NA-MIC Project Weeks

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Visual Evaluation and 3D Inspection of Cortical Surface Reconstructions from MRI Using 3D Slicer

Key Investigators

• Kaveh Moradkhani (ÉTS, Canada)
• Sylvain Bouix (ÉTS, Canada)
• Jarrett Rushmore (Boston University, USA)

Presenter location: Online

Project Description

We will visually evaluate and inspect the outputs obtained from the cortical surface reconstructions generated by our designed model. We will ensure the accuracy and correctness of these reconstructions, focusing on white matter and pial surfaces to assess their structural integrity and reliability.

Objective

1. Objective A: Visually evaluate cortical surface reconstructions from MRI images. Focus on assessing white matter and pial surfaces in .stl and .ply formats to ensure high-quality reconstructions.
2. Objective B: Visualize and inspect these reconstructions using 3D Slicer. Examine surface topology and detect self-intersections to ensure structural integrity and accuracy.

Approach and Plan

No response

Progress and Next Steps

Progress

During the NA-MIC Project Weeks, significant progress was made in the following areas:

1- Neuroanatomy and Neurosegmentation Overview: Attended sessions led by Professor Jarrett Rushmore on neuroanatomy, neurosegmentation, and the evaluation of brain structures.

2- Freesurfer Outputs Examination: Analyzed the outputs of Freesurfer, identifying inaccuracies, such as regions mistakenly classified as cortical surface, like the hippocampus, and parts including gray matter instead of cortex.

3- Sinus Examination in MRA Images: Investigated the presence and structure of sinuses in MRA images.

4- Model Comparison: Compared the outputs of our model against those from Freesurfer and Vox2Cortex models, identifying strengths and weaknesses. Notably, Fastsurfer was found to be inferior to Freesurfer in certain cases.

5- Model Evaluation and Problem Identification: Evaluated the outputs of our cortical surface reconstruction model at critical points, identifying various issues and areas for improvement.

6- 3D Slicer Extension Development: Developed approximately 70% of the extension for 3D Slicer to support cortical surface reconstruction tasks.

Next Steps

Moving forward, the following steps will be undertaken:

1- Problem Resolution: Address the issues identified during the visual evaluation of the model’s outputs, ensuring higher accuracy and structural integrity.

2- Extension Completion: Finalize the development of the 3D Slicer extension to fully support the cortical surface reconstruction workflow.

Illustrations

No response

Background and References

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