Sources, coverage, and interpretation
This educational reference combines documented surface labels with a matching reference MRI. Internal numerical checks do not replace qualified neuroanatomical review. The atlas is not a patient scan or a treatment planning system.
What each view represents
| View | Source and coverage | Interpretation |
|---|---|---|
| Whole brain | Two fsaverage cerebral cortical surfaces, cerebellar cortex and white matter (aseg 7, 8, 46, 47), and brainstem (aseg 16), using the matching reference MRI described below. | Seven independently selectable source components retain their native coordinates. The overview is not an exhaustive tissue segmentation. Cerebellar white matter remains distinct from cortex. Separation is illustrative; inflation is disabled in this mixed surface and volume view. |
| Anatomy and lobes | Desikan–Killiany cortical parcellation, 34 named cortical parcels per hemisphere. | Lobes aggregate source parcels. Cingulate cortex is separate. Paracentral is assigned frontal despite spanning the central region; fusiform is assigned temporal. These are cortical surfaces, not whole lobar volumes. |
| Gyri and sulci | Destrieux et al., 2010, FreeSurfer aparc.a2009s, 74 named units per hemisphere. Native fsaverage annotations are included in the same verified reference archive. | Gyral, sulcal, fissural, and combined sulcogyral labels remain distinct. Sulcal labels represent cortical surface within a groove. Native vertex identities are preserved when sampling at fsaverage5 resolution; no invented solid sulcal anatomy is added. |
| Brodmann | ggsegBrodmann, Athanasia Mo Mowinckel / ggsegverse; Dutch Connectome Lab annotations. Pijnenburg et al., 2021. 39 labels per hemisphere. | Historical reconstruction projected to fsaverage5. Combined BA1_3, BA26_29_30, BA35_36, and BA41_42_52 remain combined. This is not an assertion of 52 individually delineated human areas or individual histology. |
| Networks | Yeo et al., 2011, original 7- and 17-network vertex assignments. | Distributed cortical groupings from functional connectivity. Display aliases supplement canonical source labels. Membership alone does not establish axonal connections, causal direction, or measured activity in a person. |
| Functional parcels | Schaefer et al., 2018, 200 and 400 parcels, Yeo 17-network order. | Parcel boundaries differ from gyral anatomy and Brodmann labels. A cortical network scheme does not automatically assign deep structures. |
| Deep structures and sections | FreeSurfer automated segmentation, fsaverage 6 reference from the MNE fsaverage archive. 33 labels and 291 MRI sections. | Surfaces extracted at original 1 mm voxel resolution, without smoothing. Ventricles are cavities. T1 sections are sampled every 2 mm. Crosshairs indicate the selected source region’s bounding-box center, which can lie outside curved tissue. |
| Brainstem study | Iglesias / FreeSurfer atlas-prior export, MNI ICBM152 nonlinear symmetric 2009c. Midbrain, pons, medulla and SCP; 291 matching MRI sections. | Approximate probabilities converted to background-inclusive maximum-probability assignments in their native world coordinates. No fsaverage registration or cortical overlay. The medulla has an open inferior edge where source coverage stops. Labels are not split by side. |
| Hypothalamic study | Neudorfer et al., version 4, MDA 990HCP template. 26 manually delineated hypothalamic regions, 13 per hemisphere; 387 matching regional MRI sections. | Native RAS coordinates, original 0.5 mm label sampling, no smoothing or registration to another atlas. This subset is not all hypothalamic tissue. Neighboring labels are excluded; source red-nucleus outliers are documented in the provenance. |
Coordinates and graphics
The brainstem study uses MNI ICBM152 symmetric 2009c world RAS with its own matching MRI; it does not use the experimental fsaverage alignment. Its source probabilities remain available for inspection. The hypothalamic study uses the separate Neudorfer MDA 990HCP reference and its matching MRI. Its region images use half-millimeter section spacing and a regional field of view; 0.25 mm display pixels linearly interpolate the 0.5 mm MRI without adding anatomical detail. Remaining modes use FreeSurfer tkregister RAS, in millimeters: positive X is right, Y anterior, and Z superior. The fsaverage5 topology has 10,242 vertices and 20,480 triangles per hemisphere. Folded positions use corresponding fsaverage 6 pial vertices. Independent subdivision checks verify the vertex mapping; export rounding is at most 0.00005 mm per coordinate. This is a numerical tolerance, not a claim about biological accuracy.
