ArticleNeuroinformatics2020
Automatic Brain Extraction for Rodent MRI Images.
Article in Neuroinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 37 citations in OpenAlex.
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- PIGSKIN: PIG SKull stripping with synthetic Images and Neural networks.AI in neuroscience · 2026Article
- In vivo imaging of glutamate uncovers the neuroprotective effects of nicotinamide riboside on excitotoxicity in an Alzheimer's mouse model.Alzheimer's research & therapy · 2026Article
- Hippocampal tissue mechanics are sensitive to fluctuations in oestrogen across the rat oestrous cycle.Brain communications · 2026Article
- Segmentation of Pulp and Pulp Stones with Automatic Deep Learning in Panoramic Radiographs: An Artificial Intelligence Study.Dentistry journal · 2025Article
- Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small-animal imaging.Magnetic resonance in medicine · 2025Review
- Mouse Brain Extractor: Brain segmentation of mouse MRI using global positional encoding and SwinUNETR.bioRxiv : the preprint server for biology · 2024Article
- Fully automated whole brain segmentation from rat MRI scans with a convolutional neural network.Journal of neuroscience methods · 2024Article
- GPU-Based Parallel Processing Techniques for Enhanced Brain Magnetic Resonance Imaging Analysis: A Review of Recent Advances.Sensors (Basel, Switzerland) · 2024Review
- Brain morphological analysis in mice with hyperactivation of the hedgehog signaling pathway.Frontiers in neuroscience · 2024Article
- MR Template-Based Individual Brain PET Volumes-of-Interest Generation Neither Using MR nor Using Spatial Normalization.Nuclear medicine and molecular imaging · 2023Article
- RU-Net: skull stripping in rat brain MR images after ischemic stroke with rat U-Net.BMC medical imaging · 2023Article
- Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks.Neuroinformatics · 2023Article
- Article
- Longitudinal manganese-enhanced magnetic resonance imaging of neural projections and activity.NMR in biomedicine · 2022Review
- Deep learning network for integrated coil inhomogeneity correction and brain extraction of mixed MRI data.Scientific reports · 2022Article
- Automated Skull Stripping in Mouse Functional Magnetic Resonance Imaging Analysis Using 3D U-Net.Frontiers in neuroscience · 2022Article
- An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery.Frontiers in bioinformatics · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Rodent models are increasingly important in translational neuroimaging research. In rodent neuroimaging, particularly magnetic resonance imaging (MRI) studies, brain extraction is a critical data preprocessing component. Current brain extraction methods for rodent MRI usually require manual adjustment of input parameters due to widely different image qualities and/or contrasts. Here we propose a novel method, termed SHape descriptor selected Extremal Regions after Morphologically filtering (SHERM), which only requires a brain template mask as the input and is capable of automatically and reliably extracting the brain tissue in both rat and mouse MRI images. The method identifies a set of brain mask candidates, extracted from MRI images morphologically opened and closed sequentially with multiple kernel sizes, that match the shape of the brain template. These brain mask candidates are then merged to generate the brain mask. This method, along with four other state-of-the-art rodent brain extraction methods, were benchmarked on four separate datasets including both rat and mouse MRI images. Without involving any parameter tuning, our method performed comparably to the other four methods on all datasets, and its performance was robust with stably high true positive rates and low false positive rates. Taken together, this study provides a reliable automatic brain extraction method that can contribute to the establishment of automatic pipelines for rodent neuroimaging data analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.