T o be able to understand what an anatomical MRI scan is, you must first understand what the brain is. The brain is composed of the cerebrum, brainstem and cerebellum which work together to make the brain function. The cerebrum, has two cerebral hemispheres — left and right —which contains an inner core made of white matter and an outer surface, the cerebral cortex, which is made of grey matter.

What is grey and white matter and what are the differences between them?

These two types of matter are composed of nerve cells called neurons which carry electrical impulses from one place to another. A neuron is composed of a long fibre, called an axon, which is insulated by a fatty myelin sheath. These axons are long so that they can carry messages up and down the body, but because they are long, this myelin sheath is used to speed up the transmission of signals by allowing signals to jump from node to node, effectively bypassing the need to travel the whole length of the nerve fibre. The cell body, also known as a soma, is the core part of the neuron which provides energy to drive activities and receives information.

Grey matter mainly consists of neuronal cell bodies and unmyelinated axons, while white matter is mainly made up of myelinated axons. As the image shows, the part of the neuron which is covered in the myelin sheath is found within the white matter. The myelin protects the nerve fibres (axons) from damage and is what gives white matter its colour, it also facilitates electrical signals to jump, by acting as an insulator, which increases the transmission speed of signals. These axons, allow for communication between different brain regions and connects various grey matter areas to each other. The cell bodies are found within the grey matter, which allows it to process information and release new information through axon signalling. Grey matter plays an important role in enabling individuals to control movement, memory, and emotions. However, an individuals grey matter volume changes over the course of ageing and is also affected by many other factors. For example, lifestyle factors, such as high alcohol consumption, has been linked with reductions in grey matter volume. People with neurological diseases, such as Alzheimer’s, have also been shown to have a reduced grey matter volume. This is why it is important to understand the structure of the brain and how it is susceptible to change.

Essentially, grey matter contains most of the brains neuronal cell bodies which conducts, processes and sends information to various parts of the body. White matter is made up of axons which allows signals to be sent, connects brain regions and interprets sensory information from parts of the body.

So now we know about grey and white matter, but how does that relate to MRI scans?

MRI scans produce detailed images, in three planes, of the tissues which make up the brain by using magnetism and radio waves. There are three common MRI sequences, known as T1 weighted (T1), T2 weighted (T2) and Fluid Attenuated Inversion Recovery (FLAIR), which produce different contrasts and brightness of the different tissues. In a T1 scan, the white matter will appear brighter than in a T2 scan. Conversely, the cerebrospinal fluid (CSF) will typically appear darker in a T1 scan, and in a T2 scan it will appear brighter. This is illustrated in the image below.

Ok, so the brightness is different in each sequence, but why is this useful?

Well because the different scans highlight different areas, they can be used for different reasons. Both T1 and T2 scans are used for anatomical detail but the brightness is flipped. This allows certain features to be highlighted by the different scans. For example, the T1 scan can be useful to detect vascular changes, if Gadolinium (a contrast enhancement agent) is injected, then the visibility of blood vessels is improved. T2 scans are useful at picking up a majority of lesions as they will appear bright, however it has trouble differentiating them from the CSF which is why FLAIR is sometimes used. FLAIR is similar to T2 but can differentiate between CSF and lesions as these will show up as bright and the CSF will show up as dark, allowing a contrast between the two. This is opposed to T2 scans where both will show up as bright so would be difficult to tell apart. The table below summarises these differences.

So you can see the reasons why we might choose different sequences depending on what we want to investigate in the image.

Earlier, I mentioned about MRI scans producing an output in three different planes, so you may be wondering what these are. These are basically the different directions which the image is taken — axial, sagittal and coronal. Axial is taken from the top-down (superior-inferior), sagittal is taken from the side and coronal is taken from the front (anterior-posterior) as illustrated in the image below.

Modern medical imaging, including MRI, often uses DICOM to store scans along with meta-data about those scans. This meta-data can include patient information (birth, gender), context data (patient history), and more importantly, acquisition data (type of modality used, settings of the scanner). These DICOM images contain the raw 3D MRI scan, but they are often converted into NIFTI file format, which is essentially a series of 2D slices, for use in analysis.

So now you know about anatomical MRI scans. In the next post, I will explain what functional MRI scans are and what they are used for. I will then later go on to explain how we can pre-process these images and run analysis.