A basic introduction to fMRI and MRI

MRI scannerfMRI (functional magnetic resonance imaging) builds on a basic MRI (magnetic resonance imaging) by looking at blood flow. An MRI works because protons, which make up atoms, are affected by magnetic fields. Basically, an MRI aligns a very small proportion of the protons in body tissue (it usually affects hydrogen the most because of hydrogen’s proton and neutron composition; hydrogen is also prevalent in body tissue and so it is easy to affect). Normally the protons in hydrogen are randomly orientated which means their minute magnetic fields are also randomly orientated. When these protons are placed in the vicinity of the strong magnetic field produced by MRI machines, some of them align with the magnetic field of the machine. The machine also produces radio waves that slightly affect the aligned protons. These waves will cause the protons to spin a certain way in response to the radio waves. The radio waves are then turned off and the protons realign themselves to the magnetic field produced by the MRI machine. The machine picks up this re-alignment and a computer processes it to create an image of the brain (or what ever else is scanned). Since protons in different tissues align at different rates, the machine can differentiate between different types of tissue (such as skull and white and gray matter).

An fMRI just builds on the MRI by focusing on the ratio between oxygenated to deoxygenated blood; this is the blood oxygenation level dependent effect (BOLD effect). Basically, an fMRI indirectly measures brain activity by measuring the change in blood levels (specifically hemoglobin as it deoxygenates). An fMRI works because as brains process information blood flows to those areas to help provide the needed oxygen and glucose. The result of this process is a scan of the brain with lighter (or darker) areas where blood is flowing in greater quantity.

One example of how an fMRI was used to test a cognitive neuroscience theory was when Deibert et al. (1999) had subjects close their eyes and try to identify objects only by touch. The researchers discovered through fMRI that the subjects’ visual cortex was activated even though their eyes were closed. There were two different explanations: first the objects were identified and then visual images were created or the visual image was created during the process of identification and thus helped the subjects recognize the objects. However, fMRI alone was not sufficient to support the correct theory. When researchers used transcranial magnetic stimulation (TMS) they discovered that they could interrupt the processing in the occipital lobe and interfere with object recognition. So the combination of fMRI and TMS showed that the visual image formed during tactile exploration is important for object recognition. While fMRI was not sufficient in this case, it was key in uncovering and explaining the theory about how tactile object recognition works in the absence of visual input.

Image courtesy of MacRonin47.

Neuroimaging and Image Analysis

A handy program I use to analyze MRI data is called FSL. “FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK” (from the FSL website). It is powerful, flexible, and well-maintained. There is a very active community listserv too.

All of my research is structural MRI-based, so the main FSL tools I use are: Brain Extraction tool (BET), SUSAN (which reduces noise nonlinearly), FAST (an automated segmentation program that can separate the MR images into different tissue types), FLIRT (a linear registration program), and FUGUE (a program that can unwarp the MR images; there is often distortion in MRIs caused at scan acquisition by head movements or other problems).

I’ve been very pleased with the software so far. It’s free software and available to pretty much anyone for use. I have no affiliation with the software developers, I am just a pleased user of the software. I would post some of the images I’ve processed with FSL, however, due to IRB, HIPPA, and confidentiality limitations, I am unable to.

Great neuroanatomy site

I came across this great site with “over 12 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet.” They have some great high-quality images of brains – great for learning neuroanatomy.


Link to neuroanatomy/MRI site

As a start towards discovering neuropsychology, understanding neuroanatomy is imperative; so here’s a great brain MRI website: The Whole Brain Atlas