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Inouye JM, Handsfield GG, and Blemker SS. Fiber tractography for finite-element modeling of transversely isotropic material structures of arbitrary shape using computational fluid dynamics. Proceedings of the 2015 Summer Simulation Multi-Conference. (2015)
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Fiber tractography is useful for studying a variety of biological phenomena associated with transversely isotropic tissues, in which fibers serve to provide functional strength along a specific axis. One useful application of fiber tractography is finite-element analysis (FEA) studies. Here, we present a method utilizing computational fluid dynamics (CFD) for efficiently determining fiber trajectories in a transversely isotropic material with arbitrary structures of any complexity (such as those determined from biomedical imaging). We demonstrate assignment of fiber directions to FEA mesh by registration with the CFD mesh. Sensitivity analysis on various solver settings, flow characteristics, and material parameters shows less than 2 degrees of average deviation from the nominal fiber vectors if the Reynolds number is <1 and the flow is laminar and incompressible with our nominal fluid properties (viscosity of 1Pa-s and density of 1g/cm^3). Flow guides can be used to help correct fiber trajectories to experimental or anatomical observations, such as twisting in the Achilles tendon. This method also provides an elegant solution to determining fiber tracts in muscles that intertwine with each other, such as in the soft palate complex. For FEA studies, this method enables efficient determination and assignment of fiber directions to any finite-element mesh.


Provides a workflow for automated fiber tractography of transversely isotropic tissues for finite element modeling using computational fluid dynamics.

License: Shared materials

This project demonstrates the process for fiber tractography of complex biological tissues with transverse isotropy, such as tendon and muscle. This is important for finite element studies of these tissues, as the fiber direction must be specified in the constitutive model. This project contains code, models, and data that can be used to reproduce the results of our publication on this technique. The supplied instructional videos will enable researchers to easily and efficiently apply this method to a variety of other tissues. The software used in the fiber tractography process and demonstrated in this project is Matlab, Autodesk Inventor (free for educators), and Autodesk Simulation CFD (free for educators). Full demonstrations and process instructions can be found in the 7 videos posted at https://vimeo.com/album/3414604:

Contents:

Chapter 1: Introduction (2:35)
This video introduces the CFD fiber tractography software pipeline

https://vimeo.com/moogaloop.swf?clip_id=129107314&force_embed=vimeo.com&fullscreen=1" />

Chapter 2: Supplementary materials code, models and data (20:21)
This video shows the shared models, code, and data posted online at simtk.org/m3lab_cfd4fea.

Chapter 3: Finite element simulations (5:38)
This video shows finite element simulations using the fiber mapping process.

Chapter 4: Iliacus example walkthrough (21:38)
This video shows the step-by-step process for fiber mapping the iliacus muscle (a hip flexor).

Chapter 5: Bflh example walkthrough (12:09)
This video shows the step-by-step process for fiber mapping the biceps femoris longhead muscle (a hamstring).

Chapter 6: Autodesk Inventor segmentation (9:09)
This video shows how to do segmentation of medical images in Autodesk Inventor in order to simplify the solid model for the CFD and FEA software.

Chapter 7: Curved inlet surfaces (6:28)
This video shows how to create curved inlet surfaces for use in Autodesk Simulation CFD.

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The code, data, and models are provided to reproduce Figures 1, 2, 3c, 3d, and 4, and Table 1.

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