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Cited by 74Medical Image Segmentation TechniquesAdvanced MRI Techniques and ApplicationsAcute Ischemic Stroke Management

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models

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Koch, Stefan, Mueller, Susanne, Foddis, Marco, Bienert, Thomas, von Elverfeldt, Dominik, Knab, Felix, Farr, Tracy D, Bernard, René +5 more·2019·Journal of Cerebral Blood Flow & Metabolism
DOI 10.1177/0271678x17726635PMC PMC6360485
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Abstract

Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registration performed equally well in in a mouse middle cerebral artery occlusion model (Pearson r = 0.976, p = 2.265e-11). Information encapsulated in the registration was used to generate maps of edema induced tissue volume changes. These showed discrepancies to simplified tissue models underlying the manual approach. The presented techniques provide biologically more meaningful, voxel-wise biomarkers of vasogenic edema after stroke.

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  • Fixation alters the magnitude of water diffusion in tissue, but measures of the directionality of diffusion are less affected.

    “Fixation does alter the magnitude of water diffusion in the tissue, but measures of the directionality of diffusion are less affected [44][45][46].”

    From Diffusion tensor imaging reveals whole-brain microstructural changes in the P301L mouse model of tauopathy. (2020) · cites this paper as [45]

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Authors
Koch, S., Mueller, S., Foddis, M., Bienert, T., von Elverfeldt, D., Knab, F., Farr, T. D., Bernard, R., Dopatka, M., Rex, A., Dirnagl, U., Harms, C., & Boehm-Sturm, P.
Affiliations
  • Center for Stroke Research Berlin (DE)
  • University of Freiburg (DE)
  • Department of Radiology – Medical Physics, and BrainLinks-BrainTools Excellence Cluster, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
  • University of Nottingham (GB)
  • German Center for Neurodegenerative Diseases (DE)
  • Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), and NeuroCure, Charité University Medicine Berlin, Berlin, Germany
ORCID
Venue
Journal of Cerebral Blood Flow & Metabolism
Publisher
SAGE Publications
Published
2017-08-22
Volume
39
Issue
2
Pages
313-323
ISSN
  • 0271-678X (ISSN-L)
  • 1559-7016
DOI
10.1177/0271678x17726635
PMC
PMC6360485
OpenAlex
W2748647778
Cited by
74
References
0
Citations by year
2026: 4 · 2025: 8 · 2024: 17 · 2023: 9 · 2022: 8 · 2021: 5 · 2020: 9 · 2019: 9 · 2018: 3 · 2017: 2
FWCI
2.61
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Cerebral Blood Flow & Metabolism (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Nottingham ePrints (University of Nottingham) (submittedVersion, cc-by-nc)
  • FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion)
  • Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
  • DZNE Pub (submittedVersion, other-oa)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by-nc)
Funders
  • Deutsche Forschungsgemeinschaft
  • Bundesministerium für Bildung und Forschung (01EO0801)
  • Center for Stroke Research Berlin
  • BrainLinks-BrainTools
Topics
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
  • Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
  • Health Sciences › Medicine › Epidemiology › Acute Ischemic Stroke Management
Keywords
brain atlas registration, Allen Brain Atlas, mouse stroke model, middle cerebral artery occlusion, automatic image registration, MATLAB toolbox
MeSH terms
Animals, Blood-Brain Barrier, Brain Edema, Disease Models, Animal, Magnetic Resonance Imaging, Male, Stroke, Mice

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