Developing subject-specific models for the study of traumatic brain injury

Submission information

Submission Number: 137

Submission ID: 241

Submission UUID: 7dd2f3b7-cff2-4f82-922e-6921e5eb451a

Submission URI: /form/project

Created: Fri, 01/28/2022 - 09:16

Completed: Fri, 01/28/2022 - 09:16

Changed: Wed, 05/01/2024 - 15:44

Remote IP address: 66.206.189.249

Submitted by: Rika Carlsen

Language: English

Is draft: No

Webform: Project

Project Title Developing subject-specific models for the study of traumatic brain injury

Program CAREERS

Project Image

Tags finite-element-analysis (588), image-processing (299), matlab (2), programming (5), unix-environment (60), workflow (365)

Status Complete

Project Leader

Project Leader Rika Carlsen

Email carlsen@rmu.edu

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Project Personnel

Mentor(s) Anu Tripathi

Student-facilitator(s) Jordan Myers

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Project Information

Project Description Our research group is developing a workflow for generating subject-specific finite element head models from medical imaging data. These head models are applied to simulate blunt impact and blast loading scenarios with a goal of predicting the severity of brain injury. The model generation process includes segmenting the functional and structural regions of the brain, generating an appropriate finite element mesh, and incorporating structural details from medical imaging data. We are seeking a student who is interested in learning the steps in the workflow and developing new methods for improving the anatomical accuracy of these models.

Project Information Subsection

Project Deliverables The project deliverables include the following: (a) Obtain the brain segmentation from subject-specific MRI scans, using the AI-based medical image processing software FreeSurfer. (2) Generate the skull segmentation for the subject using the software FSL, (3) Combine the segmentations and manually add remaining anatomical segmentations (CSF, dura, falx, tentorium) using the software 3D Slicer, (4) Run in-house MATLAB codes to generate finite element mesh from the segmentations, (5) Repeat process (Steps 1 – 4) for additional subjects.

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Student Research Computing Facilitator Profile The candidate should have some MATLAB programming experience. Ability to program in a Linux/Unix environment is desirable. Experience/knowledge in medical image processing and finite element analysis (Abaqus) is a plus.

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Student Facilitator Programming Skill Level One programming class

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Project Institution Robert Morris University

Project Address 6001 University Blvd
Moon Township, Pennsylvania. 15108

Anchor Institution CR-Penn State

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Start as soon as possible. Yes

Project Urgency Already behind5Start date is flexible

Expected Project Duration (in months) 3 months

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Launch Presentation Date 06/08/2022

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Project Milestones

Milestone Title: Brain Segmentation
Milestone Description: Obtain brain segmentation from a subject-specific MRI scan, using the AI-based medical image processing software FreeSurfer (1 week)
Completion Date Goal: 2022-07-08
Milestone Title: Skull Segmentation
Milestone Description: Generate the skull segmentation for the subject using the software FSL (1 week)
Completion Date Goal: 2022-07-15
Milestone Title: Segmentation of Remaining Anatomical Structures
Milestone Description: Combine the segmentations and manually add remaining anatomical segmentations (CSF, dura, falx, tentorium) using the software 3D Slicer (2 - 3 weeks)
Completion Date Goal: 2022-08-05
Milestone Title: Create Finite Element Mesh
Milestone Description: Run in-house MATLAB codes to generate finite element mesh from the segmentations (1 week)
Completion Date Goal: 2022-08-12
Milestone Title: Repeat for Additional Subjects
Milestone Description: Repeat process (Steps 1 – 4) for additional subjects (4 - 6 weeks)
Completion Date Goal: 2022-09-23

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Planned Publications (if any) The generated models will be used in future finite element modeling studies of traumatic brain injury, which will be published.

What will the student learn? The student will learn about subject-specific modeling, gain hands on experience in medical image analysis, and learn how to generate a voxel-based finite element mesh.

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HPC resources needed to complete this project? Our current XSEDE allocation can be used to test the results. Several open-source software packages will be used (Freesurfer, FSL, 3D Slicer), and the only required commercial software package is MATLAB.

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Final Report

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