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Updated: Apr 26, 2026

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Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images
Published on: January 7, 2019
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Bringing CLARITY to gray matter atrophy
Rory D Spence1, Florian Kurth1, Noriko Itoh2
1Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA.
Neuroimage
|July 20, 2014
Summary
This study links gray matter atrophy in experimental autoimmune encephalomyelitis (EAE) to spinal cord axonal damage. Cortical volume loss directly correlated with axonal end bulbs, revealing a key relationship in this multiple sclerosis model.
Area of Science:
- Neuroscience
- Immunology
- Biomedical Imaging
Background:
- Gray matter atrophy correlates with disability in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE).
- The link between gray matter atrophy and spinal cord pathology in EAE remains unclear.
Purpose of the Study:
- To investigate the relationship between cortical volume changes and spinal cord axonal pathology in EAE.
- To establish correlations between in vivo MRI findings and ex vivo tissue analysis using CLARITY.
Main Methods:
- Experimental autoimmune encephalomyelitis (EAE) induced in Thy1.1-YFP mice.
- In vivo magnetic resonance imaging (MRI) of brains.
- Optical clearing of brains and spinal cords using Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging-compatible Tissue-hYdrogel (CLARITY).
- 3D axonal tracing in spinal cords and analysis of cortical neuron morphology.
Main Results:
- EAE mice showed decreased cortical volumes and reduced layer V pyramidal neuron apical dendrite length.
- Significant axonal damage observed in spinal cords, including axonal ovoids and end bulbs.
- Direct correlation found between decreased cortical volume and the number of axonal end bulbs in the spinal cord.
Conclusions:
- This study establishes a direct relationship between cortical volume loss and spinal cord axonal pathology in EAE.
- The findings highlight the utility of combining MRI and CLARITY for studying neurodegenerative processes in animal models.
- This research provides novel insights into the neuropathological mechanisms underlying EAE and potentially MS.
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