ArticleNeuroImage2020
A comparison of Freesurfer and multi-atlas MUSE for brain anatomy segmentation: Findings about size and age bias, and inter-scanner stability in multi-site aging studies.
Article in NeuroImage, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring approaches to tackle cross-domain challenges in brain medical image segmentation: a systematic review.Frontiers in neuroscience · 2024Pooled it
- A randomized controlled trial examining the effects of behavioral weight loss treatment on hippocampal volume and neurocognition.Physiology & behavior · 2023Trial
- Machine learning-derived Alzheimer's disease dimensions: neuroanatomical, cognitive, clinical, functional, and genetic risk heterogeneity signatures.medRxiv : the preprint server for health sciences · 2026Article
- A unified model for staging amyloid and tau pathology in Alzheimer's disease.medRxiv : the preprint server for health sciences · 2026Article
- Comparative analysis of freesurfer and brainsuite in thickness, surface area, and volume measurements for morphometric group comparisons.Brain imaging and behavior · 2026Article
- CSF Levels of NPTX2 Are Associated With Less Brain Atrophy Over Time in Cognitively Unimpaired Individuals.Annals of clinical and translational neurology · 2026Article
- Modeling the age-specific incidence of mild cognitive impairment incorporating the time-varying relationship of Alzheimer's disease biomarkers over 28 years.Journal of Alzheimer's disease : JAD · 2026Article
- Adult lifespan effects on functional specialization along the hippocampal long axis.Frontiers in cognition · 2026Article
- Estimation of reference curves for brain atrophy and analysis of robustness to machine effects.Scientific reports · 2025Article
- Multivariate whole brain neurodegenerative-cognitive-clinical severity mapping in the Alzheimer's disease continuum using explainable AI.medRxiv : the preprint server for health sciences · 2025Article
- Quality and efficiency of a semi-automatic anatomy-based method for tractography of associative white matter fascicles in brain tumor patients, a case series.Neurosurgical review · 2025Article
- Machine learning reveals distinct neuroanatomical signatures of cardiovascular and metabolic diseases in cognitively unimpaired individuals.Nature communications · 2025Article
- Lower hippocampal volumes at baseline are associated with higher volume loss in healthy elderly.Frontiers in aging neuroscience · 2025Article
- Inter-Software Consistency on the Estimation of Subcortical Structure Volume in Different Age Groups.Human brain mapping · 2024Article
- The effects of psychotherapy for anhedonia on subcortical brain volumes measured with ultra-high field MRI.Journal of affective disorders · 2024Article
- Choroid plexus volumes and auditory verbal learning scores are associated with conversion from mild cognitive impairment to Alzheimer's disease.Brain and behavior · 2024Article
- Deep learning-based, fully automated, pediatric brain segmentation.Scientific reports · 2024Article
- Superpixel-ComBat modeling: A joint approach for harmonization and characterization of inter-scanner variability in T1-weighted images.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Alzheimer's disease genetic risk and changes in brain atrophy and white matter hyperintensities in cognitively unimpaired adults.Brain communications · 2024Article
- Cognitive and gray matter volume predictors of learning across two types of casual video games in older Adults: Action vs Strategy.Aging brain · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Automatic segmentation of brain anatomy has been a key processing step in quantitative neuroimaging analyses. An extensive body of literature has relied on Freesurfer segmentations. Yet, in recent years, the multi-atlas segmentation framework has consistently obtained results with superior accuracy in various evaluations. We compared brain anatomy segmentations from Freesurfer, which uses a single probabilistic atlas strategy, against segmentations from Multi-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters and locally optimal atlas selection (MUSE), one of the leading ensemble-based methods that calculates a consensus segmentation through fusion of anatomical labels from multiple atlases and registrations. The focus of our evaluation was twofold. First, using manual ground-truth hippocampus segmentations, we found that Freesurfer segmentations showed a bias towards over-segmentation of larger hippocampi, and under-segmentation in older age. This bias was more pronounced in Freesurfer-v5.3, which has been used in multiple previous studies of aging, while the effect was mitigated in more recent Freesurfer-v6.0, albeit still present. Second, we evaluated inter-scanner segmentation stability using same day scan pairs from ADNI acquired on 1.5T and 3T scanners. We also found that MUSE obtains more consistent segmentations across scanners compared to Freesurfer, particularly in the deep structures.
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