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Archive for the ‘neuroimaging’ Category

Art of Neuroimaging

November 18th, 2010 No comments

Check out more images on my neuroimaging site.

Video Introduction to the Cingulum

September 15th, 2010 2 comments

I posted this on my neuroimaging blog and thought I should post it here too. This is a video I put together about the cingulum, a prominent white matter fiber track in the brain that is involved in emotion, attention, memory, among many other functions. All images except one from Gray’s Anatomy (the anatomy book, not the T.V. show) were created by me using some fairly advanced imaging techniques. If you are interested about some of the techniques, read my neuroimaging blog.

New Neuroimaging Website

May 16th, 2010 No comments

I’ve started an online structural neuroimaging guide for users of Mac OS X. The site can be found here. I am just beginning with it so there is not much information there yet but I hope to slowly expand it and make it a good resource for things related to neuroimaging, particularly structural MRI (including diffusion weighted images). My primary interests are with neuroimaging, neuroanatomy, and neuropsychology; I spend the bulk of my research time doing one of my favorite things – dealing with methods of neuroimaging analysis. While my role is not as technical as some of our collaborators, I enjoy the process of processing MRIs. In the process I have learned a great deal about imaging and wanted to put together a series of guides that will allow others, especially students and novices, to conduct their own analyses. There is a lot of very useful information out there but it is not consolidated into any one locale. One thing I plan on doing is consolidating much of the information into one place and making it easy to follow.

Leukoaraiosis and Lacunes – A Very Brief Overview

March 12th, 2008 No comments

As people age, it is common for their brain white matter to change. These changes often appear as bright white spots on T2-weighted MR scans. These areas or spots of hyperintensity (i.e., white matter hyperintensities {WMH}) are also called leukoaraiosis (LA). Researchers are still investigating the exact nature and pathology of these abnormalities but our understanding of them is increasing. They most often seem to start around the lateral ventricles and spread from there, although it is possible to have punctate WMH throughout the brain white matter (i.e., WMH that are not connected to other regions). WMH on brain MRIs represent rarefaction of the white matter, including swelling, demyelination, and damage, although the exact nature and combination of the white matter changes is not known. These WMH can interfere with normal cognitive functioning, including processing speed, attention, inhibition, as well as global executive functioning (although these claims are still being investigated).

Other damage to white matter includes lacunes, which are little holes in the brain, much like the holes in Swiss cheese. They are caused by mini infarcts, or strokes, or other processes. Most of the time they are due to “silent strokes”, or strokes that are small enough that the person does not have any noticeable stroke symptoms. These lacunes can have similar impact on cognition as WMH. Both WMH and lacunes are related to vascular risk factors, such as hyper- or hypo-tension, diabetes, etc.

Moral Development and the Brain

November 29th, 2007 No comments

Moral reasoning is the ability a person has to reason in and through social, ethical, and emotional situations. One component of moral reasoning is moral behavior, which is the intentional and voluntary acting in a prosocial manner (Walker, 2004). Moral behavior and reasoning are the foundation for “many human social and cultural institutions such as family structures, legal and political government systems that affect the lives of virtually every person” (Eslinger, Flaherty-Craig, & Benton, 2004, p. 100). Often situations in life are morally ambiguous and involve a choice between two actions that both have consequences that may or may not be in opposition to each other. Some researchers, such as Lawrence Kohlberg, believe that people will reason through these situations at varying levels or stages, with some in a very concrete and egotistic manner and others in an abstract and universal manner.

Lawrence Kohlberg was the first researcher to come up with a major testable theory of moral development. He formulated six stages of development, with most adults reaching stage four, a few five, and very few stage six. The first two stages are at the pre-conventional level (typically self-centered and concrete reasoning), stages three and four are at the conventional level (recognition of social norms and laws), and the last two stages at the post-conventional level (recognition of universal rights and responsibilities). While Kohlberg’s theory of moral development is a stage model, the progression through the stages is not necessarily viewed as invariant. This means that people reach them at different rates and do not always reason at a particular stage with any given dilemma. There is significant variability within and between people in moral reasoning abilities. Most research focuses on between-person variability.

Read more…

MedINRIA MRI Visualization and Processing

November 20th, 2007 No comments

I just ran across a site that has a few medical imaging software packages. One of them is MedINRIA.

“MedINRIA aims at providing to clinicians state-of-the-art algorithms dedicated to medical image processing and visualization. Efforts have been made to simplify the user interface, while keeping high-level algorithms. Each application is called a module, and can be loaded dynamically from a single main window. MedINRIA is available for Microsoft Windows XP/Vista, Linux Fedora Core, MacOSX, and is fully multithreaded.”

Link to a description and download.

