🧠 Seeing the Brain in Action: A Beginner’s Guide to Neuroimaging

You’ve learned to listen to the brain’s electrical activity with EEG — now it’s time to see it. Neuroimaging gives us a window into the brain’s structure, guiding diagnosis, understanding, and treatment. 

But no single scan tells the full story. Each modality sees the brain differently — some reveal anatomy, others show activity — and choosing the right one means knowing what you’re asking, and what the scan can answer. This is just a primer to get you started - imaging is a long journey of learning to come !

🧠 Why Do We Image the Brain?

We order neuroimaging when we want to:

• Check for strokes, tumours, or bleeding
• Investigate sudden weakness, sensory loss, or confusion
• Explore causes of seizures or changes in behaviour
• Evaluate trauma or suspected raised intracranial pressure

Imaging isn’t about guessing — it’s about matching the right scan to the right clinical question.

⚙️ Types of Neuroimaging and What They Show

Let’s break down the key modalities:

💠 CT Scan (Computed Tomography)

What it shows: Bone, blood, and acute trauma
When to use it: Head injury, suspected bleed, rapid assessment
Why it’s useful: Fast, widely available, picks up haemorrhage clearly
What it misses: Subtle soft tissue and ischemic changes in early stroke

🧭 CT is your go-to for quick answers — especially when time matters

🖼️ CT Scans Explained

CT scans use X-rays to take multiple cross-sectional images from different angles. These beams pass through the body, and a computer reconstructs them into slices that show varying densities — bone appears bright white, blood is grey, and air is black. Because it’s fast and excellent at spotting acute bleeding or fractures, CT is ideal in emergencies.

🧠 Analogy: Think of it like slicing a loaf of bread — each slice reveals more detail about what’s inside.

💠 Follow the density trail

• Start with symmetry — compare left to right
• Check for hyperdense (bright) areas — blood, calcification, or contrast
• Look for effacement of sulci or ventricles — signs of swelling or mass effect
• Ask where bone ends and brain begins — skull fractures can be subtle
• Think in emergencies: "Is there blood, fracture, or shift?"

🧠 CT gives you a grayscale puzzle — learn what’s normal before hunting for what’s not.

🌀 MRI (Magnetic Resonance Imaging)

What it shows: Soft tissue detail, brain anatomy, white matter
When to use it: Stroke, tumours, MS, detailed follow-up
Why it’s useful: Excellent resolution, detects early ischemia
What it misses: It’s slower and less available in emergencies

🧭 MRI lets us zoom in — especially when the diagnosis isn’t obvious.

🧲 MRI Scans Explained

MRI uses strong magnets and radio waves to generate images based on how hydrogen atoms behave in a magnetic field. Tissues like fat, fluid, and brain matter all respond differently — giving us contrast between grey matter, white matter, and CSF. There’s no radiation, and sequences like T1, T2, and FLAIR can highlight pathology depending on water content, timing, and pulse techniques.

🧠 Analogy: MRI is like tuning into different radio stations — each setting reveals a different layer of anatomical detail.

🌀Choose your sequence, read the rhythm

• T1 vs T2 vs FLAIR — understand what’s bright and why
• Follow anatomical landmarks — corpus callosum, ventricles, sulci
• Look for asymmetry in signal — abnormal brightness or darkness
• Zoom in on grey-white differentiation — early ischemia can blur this line
• Ask why this sequence was chosen: “What pathology does this highlight?”

🧠 MRI Sequences: T1, T2, and FLAIR Explained

T1, T2, and FLAIR (Fluid-Attenuated Inversion Recovery) are all types of MRI sequences used to image the body, particularly the brain, and each provides different information.

T1-weighted images are useful for visualizing anatomical structures like gray and white matter.
T2-weighted images are excellent for detecting edema and inflammation and are often used to identify lesions.
FLAIR sequences are specifically designed to suppress the signal from cerebrospinal fluid (CSF), making lesions and other abnormalities near the CSF more visible.

🧠 MRI reveals more than images — it shows tissue behaviour. Learn the visual language of each sequence.

🔆 fMRI (Functional MRI)

What it shows: Blood flow linked to neural activity
When to use it: Research, pre-surgical planning, cognitive studies
Why it’s useful: Maps active regions during tasks or rest
What it misses: Structural abnormalities — this is about function

🧭 fMRI allows us to ask: “Which part of the brain lights up when you think?”

🧠 fMRI: Mapping Brain Function

fMRI builds on traditional MRI by using a technique called BOLD (Blood Oxygen Level Dependent) imaging. When a region of the brain becomes active, it uses more oxygen — changing local blood flow. fMRI detects these changes and maps them to brain function in real time.

It’s used in research and pre-surgical planning to see which areas light up during tasks (e.g. language or motor activity).

🧠 Analogy: So instead of just anatomy, fMRI shows function — a kind of “brain activity heat map.”

🔆 What lights up when the brain works

• Map regions activated during specific tasks
• Look for lateralization — e.g. language dominance
• Interpret changes with caution — not all activation equals pathology
• Use overlays with structural MRI to locate functional areas

🧠 fMRI is like watching thoughts unfold — ideal for planning, not diagnosis.

🔬 PET Scan (Positron Emission Tomography

What it shows: Metabolic activity — where cells are working hard
When to use it: Epilepsy localisation, tumours, neurodegeneration
Why it’s useful: Highlights areas of hyperactivity or hypometabolism
What it misses: Fine structural detail — best used with MRI

🧭 PET sees how the brain is behaving — not just how it looks

🔬 PET Scans: Physiology in Action

PET scans involve injecting a radioactive tracer, usually linked to glucose, which gets taken up by active cells. The scanner detects positrons emitted during decay and builds a 3D image of metabolism.

It shows how tissues are behaving — making it useful in epilepsy, cancer, and neurodegeneration. Areas using lots of energy light up; underactive areas appear dim.

🧠 Analogy: PET is like night-vision for physiology: it doesn’t show structure, but reveals where cells are working hard.

🔬 Follow the sugar trail

• Spot hypermetabolic regions — often tumours or seizure foci
• Note hypometabolism — possible degeneration or old injury
• Match uptake patterns to known disease templates
• Always cross-reference with MRI — structure plus function matters

🧠 PET shows how cells use energy — understanding the metabolic map reveals hidden dysfunction.

🔬 SPECT Scan (Single Photon Emission Computed Tomography)

What it shows: Blood flow to different brain regions

When to use it: Seizure localisation (interictal/ictal), dementia

Why it’s useful: Functional insight into perfusion

What it misses: High-resolution detail — it’s not anatomical imaging

🧭 SPECT shows stormy zones — increased blood flow — and calm ones too

🌦️ SPECT: Blood Flow and Brain Function

SPECT also uses radioactive tracers, but instead of detecting positrons like PET, it tracks gamma rays emitted from the tracer. It’s especially useful for showing blood flow to different brain regions — often used in seizure localisation and dementia.

SPECT gives functional insights, though resolution is lower than MRI or CT.

🧠 Analogy: Picture it as a weather radar for blood flow — you can see stormy areas (hyperactivity) and calm zones (reduced perfusion).

🔬 SPECT – Trace the blood flow

• Identify areas with increased or reduced perfusion
• Useful in seizure evaluation — ictal vs interictal flow can guide surgery
• Interpret in clinical context — perfusion changes may overlap conditions
• Overlay with MRI/CT if available for anatomical clarity (below)

🧠 SPECT isn’t sharp — but its insights into perfusion are powerful when paired with anatomy.

🚫 Why Not X-ray or Ultrasound?

❌ X-ray: Good for bones, bad for brains

• X-rays are great for showing hard tissues like bone — they reveal fractures, calcifications, and alignment.
• But the brain is made of soft tissue, which X-rays can’t distinguish well. You can’t see the cortex, ventricles, or CSF.
• The skull also blocks the view — it's like trying to photograph a person through a brick wall.

🧠 We use X-rays for skull injuries, not brain insight.

❌ Ultrasound: Perfect for babies, limited for brains

• Ultrasound uses sound waves, which reflect off tissues to create live images.
• But in adults, the skull blocks sound waves, so we can’t see the brain clearly.
• In babies, we use it through the fontanelle (soft spot) — making it useful for neonatal hydrocephalus or bleeding.
• Outside of that, it’s mostly used for carotid arteries, not the brain itself.

🧠 Ultrasound is great for vessels and infants — not adult brain tissue.

Case studies 

🧑‍⚕️ Case 1: Jasmine’s Collapse at Work

Jasmine, 28, is brought to ED after collapsing at work. Witnesses describe stiffening, limb jerking, and brief confusion afterwards.

