mlsanityData to 7 Oct 2026

Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets

arXiv 2209.02032 ↗First posted 5 Sep 2022eess.IV cs.CVcited by 50

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Abstract (arXiv)

Every year, millions of brain MRI scans are acquired in hospitals, which is a figure considerably larger than the size of any research dataset. Therefore, the ability to analyse such scans could transform neuroimaging research. Yet, their potential remains untapped, since no automated algorithm is robust enough to cope with the high variability in clinical acquisitions (MR contrasts, resolutions, orientations, artefacts, subject populations). Here we present SynthSeg+, an AI segmentation suite that enables, for the first time, robust analysis of heterogeneous clinical datasets. In addition to whole-brain segmentation, SynthSeg+ also performs cortical parcellation, intracranial volume estimation, and automated detection of faulty segmentations (mainly caused by scans of very low quality). We demonstrate SynthSeg+ in seven experiments, including an ageing study on 14,000 scans, where it accurately replicates atrophy patterns observed on data of much higher quality. SynthSeg+ is publicly released as a ready-to-use tool to unlock the potential of quantitative morphometry.

Key facts. Cited by 50 papers in the map (data through 7 Oct 2026). Builds on 21 of its 64 references that are in the map. First posted on arXiv 5 Sep 2022.

Builds on

21 of 64 references.

References · 21

  1. 2014Adam: A Method for Stochastic Optimizationcited by 36,960
  2. 2015U-Net: Convolutional Networks for Biomedical Image Segmentationcited by 19,604
  3. 2016V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentationcited by 2,284
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  6. 2019Synergistic Image and Feature Adaptation: Towards Cross-Modality Domain Adaptation for Medical Image Segmentationcited by 121
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  8. 2017Anatomically Constrained Neural Networks (ACNN): Application to Cardiac Image Enhancement and Segmentationcited by 109
  9. 2020Test-Time Adaptable Neural Networks for Robust Medical Image Segmentationcited by 102
  10. 2017Transfer Learning for Domain Adaptation in MRI: Application in Brain Lesion Segmentationcited by 66
  11. 2020Post-DAE: Anatomically Plausible Segmentation via Post-Processing with Denoising Autoencoderscited by 38
  12. 2017Reverse Classification Accuracy: Predicting Segmentation Performance in the Absence of Ground Truthcited by 35
9 more
  1. 2020A Learning Strategy for Contrast-agnostic MRI Segmentationcited by 35
  2. 2018An application of cascaded 3D fully convolutional networks for medical image segmentationcited by 34
  3. 2020Atlas-ISTN: Joint Segmentation, Registration and Atlas Construction with Image-and-Spatial Transformer Networkscited by 25
  4. 2020Deep Generative Model-based Quality Control for Cardiac MRI Segmentationcited by 21
  5. 2020Partial Volume Segmentation of Brain MRI Scans of any Resolution and Contrastcited by 16
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  8. 2019An Alarm System For Segmentation Algorithm Based On Shape Modelcited by 8
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Citing papers per year: 2023: 9; 2024: 14; 2025: 13; 2026: 14.

