Brain MRI Anatomy: Basal Ganglia, Ventricles and Internal Capsule Step by Step

By the DecodeMed TeamOctober 23, 20267 min read

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The fastest way to orient yourself on an axial brain MRI is to find the CSF spaces in the midline first—the frontal horns of the lateral ventricles and the slit-like third ventricle—and then read the deep grey nuclei arranged around the V-shaped white matter of the internal capsule. You can scroll this exact volume with 3D reconstructions in the free DecodeMed radiology atlas or ask the AI tutor in RadioAnato AI to highlight the caudate, putamen, globus pallidus and thalamus in 3D.

Brain MRI in the DecodeMed radiology atlas with the cortex, white matter, ventricles, caudate, putamen, pallidum and thalamus labelled on the 3D volume — A brain MRI in the free radiology atlas, with the deep grey nuclei and the ventricles labelled. Image sources and licences.

Step 1: Confirm the sequence and the midline

Check the CSF in the ventricles first. If the ventricular fluid is dark and white matter is brighter than cortical grey matter, you are looking at a T1-weighted image (the classic “anatomical” sequence). If the CSF is bright white, you are on T2. See T1 vs T2 MRI: how to tell them apart.
Trace the midline from anterior to posterior: the falx cerebri between the frontal lobes, the septum pellucidum separating the two frontal horns, and the narrow third ventricle between the two thalami.

Step 2: The “star” level — basal ganglia and internal capsule

Scroll to the axial slice where both the frontal horns of the lateral ventricles and the third ventricle are visible together. Everything important in the deep brain sits around a boomerang-shaped band of white matter called the internal capsule:

Structure	Where it sits on the axial slice	Key clinical role
Caudate nucleus (head)	Bulges into the lateral wall of the frontal horn, anterior and medial to the internal capsule	Atrophies in Huntington disease, enlarging the frontal horns
Internal capsule (anterior limb, genu, posterior limb)	V-shaped white-matter highway pointing medially toward the third ventricle	The posterior limb carries the corticospinal tract; a tiny lacunar infarct here causes pure motor hemiparesis
Lentiform nucleus (putamen + globus pallidus)	Wedge-shaped grey mass tucked lateral to the internal capsule (putamen is outer, pallidus is inner)	Common site of hypertensive intracerebral haemorrhage
Thalamus	Large oval grey nucleus medial to the posterior limb of the internal capsule, flanking the third ventricle	Main sensory relay to the cortex
Insular cortex & Sylvian fissure	Lateral to the lentiform nucleus, separated by the external capsule and claustrum	Supplied by the middle cerebral artery (MCA); loss of the insular ribbon is an early sign of stroke

Step 3: Follow the ventricular system from top to bottom

Bodies and frontal horns of the lateral ventricles sit high beneath the corpus callosum, separated by the septum pellucidum.
Trigone (atrium), occipital and temporal horns sweep posteriorly and inferiorly into the occipital and temporal lobes.
Foramina of Monro connect the lateral ventricles to the midline third ventricle between the thalami.
Cerebral aqueduct (of Sylvius) runs through the midbrain into the fourth ventricle, which sits between the pons/medulla anteriorly and the cerebellum posteriorly.

Abdominal CT in the DecodeMed radiology atlas: 3D models of the organs beside the CT volume, with liver, kidneys, spleen, pancreas, stomach and adrenal glands labelled — An abdominal CT in the free radiology atlas: the organs as 3D models and labelled on the CT volume; the slices open below in axial, coronal and sagittal planes. Image sources and licences.

Study it in RadioAnato AI

RadioAnato AI, the DecodeMed app, puts 3D anatomy, CT and MRI studies, histology slides and an AI tutor that answers on them in your pocket. Free to download for iPhone, iPad and Android.

Four screens of the RadioAnato AI app: a labelled PET scan, a brain MRI with a 3D brain, 3D lungs with CT slices, and a labelled lung CT — RadioAnato AI on a phone: PET, MRI and CT studies with every structure labelled, next to its 3D model. Download the app. Image sources and licences.

Step 4: Three levels above and below the basal ganglia

High convexity (centrum semiovale): above the ventricles, where the central sulcus separates the precentral gyrus (motor strip) from the postcentral gyrus. Look for the “omega sign” of the hand motor area.
Midbrain level: shaped like Mickey Mouse’s ears (the cerebral peduncles anteriorly) with the cerebral aqueduct and quadrigeminal cistern posteriorly.
Pons and cerebellopontine angle: the belly of the pons anteriorly, the fourth ventricle behind it, and the middle cerebellar peduncles reaching into the cerebellum.

Open the labelled brain MRI volume in the free radiology atlas to rotate the 3D deep grey nuclei while scrolling the slices. For more cross-sectional guides, read chest CT anatomy, how to read an abdominal CT and how to learn radiology with AI.

Frequently asked questions

How do you tell the caudate, putamen and thalamus apart on an axial brain MRI?

Find the V-shaped white-matter band of the internal capsule first. The caudate head is anterior and medial (hugging the frontal horn of the lateral ventricle), the thalamus is posterior and medial (hugging the third ventricle), and the wedge-shaped lentiform nucleus (putamen and globus pallidus) sits laterally in the crook of the V.

Which MRI sequence is best for learning normal brain anatomy?

T1-weighted MRI is best for normal anatomy because CSF is dark, grey matter is grey and white matter is lighter grey, matching how the brain looks in neuroanatomy lab.

Where can I practise scrolling a labelled brain MRI for free?

Open the DecodeMed radiology atlas at decodemed.app/rad-atlas in your browser or download RadioAnato AI for free on iPhone, iPad and Android to scroll a real brain MRI with the cortex, white matter, ventricles, caudate, putamen, globus pallidus and thalamus labelled in 2D and 3D.