Inflation is an explicit visualization deformation. MRI locations always use folded scientific coordinates. In a mixed-label triangle, categorical borders are interpolated through edge midpoints and the triangle centroid. This preserves the original triangular surface but does not recover microscopic borders. Explosion adds reversible presentation offsets. It does not change anatomical distance or tissue size.
Coronal and axial MRI images use radiological display, with anatomical right on the image’s left. Sagittal images show anterior on the right and superior at the top. A camera view in the 3D atlas remains distinct from a section image.
Teaching coverage
39 of the 39 mapped Brodmann source labels currently have detailed location, functional-association, uncertainty and evidence sections, shown for both hemispheres. These accounts include explicit limits where a specific function is not established. Detailed teaching for other atlas classifications remains incomplete. Learning aliases support search without changing any atlas boundary. Number searches such as BA4 are exact; a combined source label remains combined when one of its numbers is searched.
Current limits
Hypothalamic study now shows 26 source-defined regional labels in its own template. These do not form every part of a complete solid hypothalamus. Ventral diencephalon in the fsaverage view remains a broader label and cannot be renamed hypothalamus. Whole brain and Deep structures retain the coarse fsaverage brainstem segmentation. Brainstem study separately presents four approximate MNI atlas-prior labels. Its medulla coverage is cropped inferiorly; it is not a newly validated segmentation of fsaverage or an individual brain. No validated scalp montage, white-matter tractography, vascular map, or individual localization is included. These limits remain visible in the atlas.
Text guide
Use Organization to choose a classification, then search or select a named region. The list and explanations work without 3D rendering. In the region list, use arrow keys to browse, Home or End to jump, and Enter or Space to select. Tab leaves the list; Read selected region opens keyboard access to its explanation. Hemisphere labels refer to the brain’s own left and right. A front-facing camera places anatomical left on the observer’s right. Use the named views, Isolate, and MRI sections to compare relationships, then return separation to zero.
The eight guided lessons include demonstrations, an action, a completion check, and an expandable text explanation. The 22-item knowledge check supplies corrective feedback and source links after each answer. The sensor lesson explains why scalp position does not uniquely identify a neural source.
Gyri-and-sulci teaching
Initial source-linked teaching covers 32 of the 148 Destrieux selections, including central, temporal and posterior visual landmarks. Each account includes an observation task and an answer explanation. The other 116 selections identify their teaching as pending. Anatomical labels remain separate from functional fields such as V3A and V6; the research cited in a card does not supply a functional boundary for its whole mesh.
Deep-structure teaching
All 33 deep selections have source-linked explanations of location, functional or fluid-space context, representation limits and an observation prompt. Matching cerebellar and brainstem selections in Whole brain use the same teaching. Bilateral labels share general context without inventing side-specific functions. Callosal divisions retain their positional source names; broad labels do not imply microscopic subdivisions.
These descriptions combine anatomical references with the actual segmentation coverage. They remain pending qualified scientific review.
Provenance and reproducibility
- Cortical input URLs, revisions, processing, and Brodmann coverage
- MRI and segmentation provenance
- Internal geometry verification
- Brainstem study provenance and geometry checks
- Original brainstem label probabilities (NIfTI)
- Brainstem channel names and IDs
- MNI MRI template notice
- Hypothalamic source, conversion, MRI and coverage
- Neudorfer dataset attribution and CC BY 4.0 notice
- Original Neudorfer source label table
- Asset checksums
Licenses and attribution
The hypothalamic study derives from Neudorfer, Germann, Elias, Gramer, Boutet and Lozano (2020), published under CC BY 4.0. Changes include selecting the 26 hypothalamic labels, unsmoothed mesh conversion, display colors and MRI resampling. The source authors derived their template from Human Connectome Project data. Their atlas includes uncertain, low-contrast boundaries and does not endorse this educational tool.
CBIG assets retain their MIT license and applicable underlying FreeSurfer terms. The Brodmann derivative retains CC BY 4.0 attribution. Changes include conversion to JSON, categorical boundary interpolation, display colors, and web rendering. No original author endorses this tool.
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