Interactive Brain Atlas

Slice MRI & real head CT, spin a 3D brain, or pick apart 283 individually-named structures. MRI / 3D = standardized templates; CT = real de-identified patient scans. Educational, not for diagnosis.

MNI152 — a population-average MRI template in standard stereotaxic space. Pick an atlas overlay to label regions (try Tracts + the 3D view for a glass-brain), switch to CT for real patient scans, or open 3D Brain to pick apart 283 named parts.

Structure—

Atlas overlay

Connectome type

Functional = resting-state co-activation (what fires together); structural = DTI streamline counts (the physical white-matter wiring). Same 200 parcels — compare how the two networks differ.

Functional networks (Yeo-7)

Click a node to trace its strongest connections, or pick a network.

Connectivity matrix

Each cell is the connectivity (functional or structural, per the toggle above) between two parcels, ordered by network — the bright blocks on the diagonal are within-network links. Hover a cell to light the two regions in 3D.

CT scan — real cases

Window

Same scan, different windows — Brain reads grey–white & bleed, Blood narrows on hyperdensity, Bone shows the skull/fractures. Scroll the slices to read top-to-bottom.

Vascular territory → stroke syndrome

ACA Lenticulostriate MCA PCA Choroidal / perforators Basilar Cerebellar (SCA/PICA/AICA)

Each shade within a family is a specific branch — click into the brain to name it.

Move the crosshair over a territory

Each colour is one artery's territory — click into the brain to see the artery and the stroke a lesion there causes.

White-matter tract → deficit

Motor (CST) Thalamic projection Association Commissural Limbic

Move the crosshair over a tract

Each colour is one tract class — slice in (clip planes) or move the crosshair to name the tract, what it carries, and the deficit a lesion there causes.

Spinal cord — tract cross-section

The brain tracts above continue into the cord. Click a tract on the cord to see what it carries and the deficit a lesion causes — the cord is as important as the brain.

Overlay opacity

View

Slice the 3D view — clip planes

Works in the 3D view. Toggle 1, 2, or 3 planes to cut in from each direction.

Base model

A real, co-registered deep-brain model (Z-Anatomy): brainstem, thalamus, basal ganglia, ventricles and limbic structures, all twelve cranial nerves, and the white-matter tracts — wrapped in a translucent whole-brain shell so you can see the tracts running inside a glass brain. Toggle any layer, click or search a structure, slice in, or isolate one.

Layers

Toggle layers to build up or strip back the brain — deep nuclei, the cranial nerves, and the white-matter tracts, all in register. Slice or click any of them.

Find a structure (283)

Selected structure

Slice (clip planes)

Flip side

Pick an atlas, then click through the image — the structure under the crosshair shows bottom-left. Use the 3D view + clip plane to slice.

Search or click a structure to name it. Toggle X / Y / Z to slice in 1, 2, or 3 directions and reveal deep structures.

Data & credits

Rendered with NiiVue (BSD-2). Base imaging: ICBM/MNI152 template. Atlases: Arterial territories — Digital 3D Brain Arterial Territories Atlas (Liu et al., © Johns Hopkins, CC BY-SA 4.0); stroke syndromes summarised from standard references (Tatu et al., arterial territories; Caplan's Stroke) — educational, not diagnostic. AAL (Tzourio-Mazoyer; Rolls et al.), CIT168 (Pauli et al.), Cerebellum (via FSL) — used for education. 3D Structures: SPL/NAC Brain Atlas (Surgical Planning Lab & NAC, BWH / Harvard, via the Open Anatomy Project); cortex parcellation: Desikan-Killiany surfaces from Brain-for-Blender (A. Winkler, brainder.org, CC BY-SA 3.0), recoloured by lobe. Cranial nerves, deep neuroanatomy, white-matter tracts & the translucent whole-brain (glass-brain) shell: Z-Anatomy (G. Kervyn et al., derived from BodyParts3D, CC BY-SA 4.0), recoloured by category — the glass shell is a surfaced envelope of the Z-Anatomy cerebrum, co-registered to the deep & tract meshes by a 10-landmark similarity transform. Rendered with three.js. Connectome: nodes = Schaefer-200 / Yeo-7 parcellation (ThomasYeoLab/CBIG, MIT; Schaefer et al. 2018); edges = the HCP group-average functional connectome bundled in the ENIGMA Toolbox (BSD-3; Larivière et al. 2021) — resting-state co-activation, not anatomical tracts. Head CT: normal reference — Rorden Clinical Toolbox (BSD-2); subarachnoid haemorrhage — RHUH SAH (CC-BY-4.0); intraparenchymal / lobar-with-mass-effect / intraventricular / posterior-fossa haemorrhage, acute & chronic subdural / epidural haematoma, and calvarial fracture — CQ500 (qure.ai, CC BY-NC-SA 4.0; Chilamkurthy et al., Lancet 2018); acute ischaemic & large MCA-territory infarct — CPAISD (Core-Penumbra Acute Ischemic Stroke Dataset, CC-BY-4.0); post-op intracranial electrodes — SCI Institute, Univ. of Utah (MIT). Real patient scans, de-identified — educational, not for diagnosis. CQ500 is CC BY-NC (non-commercial): the CQ500-derived cases must be removed if this app is ever monetized. Template / atlas data otherwise; not for diagnostic use.