Wednesday, July 30, 2014

Introduction to Diffusion Tensor Imaging: From Hospital Horror Story to Neuroimaging

It is well known that one of the deepest human fears is to be a patient in a hospital late at night, all alone, while a psychotic nurse injects you with a paralyzing agent, opens up your skull with a bone saw, and begins peeling away layers of your cortex while you are still awake.*

As horrifying as this nightmare scenario may be, it also lends an important insight into an increasingly popular neuroimaging method, diffusion tensor imaging (DTI; pronounced "diddy"). To be more gruesomely specific, the psychotic nurse is able to peel away strips of your brain because it has preferred tear directions - just like string cheese. These strips follow the general direction of fascicles, or bundles of nerves, comprising grey and white matter pathways; and of these pathways, it is white matter that tends to exhibit a curious phenomenon called anisotropy.

Imagine, for example, that I release a gas - such as, let's say, deadly neurotoxin - into a spherical compartment, such as a balloon. The gas, through a process called Brownian motion (not to be confused with the Dr. Will Brown frequently mentioned here) will begin to diffuse randomly in all directions; in other words, as though it is unconstrained.

However, release the same gas into a cylindrical or tube-shaped compartment, such as one of those cardboard tubes you used to fight with when you were a kid,** and the gas particles will tend to move along the direction of the tube. This is what is known as anisotropy, meaning that the direction of the diffusion tends to go in a particular direction, as opposed to isotropy, where diffusion occurs in all directions with equal probability.

Left two figures: Ellipsoids showing different amounts of anisotropy, with lambda 1, 2, and 3 symbolizing eigenvalues. Eigenvalues represent the amount of diffusion along a particular direction. Right: A sphere representing isotropy, where diffusion occurs with equal probability in all directions.

This diffusion can be measured in DTI scans, which in turn can be used to indirectly measure white matter integrity and structural connectivity between different areas of the brain. A common use of DTI is to compare different populations, such as young and old, and to observe where fractional anisotropy (FA) differs between groups, possibly with the assumption that less FA can be indicative of less efficient communication between cortical regions. There are other applications as well, but this is the one we will focus on for the remainder of the tutorials.

The data that we will be using can be found on the FSL course website, after scrolling down to Data Files and downloading File 2 (melodic and diffusion). I haven't been able to find any good online repositories for DTI data, so we'll be working with a relatively small sample of three subjects in one group, and three subjects in the other. Also note that while we will focus on FSL, there are many other tools that process DTI data, including some new commands in AFNI, and also a program called TORTOISE. As with most things I post about, these methods have already been covered in detail by others; and in particular I recommend a blog called, which covers both the AFNI and TORTOISE approaches to DTI, along with other tutorials that I thought I had been the first to cover, but which have actually already been discussed in detail. I encourage you to check it out - but also to come back, eventually.

*Or maybe that's just me.
**And maybe you still do!

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