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  1. 2023A comprehensive survey on deep active learning in medical image analysiscited by 32
  2. 2024Learning General-Purpose Biomedical Volume Representations using Randomized Synthesiscited by 27
  3. 2023AnyStar: Domain randomized universal star-convex 3D instance segmentationcited by 14
  4. 2023Brain-ID: Learning Contrast-agnostic Anatomical Representations for Brain Imagingcited by 10
  5. 2023SE(3)-Equivariant and Noise-Invariant 3D Rigid Motion Tracking in Brain MRIcited by 10
  6. 2025MultiMorph: On-demand Atlas Constructioncited by 9
  7. 2024Boosting Skull-Stripping Performance for Pediatric Brain Imagescited by 8
  8. 2023Comprehensive analysis of synthetic learning applied to neonatal brain MRI segmentationcited by 7
  9. 2024Improving cross-domain brain tissue segmentation in fetal MRI with synthetic datacited by 7
  10. 2024MRISegmentator-Abdomen: A Fully Automated Multi-Organ and Structure Segmentation Tool for T1-weighted Abdominal MRIcited by 7
  11. 2024Recon-all-clinical: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRIcited by 6
  12. 2024Towards General Text-guided Image Synthesis for Customized Multimodal Brain MRI Generationcited by 5
38 more
  1. 2023A 3D generative model of pathological multi-modal MR images and segmentationscited by 4
  2. 2024Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients for Brain Image Segmentationcited by 4
  3. 2025Unraveling Normal Anatomy via Fluid-Driven Anomaly Randomizationcited by 4
  4. 2024Evaluating Synthetic Data Generation for Domain Generalization in Fetal Brain MRI Segmentationcited by 3
  5. 2026Deep learning-based neurodevelopmental assessment in preterm infantscited by 3
  6. 2023FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRIcited by 2
  7. 2025Evaluation of 3D Counterfactual Brain MRI Generationcited by 2
  8. 2025Towards Robust In-Context Learning for Medical Image Segmentation via Data Synthesiscited by 2
  9. 2023Brain MRI Segmentation using Template-Based Training and Visual Perception Augmentationcited by 1
  10. 2024Opportunities and challenges in the application of large artificial intelligence models in radiologycited by 1
  11. 2024Guided Synthesis of Labeled Brain MRI Data Using Latent Diffusion Models for Segmentation of Enlarged Ventriclescited by 1
  12. 2025TractCloud-FOV: Deep Learning-based Robust Tractography Parcellation in Diffusion MRI with Incomplete Field of Viewcited by 1
  13. 2025Integrating Anatomical Priors into a Causal Diffusion Modelcited by 1
  14. 2026Cortex-Grounded Diffusion Models for Brain Image Generationcited by 1
  15. 2026Rectified flow-based prediction of post-treatment brain MRI from pre-radiotherapy priors for patients with gliomacited by 1
  16. 2023USLR: an open-source tool for unbiased and smooth longitudinal registration of brain MRcited by 0
  17. 2024SYNCS: Synthetic Data and Contrastive Self-Supervised Training for Central Sulcus Segmentationcited by 0
  18. 2024Deep learning-based brain segmentation model performance validation with clinical radiotherapy CTcited by 0
  19. 2024Impact of Initialization on Intra-subject Pediatric Brain MR Image Registration: A Comparative Analysis between SyN ANTs and Deep Learning-Based Approachescited by 0
  20. 2024A Contrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentationcited by 0
  21. 2025Full-Head Segmentation of MRI with Abnormal Brain Anatomy: Model and Data Releasecited by 0
  22. 2025Reference-Free 3D Reconstruction of Brain Dissection Slabs via Learned Atlas Coordinatescited by 0
  23. 2025FLAIRBrainSeg: Fine-grained brain segmentation using FLAIR MRI onlycited by 0
  24. 2025Learning to Upscale 3D Segmentations in Neuroimagingcited by 0
  25. 2025Benchmarking of Deep Learning Methods for Generic MRI Multi-Organ Abdominal Segmentationcited by 0
  26. 2025MRExtrap: Longitudinal Aging of Brain MRIs using Linear Modeling in Latent Spacecited by 0
  27. 2025Comparison of different segmentation algorithms on brain volume and fractal dimension in infant brain MRIscited by 0
  28. 2026Unified Multi-Site Multi-Sequence Brain MRI Harmonization Enriched by Biomedical Semantic Stylecited by 0
  29. 2026GOUHFI 2.0: A Next-Generation Toolbox for Brain Segmentation and Cortex Parcellation at Ultra-High Field MRIcited by 0
  30. 2026Improving Neuropathological Reconstruction Fidelity via AI Slice Imputationcited by 0
  31. 2026CRIS: Cross-Plane Self-Supervised Isotropic Restoration for Anisotropic Volumetric Imaging Across Modalitiescited by 0
  32. 2026PhyMRI-SR: Toward Physics-Aware MRI Image Super-Resolutioncited by 0
  33. 2026Patient-Agnostic Synthetic Pretraining for Efficient Patient-Specific Intraoperative 2D/3D Registrationcited by 0
  34. 2026The microscope is the mask: privileged views and labels from a cryo-ET forward modelcited by 0
  35. 2026Brain-PACE: A Deep Siamese MRI Framework for Modelling Longitudinal Brain Accelerationcited by 0
  36. 2026Uncertainty-Aware 3D Residual Wavelet Diffusion for Ultra Low-Field MRI Super-Resolutioncited by 0
  37. 2026Structural Alignment for Reliable Industrial AI: Bridging Physical Reality, Data, Models, and Human Intentcited by 0
  38. 2026Synthetic training for long-tail haemorrhagic lesion segmentation in data-scarce settingscited by 0