MedINRIA screenshot

I have not tried the software yet – my MRI analysis software is FSL – but this software looks promising. Plus it runs natively on Windows, Linux (Fedora Core), and Mac OS X (FSL only runs natively in OS X and Linux – it’s a little tricky to run in Windows). Not that running in Windows is necessarily a perk – our preferred MRI processing workstation is a Mac – but many people are using Windows. If I get around to installing the software, I’ll post a review of it later. I’m always looking to user-friendly ways to analyze MRI data. Best of all, like FSL, it is free. It is based, in part, on the open-source and excellent ITK and VTK packages.

Categories: FSL, mri, neuroimaging, neuroscience Tags:

The beginnings of functional neuroimaging

November 7th, 2007 No comments

Angelo MossoAngelo Mosso was an Italian physiologist, interested in many things but among them, blood flow and blood pressure in humans. He was born in Turin in 1846 to a father who was a carpenter by trade. Showing great promise in school, Mosso was able to attend the University of Turin and study the natural sciences. Always the consummate and prodigious researcher, over the course of his career he published more than 200 articles and books. Mosso’s work helped lay the foundation for many important (and modern) neuroscientific research methods, such as fMRI and the polygraph.

Mosso demonstrated in the late 1800s an increase in brain blood vessel pulsation as people thought about things. He interpreted this to mean that blood flow increased to the brain when people had thoughts. This particular study was one of the first (documented) functional neuroimaging (of sorts) studies. Both fMRI and PET are based on the idea that increased blood flow to the brain is associated with changes in cognition. It’s doubtful that he could have imagined how influential this research would be.

Visit this site for a longer biography of Mosso.

Categories: neuroimaging, neuroscience, psychology Tags:

MRI Quenching

October 18th, 2007 3 comments

I learned something new this week. Modern MRI scanners produce high-strength magnetic fields (typically 1.5T up to about 20T – scanners for use with humans max out at about 7T right now {those are very rare though, 1.5T and 3T are more common). To produce these fields the scanners need to have strong electric currents. In order to handle large currents, scanners use superconductors cooled with liquid helium. In cases of serious malfunction or emergency the MRI scanner can be quenched, which releases all of the liquid helium. The helium turns into a gaseous state rapidly and expands to fill the room. The quench will make a loud sound like a jet engine or a pop. If the room is small enough, all of the air can be pushed out as the helium expands and increases the pressure. Most MRI rooms have fail-safe systems that release the helium outside, which prevents the occupants from suffocating.MRI Quench

Image from here.

Categories: mri, neuroimaging Tags:

Cool Image of Ventricles in the Brain

October 8th, 2007 No comments

For my research, I’ve been spending time processing brain MRIs and measuring the volume of the brain and lateral ventricles. Here is an image of one of the brains (visualization by FSLView 3.0, with ventricles measured by ITK-Snap). The image is slightly messy because the brain did not extract perfectly (separating brain from non-brain). Also, portions of the ventricles are missing (especially the occipital and temporal horns) due to imperfect MRI resolution and processing. The ventricles are viewed through a cut-away of the 3D-rendered brain.

Ventricles in brain

Note: You MAY NOT use this image without express written consent from me.

Categories: brain, neuroimaging Tags:

Diffusion Tensor Imaging and High Angular Resolution Diffusion Imaging

September 21st, 2007 No comments

I attended an interesting lecture this week. The professor who spoke talked about Diffusion Tensor Imaging (DTI) as well as about a newer technology they are trying to help develop – High Angular Resolution Diffusion Imaging (HARDI). DTI is based on tensor mathematics and physics. The tensor in DTI is basically a 3×3 matrix (x, y, and z planes) of numbers that represent the diffusion per voxel in the brain. A voxel is a volumetric pixel – a 3D portion of the brain in MR imaging. The highest resolution we can typically get with clinical MR scanners is a cubic mm voxel. So with DTI we have a tensor, a matrix, that describes the diffusion of water molecules within each voxel in the brain. Diffusion in a jar of water or in the ventricles of the brain tends to be fast and spherical. It is less spherical in the gray matter and even less so in the white matter. In fact, the diffusion of water is highly directional in white matter (the myelinated axons of neurons). This means that the water molecules tend to diffuse somewhat parallel to the length of the axon. The movements of these water molecules are picked up by the MR scanner (which is technically “focusing” on the hydrogen atoms in water).
The diffusion per voxel can be quantified by measures of fractional anisotropy (how directional is the movement), Mean Diffusivity (total diffusion within the voxel), and by the eigenvalues of the matrix (basically how far the molecules moved in the direction of the eigenvector).
Back to HARDI. HARDI improves upon DTI by allowing for more directions of the white matter fibers to be separated out than is possible with DTI. There are some areas of the brain where there are a lot of crossing fibers and these areas show up as dark spots on DTI (which looks like a hole in the brain). With HARDI, you can see that the fibers are just more complex than is possible to calculate with DTI.
Both of these methods are useful for measuring the overall integrity (and potentially connectivity) of the white matter in the brain.

Categories: brain, mri, neuroimaging Tags: