A brief beginner's guide to the brain and MRI

As some of you know, I often answer posts on here asking for help to understand what a neurologist’s letter or radiologist’s report means. What you probably don’t know is that it is a pretty time-consuming task and, every time I find myself typing the same stuff, I say to myself, “I absolutely must put something together that I can copy and paste from!”

Well, I have finally done it :slight_smile:

It occurred to me that some of you might be interested in reading the whole thing and that you might use it as a “starter for 10”, to give you more confidence to go and do some research on your own when you come across something in a letter or report that doesn’t make any sense.

I’ll still be happy to help, especially as the stuff I’m posting here only really scratches the surface, so don’t take this as me telling everyone to start doing it on their own :slight_smile:

I think the whole document is too long to post in one go, so I’m going to do a reply below this about the brain and a reply after that about MRI. My apologies – the spinal cord is noticeable by its absence. Maybe I’ll add something about that at a later date.

A couple of caveats. I have made this as easy as I could. That means that an expert would no doubt shake their head at bits and laugh their heads off at other bits, but on the whole I think it’s an acceptable explanation. However, I am not a neurologist or a radiologist; my knowledge comes from a background of neuroscience research using MRI followed by a lot of self teaching. In other words, please don’t assume that this is fault-free!

I hope you find it helpful.

Karen x

PS This would never make a best seller list - prepare to be rather bored!!!


The brain

The brain has three main parts: the cerebrum, the cerebellum and the brain stem. The cerebrum is the big part on the top which most people think of as the brain. The cerebellum is the smaller, roundish part that lies underneath the back of the cerebrum. The brain stem is the part that joins the brain to the spinal cord. It lies underneath the cerebrum, in front of the cerebellum and is at the top of the spinal cord.

The brain has three main types of “matter”, i.e. stuff. Gray matter is the stuff that does all the processing, encoding and storage – basically the “thinking”. White matter is the stuff that carries the signals between different parts of gray matter. If you imagine your phone connected to your computer via a USB cable, the phone and the computer are different parts of gray matter and the USB cable is the white matter allowing them to communicate with each other. Gray and white matter are made up of billions of neurons, or nerves: gray matter contains the main bodies of the nerves and white matter contains the tails of the nerves, called axons. Nerves that need to transmit fast signals have a myelin coating on their axons.

The third type of matter is CSF (cerebrospinal fluid). It bathes the brain, cushioning it and providing nourishment. There are reservoirs of CSF in the brain, the contents of which are continually refreshed by our bodies. These reservoirs are called ventricles. The biggest of these are called the lateral ventricles. If you slice the head from the eyes to the back of the skull and look down at it, you will see the lateral ventricles, one on either side of the line down the middle of the cerebrum, looking a bit like a butterfly.

Humans have evolved to have a lot of brain matter, so the only way to fit it all into the skull is to squeeze it together, like squishing up a piece of cloth to fit it into a tight space. This means that the cerebrum has lots of folds in it. The bits that go in are called sulci (a single sulci is called a sulcus) and the bits that go out are called gyri (a single gyri is called a gyrus) and they all have names. [Mammals that aren’t as intelligent as humans have smoother cerebrums, with fewer sulci and gyri, if any.]

The cerebrum has two halves, or hemispheres, which are approximate mirror images of each other. They are joined only by some tracts of white matter (like a bunch of USB cables instead of just one), so the two halves can work together. The main tract of white matter joining the two hemispheres is called the corpus callosum. It is in the middle of the cerebrum, next to the lateral ventricles. If you cut the corpus callosum, the left side and right side of the cerebrum cannot communicate properly. It is quite common for people with MS to have lesions on the corpus callosum. (A lesion is an area of damage or abnormality.)

The cerebrum is split into four “lobes” (areas): frontal, parietal, temporal and occipital. Because the cerebrum has two halves, there are right and left frontal lobes, right and left parietal lobes, etc. The frontal lobe is more or less the front half of the cerebrum. It stops at the “central sulcus”. The parietal and temporal lobes lie behind the frontal lobe with the parietal lobe at the top of the head and the temporal lobes at the sides, more or less behind your ears. The occipital lobe is right at the back. The frontal lobe is important for personality, working memory, decision making, controlling inhibition, movement, etc. The parietal lobe is important for sensation, maths, music, humour, spatial tasks, etc. The temporal lobe is important for hearing, memory, language, emotions, object recognition, etc. The occipital lobe is dedicated to vision.

The outer layers of the cerebrum are made up of gray matter. Together, these layers are called the cortex or cerebral cortex. Anything to do with the cortex is referred to as cortical. (Anything to do with the cerebrum is called cerebral and anything to do with the cerebellum is called cerebellar.) White matter lying close to the cortex is called subcortical (or superficial). White matter lying deeper into the brain is called deep white matter. There is also deep gray matter, found in the centre of the brain and the brain stem as well as white and gray matter in the spinal cord.

Amongst other things, the cerebellum is important for making all kinds of movement smooth, for balance and for learning new motor skills. The brain stem is important for many fundamental functions like sleeping, breathing and heart rate. Many of the “cranial nerves” come from the brain stem, controlling things like eye movements, sensation and movement of the face, mouth and tongue, and swallowing.

In general, the left side of the cerebrum controls the right side of the body and vice versa. This is not the case in the cerebellum where the right side controls the right side of the body and the left, the left. All the nerves from the cerebrum and the cerebellum go through the brain stem to get to the spinal cord. The cerebral nerves cross in the brain stem so that the right side of the spinal cord controls the right side of the body and the left, the left. This means that a problem with the right side of the body might come from a left hemisphere cerebral lesion, a right hemisphere cerebellar lesion, the left or right side of the brain stem (depending on whether it is above or below where the nerves cross) or a lesion on the right hand side of the spinal cord.

The McDonald criteria stipulate that, to be diagnosed with relapsing remitting MS, patients need to have at least two attacks and at least one lesion in at least two of four specified areas of the central nervous system: three in the brain and one in the spinal cord. (You can download the full paper for free: it’s Polman et al. Diagnostic criteria for multiple sclerosis: 2010 revisions to the McDonald criteria. ANN NEUROL 2011; 69:292-302.) The criteria for primary progressive MS are a gradual progression of symptoms (normally of at least a year’s duration) and two of the following: a positive lumbar puncture, at least two spinal cord lesions, at least one lesion in at least one of the three specified brain areas.

The three brain areas in the McDonald criteria are juxtacortical, periventricular and infratentorial. Juxtacortical means next to / into the cortex, i.e. a lesion that lies right at the border of the gray and white matter close to the outer edge of the cerebrum. Periventricular means next to the ventricles. Lesions next to the lateral ventricles are very common in MS. They often form at right angles to the ventricles which, when looked at side on, look a bit like fingers poking up over a wall. These are called Dawson’s fingers and are a classic sign of MS. Infratentorial means the brain stem and cerebellum; the areas under the cerebrum.

There are some parts of the cortex that are named after what they do. The most obvious of these are the visual cortex, the motor cortex and the somatosensory cortex. The visual cortex is the cortex in the occipital lobe; the gray matter that makes sense of all the information that your eyes gather. The motor cortex is the last gyri of the frontal lobe, the precentral gyrus. It is in charge of movement. The somatosensory cortex is the first gyri of the parietal lobe, the postcentral gyrus. It is on the other side of the central sulcus to the motor cortex and it controls sensation in your body. If you put your hands loosely on both ears, your thumbs are pointing towards your visual cortex, your left and right ring fingers are pointing roughly towards your left and right motor cortices and your middle fingers are pointing roughly towards your somatosensory cortices.

Finally, a few terms that you might come across:

- Anterior: in front; towards the front of the brain

- Posterior: behind; towards the back of the brain

- Superior: above; towards the top of the brain

- Inferior: below; towards the spinal cord

- Horn/tip: refers to the ends of the lateral ventricles; the “wing tips” of the butterfly shape.


MRI: Magnetic Resonance Imaging

When you have an MRI scanning session, they run a number of different scans. The standard ones, that are run for pretty much all medical conditions, are called T1 and T2. Scan types are constantly being developed, but the most commonly used additional scan type for MS investigations is FLAIR. You will also hear of PD, FSE, STIR, DWI and others, but I’m not covering them here.

The way MRI works is that different types of matter give off different levels of energy when they are placed in a magnetic field. The computer slices the thing being scanned and collects the energy signal from one slice at a time. Because of some of the loud banging noises the scanner makes, it can also work out the signal from small cubes of each slice. These cubes are called voxels (short for volume pixels).

Each slice provides the information for one image and each voxel provides the information for one pixel in that image. The whole process uses some very advanced mathematics, but ultimately, the higher the overall signal from a voxel, the brighter the pixel is on the final image (and the lower the signal, the darker the pixel). This is where the terminology gray and white matter is less than helpful so bear with me!

In a T1 scan, gray matter gives off a low signal and looks darker in the images than white matter which gives off a higher signal and looks pale gray. CSF meanwhile gives off the lowest signal and looks black. Everything is reversed in a T2 scan: gray matter looks pale gray, white matter looks darker gray and CSF looks white. FLAIR is a clever adjustment of a T2 scan which suppresses the signal from CSF. This means that we end up with gray matter looking pale gray, white matter looking darker gray and CSF looking black.

Different lesions give off different signals too. In general, a white matter MS lesion gives off a high signal in T2 and FLAIR scans, leading to it looking like a “white spot” against the white matter which looks relatively dark in these scan types. T1 is usually rubbish for spotting MS lesions unless the lesion has caused the area to die, or “atrophy”, in which case it is called a “black hole” – because it is a wee black hole on a T1 image. The terms “hyperintensity”, “hyperintense”, “high signal”, etc, all refer to the fact that somewhere is brighter / whiter than it should be. “Hypointensity”, “hypointense area”, etc, refers to somewhere that is darker than it should be. Exactly what relevance these have depends on their size, shape, location and the type of scan though.

Remember that I mentioned CSF bathes the brain? That means that all the sulci of the brain are full of CSF and so there is a lot of white on T2 images. Spotting a lesion in amongst lots of perfectly normal white stuff can be tricky, however it is really quite easy in FLAIR images – because there shouldn’t be very much white; all the CSF is black. (Please note that some small white spots can be perfectly normal – they are usually blood vessels.)

Sometimes, neuros ask for a scan with contrast. This is a T1 scan taken after the patient has been injected with a “contrast agent”. This is usually gadolinium which looks bright white on a T1 scan. The central nervous system, i.e. the brain and spinal cord, is protected by the blood brain barrier (bbb) which stops things that might harm it from getting in; gadolinium normally can’t get through the bbb.

In MS, cells from the immune system get through the bbb and attack the myelin coating of nerves in that area, causing inflammation and damage: a lesion. While this is happening, the lesion is called “active”, “enhancing” or “contrast enhancing”. The gap the immune system has caused in the bbb allows gadolinium to get in. If there are no breaches in the bbb, there should be no bright white signs of gadolinium inside the brain or spinal cord. If there are, these show where there are breaches, in other words, where the immune system is actively causing new damage.

Contrast is used for two main reasons: to show up very new lesions (typically lesions newer than about six weeks) because these can be difficult to see on normal MRI and to help show which lesions are active and which are not as this can be important for deciding on meds. Newer types of scans, e.g. DWI (diffusion weighted imaging) which measures water flow, can be used to do this too so contrast is being used less often these days.

Some terms you might come across:

- Sagittal: images taken from ear to ear, parallel to the nose

- Axial: images taken from front to back, at right angles to the nose

- Coronal: images taken from the front to back, parallel to the nose and so that one slice goes through both ears

- Artefact/artifact: a computer error, nothing to worry about

- 1.5T (and other numbers followed by a T): This is scanner strength, i.e. how strong the magnetic field is that the scanner produces. The T is short for Tesla, but has nothing to do with the T in T1 and T2 scans.

Most NHS scanners are 1.5T. There are a few 3T (and stronger) scanners that are much more powerful than 1.5T scanners, but these are usually run by Universities. Do not assume that private MRI scanners (or scans) are better than NHS scanners (or scans) – they are mostly the same, but can be worse.

For those of you who aren’t quite brain dead yet(!)…

“Partial volume effects” are an important factor in how good a scan is and are particularly relevant if you are told your MRI is clear or you have no new lesions when you are having new symptoms. Remember that the computer slices up whatever’s being scanned and then splits the slices into little cubes, the signal from these determining how dark or light a pixel will be in the image? Well, the size of those cubes has a major effect. Imagine a voxel that only contains white matter.

In a T2 scan, that voxel will give a low signal and the resultant pixel will look dark gray. Now imagine a voxel that is mostly white matter, but also has a bit of a lesion in it. In a T2 scan, lesions give high signals, so the pixel will now look brighter than the last one. But by how much? If it’s a small voxel and the lesion provides a decent proportion of the signal, the pixel will be obviously brighter than its neighbour and a radiologist should spot it easily.

However, if it’s a big voxel, the extra signal from the lesion might only make the pixel a wee bit paler than its neighbour and make it very easy to miss. So, the moral of the story: it’s important to have thin slices and small voxels! 3mm slices are fine. Less than that is great, more than that and you are losing a lot of definition and increasing the chances of missing small lesions.

By the time you get to 6mm and thicker, you could miss average and even bigger than average lesions too. (The average MS lesion is 7mm.) The slice thickness is not usually written in reports or on images, but the number of images is the same as the number of slices so the greater the number of images in one scan, the thinner the slices.

The best images generally come from thin slices with small voxels on a stronger scanner, but small voxels on a 1.5T scanner will be better than big voxels on a 3T scanner every time.


Thank you so much xxx

Amazing…am in awe !! Xx

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Wow, thats my evening’s reading sorted! Thank you Karen

I take my hat off to you Karen…thanks.

Pam x

This is wonderful Karen. You have done a great job. I can just about understand it which is great for a non-scientist like me! Thank you so much! Teresa xx

Thank you so much Karen, it’s fascinating stuff, made even more so by being written by someone who wants people to be able to understand what’s going . You’ve helped pass the wee small hours for a newbie with steroid induced insomnia!!




I did brain and brief neuro-anatomy over 10years ago in my first year at uni. If only they’d explained it as simply as this! Great stuff!

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Made it sticky. Thanks for the post Karen. The functionality for bullet points is a little wanting. Well, it doesn’t work, to be honest, so emboldened dashes was the best I could manage.

Stewart (admin)

Me too, only this was 30 years ago. I was told this week that I’d had a small stroke in the white matter and this has clarified things for me. Brilliant explanations, Karen. Thanks!

[quote=“Stewart Cumiskey”]

Made it sticky. Thanks for the post Karen. The functionality for bullet points is a little wanting. Well, it doesn’t work, to be honest, so emboldened dashes was the best I could manage.

Stewart (admin)

[/quote] Thanks Stewart. Could you do the bullet points in the MRI post too please? (The last one starts with 1.5T…) Thanks everyone else too - I’m glad it’s proving helpful :slight_smile: Kx

Well done Karen,and a big thank you for finding the time and energy to word it so well.

I bet I am one of many to get their letters out and go through them to translate them into normal speak.


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Absolutely superb.

Thank you taking the time and effort to do this.

It gives us, less likely to know people, a better knowledge.

Fantastic, Thanks.

loverly jubbly Karen just what l needed. F.xx

I read this on the train last week, a few times. Just collected a copy of my MRI, and using your brilliant explanation, I think I have found two of my three lesions!

Thank you again Karen

Thank you so much Karen, I will print it off and laminate for reference. We are so lucky to have you here to help.

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Well done Karen!

Also means that the rest of us can reply to others “Read the sticky post by Rizzo for more info”.

A huge help,

Pat x