She’s otherwise healthy, with no prior neurological history. You’re asked to consider possible causes and next steps.

📊 EEG Findings

Jasmine’s EEG shows intermittent spikes and sharp waves in the left temporal region, with occasional rhythmic discharges during drowsiness. This pattern suggests focal epilepsy, likely with a left-sided origin.

🧠 Learning point: EEG can help localise seizure focus — even between events — and guide further investigation.

🖼️ Neuroimaging Clue

An MRI is ordered to explore potential structural causes. It reveals a small, gliotic scar in the left hippocampus — consistent with mesial temporal sclerosis (MTS). This subtle finding reflects old injury, possibly from childhood febrile seizures or unrecognized trauma.

🧠 Learning point: Not all seizure triggers are active pathologies. Old scars can irritate surrounding tissue and lower seizure threshold — imaging shows us where, and how.

🎯 Why This Matters

This case highlights:

• EEG helps localise the epileptogenic zone
• MRI reveals structural correlates like scarring or sclerosis
• Together, they inform treatment — antiepileptics or even surgical options if seizures persist

🧑‍⚕️ Case 2: Theo’s Sudden Collapse

Theo, 35, collapses at home with brief limb shaking and confusion. No prior history, no fever, no trauma.

He’s oriented within minutes, and there’s no clear trigger. You start to wonder: seizure? Syncope? Something else?

📊 EEG Findings

Theo undergoes routine EEG the next morning. It’s completely normal — no interictal spikes, slowing, or epileptiform discharges. You’re told this lowers the chance of epilepsy. But something doesn’t sit right.

🧠 Learning point: A normal EEG doesn’t rule out seizures — especially if the event was focal or brief, or if it's his first. EEG captures a snapshot, not the full picture

🖼️ Neuroimaging Clue

An MRI is requested to investigate further. It reveals a small low-grade glioma in the left frontal lobe — subtly distorting cortical architecture without mass effect. This explains the seizure, and also why the EEG missed it: the abnormal area may not have been electrically active during recording.

🧠 Learning point: Structural lesions like tumours or cortical dysplasia can cause seizures even when the EEG is silent. Imaging fills in the anatomical context EEG can’t reach.

🎯 Why This Matters

This case highlights:

• EEG can be normal despite underlying pathology
• MRI reveals structural causes even when electrical findings are absent
• Clinical reasoning drives investigation — not just test results

🧑‍⚕️ Case 3: Zahra’s Festival Collapse

Zahra, 22, has a seizure at a music festival after 48 hours of poor sleep, no food, and mixing alcohol with party drugs.

She convulses briefly, recovers quickly, and recalls nothing unusual before the event.

📊 EEG Findings

Her EEG is completely normal. No epileptiform activity, no slowing. It’s repeated after sleep and shows no abnormalities.

🧠 Learning point: Normal EEG findings suggest the seizure may be provoked — not a sign of epilepsy.

🖼️ Neuroimaging Clue

CT and MRI are also entirely normal. No tumours, scars, bleeds, or anatomical abnormalities.

🧠 Learning point: Not all seizures come from brain pathology. In Zahra’s case, the cause was provocation: sleep deprivation, dehydration, and substance use lowered her seizure threshold.

🎯 Why This Matters 

This case highlights:

• EEG and MRI may both be normal when seizures are provoked, rather than spontaneous
• Diagnosis hinges on history, not just tests
• Not every seizure equals epilepsy — context defines management

🔍 What’s Next?

Now that you can see inside the brain, we can look in a week or so at how imaging patterns reflect specific pathologies — strokes, tumours, trauma, and seizures. Stay tuned for a visual walkthrough of classic neuroimaging findings and how to read them like a clinician.

📦 Want to learn more?

• 📝 All posts on the nervous system →
• 📝 Structure and function of the CNS →
• 📝 Pathophysiology of seizures →
• 📝 Understanding seizure classification →
• 📝 Localisation of seizures →
• 📝 Neurotransmitters 101 →
• 📝 Consciousness and how we can lose it →
• 📝 Clinical cases in seizure localisation →
• 📝Principles of seizure management →
• 📝Neurotransmitters on drugs! →
• 📝A beginner's guide to EEG →
• 📝A beginner's guide to neuroimaging →