ArticleScientific reports2019
atlasBREX: Automated template-derived brain extraction in animal MRI.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 30 citations in OpenAlex.
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- MBV-Pipe: A One-Stop Toolbox for Assessing Mouse Brain Morphological Changes for Cross-Scale Studies.Neuroinformatics · 2024Article
- Automatic brain extraction and brain tissues segmentation on multi-contrast animal MRI.Scientific reports · 2023Article
- HC-Net: A hybrid convolutional network for non-human primate brain extraction.Frontiers in computational neuroscience · 2023Article
- Brief isoflurane administration as an adjunct treatment to control organophosphate-induced convulsions and neuropathology.Frontiers in pharmacology · 2023Article
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- Fibrin-targeting molecular MRI in inflammatory CNS disorders.European journal of nuclear medicine and molecular imaging · 2022Article
- U-net model for brain extraction: Trained on humans for transfer to non-human primates.NeuroImage · 2021Article
- Early postnatal irradiation-induced age-dependent changes in adult mouse brain: MRI based characterization.BMC neuroscience · 2021Article
- Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates.NeuroImage · 2021Article
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- A MRI-Based Toolbox for Neurosurgical Planning in Nonhuman Primates.Journal of visualized experiments : JoVE · 2020Article
- Automatic Skull Stripping of Rat and Mouse Brain MRI Data Using U-Net.Frontiers in neuroscience · 2020Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We proposed a generic template-derived approach for (semi-) automated brain extraction in animal MRI studies and evaluated our implementation with different animal models (macaque, marmoset, rodent) and MRI protocols (T1, T2). While conventional MR-neuroimaging studies perform brain extraction as an initial step priming subsequent image-registration from subject to template, our proposed approach propagates an anatomical template to (whole-head) individual subjects in reverse order, which is challenging due to the surrounding extracranial tissue, greater differences in contrast pattern and larger areas with field inhomogeneity. As a novel approach, the herein introduced brain extraction algorithm derives whole-brain segmentation using rigid and non-rigid deformation based on unbiased anatomical atlas building with a priori estimates from study-cohort and an initial approximate brain extraction. We evaluated our proposed method in comparison to several other technical approaches including "Marker based watershed scalper", "Brain-Extraction-Tool", "3dSkullStrip", "Primatologist-Toolbox", "Rapid Automatic Tissue Segmentation" and "Robust automatic rodent brain extraction using 3D pulse-coupled neural networks" with manual skull-stripping as reference standard. ABX demonstrated best performance with accurate (≥92%) and consistent results throughout datasets and across species, age and MRI protocols. ABX was made available to the public with documentation, templates and sample material ( https://www.github.com/jlohmeier/atlasBREX ).
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