Methods
How Robotic Brain Universe is built: which data it uses and under which licences, how coordinates are defined, how the meshes are made, how content is governed, and what the model cannot tell you.
Background reading
- How MRI sees the brain
Nuclear magnetic resonance, relaxation and k-space; structural, diffusion and functional MRI; their pitfalls; and AI, portable and 11.7 T scanners.
Intermediate
- The cerebral cortex and its maps
What the folded outer layer of the brain is made of, why it folds, and how scientists map it from Brodmann's microscope to petabyte connectomes.
Introductory
- White matter and tractography
The brain's wiring, how diffusion MRI reveals it, the maths of tensors and networks, and the limits of mapping tracts.
Intermediate
- Blood supply and stroke
The arteries of the brain and their territories, how flow is regulated, what a stroke destroys minute by minute, and the trials that changed treatment.
Intermediate
Sources and licences
Commercial use was assumed (the stricter setting): every bundled dataset is licensed for commercial use. Inputs are pinned by SHA-256 in data/raw-checksums.json.
| Dataset | Version | Licence | Commercial use | Status |
|---|---|---|---|---|
| FreeSurfer fsaverage template subject Surfaces, sulcal depth, Desikan-Killiany and Destrieux parcellations, BA_exvivo labels, aseg segmentation. Modified: subsampled, transformed to MNI152, compressed. | build stamp freesurfer-x86_64-redhat-linux-gnu-dev4-20090216; MNE-Python mirror (OSF 3bxqt, version 2) | FreeSurfer Software License Agreement 1.0, Part B | permitted | used |
| FreeSurferColorLUT.txt Names and colours for aseg labels and the BA_exvivo areas. | SHA-256 d65dd6e4550106d9eb3bc116ef95dd9e2248e0299dad5fd8668209394bd68750 | FreeSurfer Software License Agreement 1.0, Part B | permitted | used |
| HCP-1065 population-averaged tractography atlas (Yeh 2022) Up to 160 streamlines per tract, resampled to 24 points. The adapted tract files are distributed under CC BY-SA 4.0. | GitHub release data-others/atlas, tag hcp1065 (files dated 2023-06-22) | CC BY-SA 4.0; HCP data use acknowledgement required | permitted | used |
| TemplateFlow tpl-fsaverage Used only to check that the derived fsaverage5 and fsaverage6 triangulations are identical, including winding. Not bundled. | den-10k and den-41k sphere surfaces | FreeSurfer licence (as the source template) | permitted | validation only |
| PALS-B12 Brodmann annotation (Van Essen), inside fsaverage FreeSurfer licence Part B §3 grants no rights in third-party data. Replaced by the MGH BA_exvivo labels. | ?h.PALS_B12_Brodmann.annot | Third-party data; no licence could be verified | not verified | excluded |
| Digital 3D Brain MRI Arterial Territories Atlas (Liu et al., Sci Data 2023) Level-1 territories (15 per hemisphere) grouped by their level-2 families (ACA, MCA, PCA, vertebrobasilar). Sampled onto the cortex and resampled onto the MRI grid; the adapted files are distributed under CC BY-SA 4.0. The probabilistic maps on NITRC require a login and are not used. | GitHub Chin-Fu-Liu/Arterial_Atlas, commit fbeb3fe70b6fb8185244d02f9c6b6e07c13235e0; Atlas_182 (FSL MNI152 1 mm grid) | CC BY-SA 4.0 (repository LICENSE and README; the NITRC page lists Creative Commons Attribution) | permitted | used |
| MNI ICBM 2009a nonlinear asymmetric template (MRI sections) Brain-masked T1, drawn on the clip plane when "MRI" is chosen as the section fill (loaded on demand). The template's copyright notice ships as public/assets/LICENSE-ICBM2009a.txt. | mni_icbm152_nlin_asym_09a_nifti.zip: T1 and brain mask, 1 mm | McConnell Brain Imaging Centre notice: use, copy, modify and distribute for any purpose, with the copyright notice in all copies | permitted | used |
| TemplateFlow tpl-MNI152NLin6Asym (FSL MNI152) brain mask Used once to check the grid assumed for the arterial atlas, whose headers carry no origin: with the FSL MNI152 sform the atlas and this brain mask overlap with a Dice coefficient of 0.946. | tpl-MNI152NLin6Asym_res-01_desc-brain_mask.nii.gz | Not verified (no licence file published with the template); validation only, not bundled | not verified | validation only |
Coordinate conventions
Source data are RAS in millimetres. fsaverage surface coordinates are MNI305: in fsaverage the scanner and surface (tkr) vox2ras matrices are equal and talairach.xfm is the identity, which the pipeline checks on every run. Positions are converted to MNI152 with the affine published in FreeSurfer's CoordinateSystems documentation, section 8a:
0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840
Reference points from the same page are unit-test fixtures: MNI305 (10, −20, 35) maps to MNI152 (10.695, −18.409, 36.137), and the published inverse maps MNI152 (10, −20, 35) to MNI305 (9.3131, −21.5849, 33.8345).
