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Updated: Mar 10, 2026
Multiple-mouse Neuroanatomical Magnetic Resonance Imaging
Published on: February 27, 2011
A Method for Whole Brain Ex Vivo Magnetic Resonance Imaging with Minimal Susceptibility Artifacts
Anwar S Shatil1, Kant M Matsuda2, Chase R Figley3
1Biomedical Engineering Graduate Program, University of Manitoba, Winnipeg, MB, Canada; Neuroscience Research Program, Winnipeg Health Sciences Centre, Kleysen Institute for Advanced Medicine, Winnipeg, MB, Canada.
Abstract:
Magnetic resonance imaging (MRI) is a non-destructive technique that is capable of localizing pathologies and assessing other anatomical features (e.g., tissue volume, microstructure, and white matter connectivity) in postmortem, ex vivo human brains. However, when brains are removed from the skull and cerebrospinal fluid (i.e., their normal in vivo magnetic environment), air bubbles and air-tissue interfaces typically cause magnetic susceptibility artifacts that severely degrade the quality of ex vivo MRI data. In this report, we describe a relatively simple and cost-effective experimental setup for acquiring artifact-free ex vivo brain images using a clinical MRI system with standard hardware. In particular, we outline the necessary steps, from collecting an ex vivo human brain to the MRI scanner setup, and have also described changing the formalin (as might be necessary in longitudinal postmortem studies). Finally, we share some representative ex vivo MRI images that have been acquired using the proposed setup in order to demonstrate the efficacy of this approach. We hope that this protocol will provide both clinicians and researchers with a straight-forward and cost-effective solution for acquiring ex vivo MRI data from whole postmortem human brains.
Insights
This study presents a simple, cost-effective method for obtaining high-quality ex vivo magnetic resonance imaging (MRI) of human brains. The protocol minimizes artifacts, improving visualization of postmortem brain structures for research and clinical applications.
Area of Science:
- Neuroimaging
- Postmortem studies
- Medical imaging techniques
Background:
- Magnetic resonance imaging (MRI) is crucial for analyzing postmortem human brains.
- Ex vivo brain MRI is often degraded by magnetic susceptibility artifacts due to removal from the natural magnetic environment.
- These artifacts hinder the assessment of anatomical features and pathologies.
Purpose of the Study:
- To describe a simple and cost-effective experimental setup for acquiring artifact-free ex vivo brain MRI data.
- To provide a detailed protocol for preparing and scanning whole postmortem human brains.
- To demonstrate the efficacy of the proposed method through representative images.
Main Methods:
- Development of a straightforward experimental setup for ex vivo brain MRI using standard clinical MRI systems.
- Detailed protocol covering brain collection, preparation, formalin handling, and MRI scanner configuration.
- Acquisition of ex vivo MRI data from whole postmortem human brains using the developed setup.
Main Results:
- The proposed setup successfully acquires artifact-free ex vivo brain images.
- Representative MRI images demonstrate high quality and clarity of brain structures.
- The method effectively overcomes common magnetic susceptibility artifacts.
Conclusions:
- The described protocol offers a practical and economical solution for obtaining high-quality ex vivo MRI data from postmortem human brains.
- This approach can significantly benefit clinicians and researchers studying brain anatomy and pathology.
- The method enhances the utility of MRI in postmortem neuroscience and diagnostics.
