetal Brain Tissue Annotation and Segmentation Challenge Results](https://mlsanity.com/paper/2204.09573/) (2022)
- [Reasoning-Enhanced Domain-Adaptive Pretraining of Multimodal Large Language Models for Short Video Content Governance](https://mlsanity.com/paper/2509.21486/) (2025)
- [Detailed delineation of the fetal brain in diffusion MRI via multi-task learning](https://mlsanity.com/paper/2409.06716/) (2024)
- [Anatomically Constrained Tractography of the Fetal Brain](https://mlsanity.com/paper/2403.02444/) (2024)
- [Atlas-Assisted Segment Anything Model for Fetal Brain MRI (FeTal-SAM)](https://mlsanity.com/paper/2601.15759/) (2026)
- [Learning Trustworthy Model from Noisy Labels based on Rough Set for Surface Defect Detection](https://mlsanity.com/paper/2301.10441/) (2023)
- [AtlasSeg: Atlas Prior Guided Dual-U-Net for Cortical Segmentation in Fetal Brain MRI](https://mlsanity.com/paper/2411.02867/) (2024)

## Abstract (arXiv)

Automatic fetal brain tissue segmentation can enhance the quantitative assessment of brain development at this critical stage. Deep learning methods represent the state of the art in medical image segmentation and have also achieved impressive results in brain segmentation. However, effective training of a deep learning model to perform this task requires a large number of training images to represent the rapid development of the transient fetal brain structures. On the other hand, manual multi-label segmentation of a large number of 3D images is prohibitive. To address this challenge, we segmented 272 training images, covering 19-39 gestational weeks, using an automatic multi-atlas segmentation strategy based on deformable registration and probabilistic atlas fusion, and manually corrected large errors in those segmentations. Since this process generated a large training dataset with noisy segmentations, we developed a novel label smoothing procedure and a loss function to train a deep learning model with smoothed noisy segmentations. Our proposed methods properly account for the uncertainty in tissue boundaries. We evaluated our method on 23 manually-segmented test images of a separate set of fetuses. Results show that our method achieves an average Dice similarity coefficient of 0.893 and 0.916 for the transient structures of younger and older fetuses, respectively. Our method generated results that were significantly more accurate than several state-of-the-art methods including nnU-Net that achieved the closest results to our method. Our trained model can serve as a valuable tool to enhance the accuracy and reproducibility of fetal brain analysis in MRI.