Scene mapping is three(x, y, z) = (R, S, −A), 1 scene unit = 1 mm. The mapping has determinant +1, so both systems are right-handed. The hover readout shows MNI152 coordinates in whole millimetres as x, y, z. On the inflated surface, which has no anatomical coordinates, it reports the corresponding pial point.
Display convention. 3D renders are never mirrored: the model always has its real handedness, and persistent L and R markers show the patient's sides. The neurological / radiological setting decides the side from which axial and coronal sections are viewed. Neurological: axial from above, coronal from behind, patient left on screen left. Radiological: axial from below, coronal from the front, patient left on screen right.
Asset pipeline
scripts/build_assets.py rebuilds every asset from the raw sources with one command and verifies its own output. fsaverage is a recursively subdivided icosahedron (ico7, 163,842 vertices per hemisphere). Its first 10,242 and 40,962 vertices are the ico5 and ico6 vertices, so the lower levels of detail are derived by reversing the subdivision. Vertex i is the same fsaverage vertex at every level. The derived fsaverage6 and fsaverage5 triangulations were compared with TemplateFlow's published meshes; face sets and winding were identical.
Each hemisphere and level of detail is one glTF binary file: pial positions, white and inflated morph targets, normals, sulcal depth, and three label attributes (Desikan-Killiany, Destrieux, Brodmann). Compression uses quantisation and meshopt without vertex reordering. A round-trip check decodes every compressed file and requires bit-identical labels, the same triangles in the same order with the same winding (the triangle codec may rotate indices), and positions within 0.05 mm. The measured maximum was under 0.01 mm. Label digests are re-checked by the unit tests.
| Level | Vertices per hemisphere | Both hemispheres | Used for |
|---|---|---|---|
| fsaverage5 | 10,242 | 434 KiB | first paint and mobile |
| fsaverage6 | 40,962 | 1,613 KiB | default on desktop (budget 2 MiB) |
| fsaverage | 163,842 | 5,909 KiB | High detail, on request, desktop only |
Subcortical, ventricular, cerebellar and brainstem meshes come from aseg.mgz: marching cubes on each label mask (scikit-image), Taubin smoothing (30 iterations, λ 0.5, μ −0.53) and simplification with meshoptimizer. Every mesh is checked to be closed after simplification; one that would open is kept unsimplified. Closed meshes let clipped sections be capped: the cut face shows grey matter, white matter and deep nuclei in their own colours. White matter and cortex labels are not meshed because the surfaces represent them. Three labels with fewer than 100 voxels (vessel, white matter hypointensities) are excluded.
Atlases and colours
Label names and colours are read from the source files at build time: the colour tables embedded in ?h.aparc.annot and ?h.aparc.a2009s.annot, and FreeSurferColorLUT.txt for aseg and the Brodmann areas. Display names expand the source abbreviations mechanically, and the source name is always shown alongside.
