ArticleJournal of neuroscience methods2016
A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head.
Article in Journal of neuroscience methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Quality Assurance Strategies for Brain State Characterization by MEMRI.bioRxiv : the preprint server for biology · 2026Article
- Reconfiguration of brain-wide neural activity after early life adversity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Reconfiguration of brain-wide neural activity after early life adversity.bioRxiv : the preprint server for biology · 2025Article
- Longitudinal monitoring of the mouse brain reveals heterogenous network trajectories during aging.Communications biology · 2024Article
- RU-Net: skull stripping in rat brain MR images after ischemic stroke with rat U-Net.BMC medical imaging · 2023Article
- Harnessing axonal transport to map reward circuitry: Differing brain-wide projections from medial prefrontal cortical domains.Frontiers in cell and developmental biology · 2023Article
- Article
- Aberrant brain functional and structural developments in MECP2 duplication rats.Neurobiology of disease · 2022Article
- Longitudinal manganese-enhanced magnetic resonance imaging of neural projections and activity.NMR in biomedicine · 2022Review
- Studying Axonal Transport in the Brain by Manganese-Enhanced Magnetic Resonance Imaging (MEMRI).Methods in molecular biology (Clifton, N.J.) · 2022Article
- Evolution of brain-wide activity in the awake behaving mouse after acute fear by longitudinal manganese-enhanced MRI.NeuroImage · 2020Article
- Automatic Brain Extraction for Rodent MRI Images.Neuroinformatics · 2020Article
- Conductive Hearing Loss Aggravates Memory Decline in Alzheimer Model Mice.Frontiers in neuroscience · 2020Article
- Imaging the evolution acute fear: Longitudinal whole brain imaging in living mice of neural activity with MEMRI.Proceedings of the International Society for Magnetic Resonance in Medicine ... Scientific Meeting and Exhibition. International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition · 2019Article
- Trastuzumab Induced Chemobrain, Atorvastatin Rescued Chemobrain with Enhanced Anticancer Effect and without Hair Loss-Side Effect.Journal of clinical medicine · 2019Article
- Decoupling the Effects of the Amyloid Precursor Protein From Amyloid-β Plaques on Axonal Transport Dynamics in the Living Brain.Frontiers in cellular neuroscience · 2019Article
- Alterations of functional circuitry in aging brain and the impact of mutated APP expression.Neurobiology of aging · 2018Article
- Neural activation imaged by MEMRI in mouse models of PTSD: Early Life Stress and Role of the Serotonergic System in Prolonged Response to Fear.Proceedings of the International Society for Magnetic Resonance in Medicine ... Scientific Meeting and Exhibition. International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition · 2018Article
- Automated Computational Processing of 3-D MR Images of Mouse Brain for Phenotyping of Living Animals.Current protocols in molecular biology · 2017Article
- In vivo microscopic voxel-based morphometry with a brain template to characterize strain-specific structures in the mouse brain.Scientific reports · 2017Article
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Authors and funding
7 authors.
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Abstract
backgroundMagnetic resonance imaging (MRI) is a well-developed technique in neuroscience. Limitations in applying MRI to rodent models of neuropsychiatric disorders include the large number of animals required to achieve statistical significance, and the paucity of automation tools for the critical early step in processing, brain extraction, which prepares brain images for alignment and voxel-wise statistics. NEW
methodThis novel timesaving automation of template-based brain extraction ("skull-stripping") is capable of quickly and reliably extracting the brain from large numbers of whole head images in a single step. The method is simple to install and requires minimal user interaction.
resultsThis method is equally applicable to different types of MR images. Results were evaluated with Dice and Jacquard similarity indices and compared in 3D surface projections with other stripping approaches. Statistical comparisons demonstrate that individual variation of brain volumes are preserved. COMPARISON WITH EXISTING
methodsA downloadable software package not otherwise available for extraction of brains from whole head images is included here. This software tool increases speed, can be used with an atlas or a template from within the dataset, and produces masks that need little further refinement.
conclusionsOur new automation can be applied to any MR dataset, since the starting point is a template mask generated specifically for that dataset. The method reliably and rapidly extracts brain images from whole head images, rendering them useable for subsequent analytical processing. This software tool will accelerate the exploitation of mouse models for the investigation of human brain disorders by MRI.
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