Three-Dimensional Shape Modeling and Analysis of Brain Structures

Jaeil Kim; Maria  del Carmen Vald&#233;s Hern&#225;ndez; Jinah Park

doi:10.3791/59172

Three-Dimensional Shape Modeling and Analysis of Brain Structures

JoVE Journal
Neuroscience

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JoVE Journal Neuroscience

Three-Dimensional Shape Modeling and Analysis of Brain Structures

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05:33 min

November 14, 2019

DOI: 10.3791/59172-v

Jaeil Kim¹, Maria del Carmen Valdés Hernández², Jinah Park³

¹School of Computer Science and Engineering,Kyungpook National University, ²Centre for Clinical Brain Sciences,University of Edinburgh, ³School of Computing and KI for Health Science and Technology (KIHST),Korea Advanced Institute of Science and Technology (KAIST)

Overview

This study introduces a semi-automatic protocol for 3D shape analysis of brain structures, focusing on hippocampal segmentation from brain MRI images. The methodology involves open software for image segmentation followed by group-wise shape analysis using an automated modeling package.

Key Study Components

Area of Science

Neuroscience
Image Analysis
Structural Brain Modeling

Background

Accurate shape recovery is essential for anatomical correspondence in brain models.
The framework includes tools for shape modeling and deformity computation.
Used with large human brain datasets for various studies.
The software was developed by Dr. Jaeil Kim and demonstrates user-friendly features.

Purpose of Study

To demonstrate a procedure for hippocampal segmentation and shape analysis.
To provide an automated framework for modeling individual and group brain shapes.
To offer tools for statistical analysis of shape variations.

Methods Used

The method utilizes a graphic user interface for MRI image and segmentation editing.
The study focuses on hippocampal structures using T1-weighted magnetic resonance images.
Users manually edit hippocampal segmentations and construct group templates.
Statistical analysis is performed using shape deformity measurements.
MATLAB code is provided for analysis at the project page.

Main Results

The approach allows for precise shape modeling of the hippocampus and computation of shape deformities.
Results demonstrate differences in hippocampal shape between groups with varying brain tissue volumes.
Individual shape characteristics are restored while minimizing distortion during modeling.
Visualization of aligned models and average shape deformity maps is included.

Conclusions

This protocol enables effective shape analysis and modeling of hippocampal structures.
The methodology enhances understanding of anatomical variations in brain research.
Applications extend to clinical studies involving conditions like Alzheimer's disease and other structural anomalies.

Frequently Asked Questions

What are the advantages of using this protocol for shape analysis?

This semi-automatic protocol enhances accuracy in shape modeling while reducing user effort through automation. It provides a robust framework for large datasets.

How is the hippocampal segmentation performed?

Segmentation begins with automatic results from the MRI, followed by manual editing to ensure that critical structures like the uncus are included in the mask.

What types of data can be obtained from this analysis?

The analysis yields detailed shape models, deformation measurements, and average shape deformity maps that reveal structural differences among populations.

Can the method be adapted for other brain structures?

Yes, while focused on the hippocampus, the framework can be applied to other brain structures requiring similar shape analysis methods.

What are the key considerations for using this approach?

Users should remain involved in critical steps that require confirmation, such as adjusting intensity parameters to fit segmentation results accurately.

How is statistical analysis integrated into this protocol?

Statistical analysis is performed on shape deformities to explore variations and correlations relevant to clinical conditions and patient populations.

We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images.

Accurately recovering the shape features against rough and noisy segmentations is critical to achieving good anatomical correspondence between individual brain shape models. Our framework provides various tools for individual shape modeling, group-wise template construction, and shape deformity computation. And it has been used for large datasets of the human brain.

Demonstrating this procedure will be Dr.Jaeil Kim, a former grad student from my laboratory who developed the software for the brain shape modeling. For manual editing of the hippocampal segmentation, open the T1 weight magnetic resonance image and the automatic hippocampal segmentation results in the graphic user interface software. Click the icon in the display window to select the coronal view and scroll through the volume until the uncus is located.

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