Brodmann areas are approximate: each vertex gets the BA_exvivo area with the highest probability (Fischl et al. 2008), if that probability is at least 0.5. Twelve areas are available (BA1, 2, 3a, 3b, 4a, 4p, 6, 44, 45, V1, V2, MT).
Lobes are derived from Desikan-Killiany labels with FreeSurfer's documented lobe mapping (CorticalParcellation wiki, after Klein and Tourville 2012). Cingulate labels form their own class, and so does the insula, which the mapping does not assign to a lobe. Lobe colours are the Okabe-Ito colour-blind-safe palette.
The colour-blind-safe alternative for parcel atlases assigns one of five CIELAB lightness levels (pairwise at least 15 L* apart) by exact graph colouring of the parcel adjacency graph. Neighbouring parcels therefore always differ in lightness, and hue alternates on a blue–orange axis where possible.
Tracts
Tracts are the HCP-1065 population-averaged tractography atlas (Yeh 2022) in ICBM 2009a space. For each of the 87 tracts, up to 160 streamlines are drawn at random with a fixed seed and resampled to 24 points by arc length. Mean lengths on the Data page use every streamline in the atlas file. Colour encodes local direction with the DTI convention (Pajevic and Pierpaoli 1999): red left–right, green anterior–posterior, blue superior–inferior. The source abbreviation table gives left-hemisphere names for two right-hemisphere tracts (C_FP_R, TR_S_R). The file name is treated as authoritative for side, and the correction is recorded.
MRI sections
A clipped section can be filled with the MNI ICBM 2009a nonlinear asymmetric T1 template (Fonov et al. 2009, 2011), the template the tracts are registered to. The template is brain-masked, cropped to the mask and stored on its own 1 mm grid (147 × 184 × 156 voxels), so no voxel is resampled: the shader samples the volume at each pixel's MNI152 position on the plane, with trilinear interpolation. Intensities are scaled linearly from 0 to the 99.5th percentile inside the mask; 0 marks voxels outside the mask, which are not drawn. The volume (1,587 KiB transferred) loads only when the MRI fill is chosen.
The pial and white surfaces are outlined where they cross the plane, so the template MRI and the fsaverage surfaces can be compared directly. They come from different templates: fsaverage was averaged in MNI305 space and is mapped to MNI152 with a linear transform. Every pial and white vertex lies inside the template brain mask (100% and 100%), and 98.1% of the displayed tract points do (most of the rest are cranial nerves leaving the brain).
Measured against the template's own tissue probability maps, white-surface vertices lie a median 1.3 mm (90th percentile 2.5 mm) from its white-matter boundary. On gyral crowns, pial vertices lie a median 4.0 mm (90th percentile 7.5 mm) inside its outer grey-matter boundary: the fsaverage surfaces are an average of surfaces, the template an average of images, and the two represent the outer cortex differently. Medial-wall vertices are excluded (scripts/measure_surface_template_fit.py).
Arterial territories
The arterial territory colour mode uses the Digital 3D Brain MRI Arterial Territories Atlas (Liu et al. 2023). It was built from the lesion distributions of 1,298 patients with acute or early subacute ischaemic stroke confined to one major arterial territory; voxels in border zones were assigned to the territory with the highest probability. Level 1 has 15 territories per hemisphere (plus the lateral ventricles), grouped at level 2 into the anterior, middle and posterior cerebral arteries and the vertebrobasilar system. Names, acronyms and levels come from the atlas lookup table; colours are a display choice (hue by level-2 family, lightness separating neighbouring territories by at least 15 L*), because the source has none.
Each cortical vertex takes the territory of the voxel at mid-thickness, halfway between the white and pial surfaces, considering only territories of its own hemisphere. 621 of 299,879 cortical vertices (0.21%) fall in unlabelled voxels and take the nearest territory within 3 mm; none remain unassigned. The medial wall is left uncoloured. On an MRI section the territories are drawn over the T1, with 1 mm borders, including the deep territories that do not reach the cortex.
