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Thesis Format

Integrated Article


Master of Engineering Science


Biomedical Engineering


Khan, Ali R

2nd Supervisor

Baron, Corey A



Diffusion MRI is used to non-invasively characterize the microstructure of the brain. However, the accuracy of the characterization is difficult to verify because no other non-invasive imaging modality provides the same information. This thesis presents a novel 3D printed axon-mimetic (3AM) diffusion MRI phantom, a synthetic object designed to mimic the brain's microstructure.

The phantoms were characterized using microscopy, synchrotron micro-computed tomography, and diffusion MRI, and found to have sufficiently axon-mimetic properties to be useful as diffusion MRI phantoms. A set of phantoms designed to have anatomically realistic and complex fibre structures was used to test the response of diffusion MRI models of white matter to fibre orientation dispersion. All tested models were found to respond to orientation dispersion, but some robust metrics were identified. The studies in this thesis demonstrate that 3AM phantoms are a novel, flexible, and inexpensive tool for validating diffusion MRI models of white matter.

Summary for Lay Audience

Magnetic resonance imaging, or MRI, is often used to generate images that we can use to safely investigate the brain. To answer some questions about the brain and how its different regions are interconnected, we need more detail than standard MRI can provide. In these cases, we can use diffusion MRI, which is sensitive to the way water molecules randomly move around. Axons, the connections between brain cells, are shaped like tubes, so it is easier for water molecules to move along the axons than across them.

We can use models, which mathematically describe what we understand about how axons change the motion of water molecules, to make predictions about the brain from diffusion MRI images. However, there is no other safe way to make the same kinds of predictions about a brain, so it is difficult to know how accurate the predictions from diffusion MRI are. What we can do to assess diffusion MRI model predictions is create artificial objects made of tube-shaped structures that mimic axons. If we make the objects and control the same properties that we investigate in the brain, we can use diffusion MRI models to ask questions about the phantoms, the answers to which we already know. If the diffusion MRI models make accurate predictions about a phantom, they probably also make accurate predictions about real brains.

This thesis presents a new kind of diffusion MRI phantom that is produced by 3D printing with a special material. Part of the 3D printed material forms fibres that dissolve in water, leaving behind holes that are tube-shaped like axons. In the thesis, we show that the tube-shaped holes are small enough to convincingly mimic axons. We then use the phantoms to show that diffusion MRI models do not always make consistent predictions when axons bend and cross.

The phantoms presented in this thesis are inexpensive and make it easier for researchers to make sure diffusion MRI models make accurate predictions even in complex parts of the brain. This will help make diffusion MRI as useful as possible for investigating the brain.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.