The atlas files carry orientation but no origin, so the FSL MNI152 1 mm grid named in their README is assumed (voxel (90, 126, 72) at MNI (0, 0, 0)). Checks: every left-named territory lies at x < 0 and every right-named one at x > 0; the atlas overlaps the FSL MNI152 brain mask with a Dice coefficient of 0.946; the level-1 and level-2 images agree on 99.986% of labelled voxels. Moving the origin by 1 mm along any axis would change the territory of 1.5%–2.1% of cortical vertices, all at territory borders. The source acronyms of four right-hemisphere territories end in “L”; the descriptive names, which the voxel data confirm, are used, and the source text is kept in arterial/art.json.
Content governance
Every statement about function, supply, drainage, deficits, surgical relevance or eloquence is a claim with at least one source. The build fails on an unsourced claim, an unknown reference, a missing atlas label, or dominance wording other than “dominant hemisphere (usually left)”. Every reference was checked against Crossref (DOI, title, authors, journal, volume, pages). Clinical reviewer: none yet. All 10 curated structures carry an “Awaiting clinical review” badge. Quantitative values come only from the cited datasets; there are no placeholder numbers.
Known limitations
- The model is a template, an average of 40 subjects. It is not patient-specific and cannot show an individual's anatomy, variability, or language dominance.
- Average surfaces are smoother than individual cortex. Template areas are smaller than individual measurements and are not norms.
- The medial walls of the average hemispheres meet at the midline. 2,722 left pial vertices lie up to 2.1 mm right of the midline, 65 of them labelled (paracentral, up to 0.6 mm). No labelled white-surface vertex crosses.
- Lower levels of detail subsample the fsaverage surface. FreeSurfer's separately averaged fsaverage5 and fsaverage6 surfaces differ from them by up to 4.8 mm at deep sulcal vertices.
- Subcortical meshes are smoothed segmentations of a template volume at 1 mm. Thin structures such as the choroid plexus and the inferior horn are approximate.
- Brodmann areas are probabilistic projections from ex vivo brains and are approximate on any template.
- Arterial territories are population maps derived from stroke lesions, not angiography; individual territories, collaterals and border zones vary and are not shown. The less stroke-prone medial lenticulostriate and anterior choroidal/thalamoperforating territories were defined from prior anatomical knowledge (Liu et al. 2023).
- The MRI sections, the tracts and the arterial atlas are on MNI152 templates; the cortex is fsaverage mapped linearly from MNI305. Against the MRI template, white surfaces are a median 1.3 mm from its white-matter boundary and pial surfaces on gyral crowns a median 4.0 mm inside its outer boundary; the surface outlines on the MRI show these differences.
Required notices
Human Connectome Project: Data were provided in part by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.
Arterial territories adapted from the Digital 3D Brain MRI Arterial Territories Atlas, © 2021 The Johns Hopkins University (Liu et al. 2023, https://doi.org/10.1038/s41597-022-01923-0), distributed under CC BY-SA 4.0. Changes: sampled onto the cortical surfaces, resampled onto the MRI grid, display colours added, two spellings and four side letters corrected. The adapted files are distributed under CC BY-SA 4.0.
MNI ICBM 2009a template copyright notice
The files in public/assets/mri/ are derived from the MNI ICBM 2009a nonlinear asymmetric template (Fonov et al. 2009, 2011), McConnell Brain Imaging Centre, Montreal Neurological Institute. Changes: brain-masked, cropped to the mask, intensities rescaled to 8 bits. The copyright notice shipped with the template (file COPYING) follows verbatim. Copyright (C) 1993-2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The authors and McGill University make no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. The authors are not responsible for any data loss, equipment damage, property loss, or injury to subjects or patients resulting from the use or misuse of this software package.
Tract data adapted from HCP-1065 (Yeh 2022) are distributed under CC BY-SA 4.0. The tract files were modified: subsampled, resampled and quantised.
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