Bring your own data: Load .nii map for a voxelwise MNI stat map, or Load .csv values
for one value per region. To use a different parcellation (.nii atlas), build a bundle with
build_bundle.py then pick it from the atlas dropdown.
Uncolored regions
Overlay opacity1.0
Overlay vividness1.0
Sparkle strength0.8
Sparkle speed1.0
Twinkle (sharpness)6
⏱ 4D frame1/1
▸🩻 Underlay
The single anatomical base image under the slices/mosaic (and what ✂ Crop to background
masks overlays to). Default is the MNI152 template — load a subject T1 / your own template
(same space as your overlays) for individual results. Tip: a plain drag-drop onto the viewport
in Slices/Mosaic also sets this.
MNI template
▸🧠 Brain extraction (BET)
Skull-strip a subject T1 / T2 — 100% original, clean-room (no FSL/ANTs/copyrighted code).
Deep-core + curvature shape prior; Refined also warps an MNI/OASIS brain-probability prior
back to the subject to trim neck & face. Then it segments CSF / GM / WM so the surface
shows real gyri & sulci. Load a subject scan (below or via 🩻 Underlay); MNI152 isn't a subject.
— none loaded —
0
1
100%
0.30
▸✂️ Segment (CHOP)
Parcel an extracted brain into tissue compartments (from the BET run above). Render any
compartment as a folded 3D surface or drop it under the slices. Run 🧠 Extract brain first.
▸🧊 Volume render
Raymarch the active overlay (incl. 4D) as a true 3D volume — glowing voxels you can
orbit/zoom. Fade the brain to a glass shell (Appearance ▸ Glass) to see the voxels inside it.
Press ▶ on a 4D overlay to animate the volume.
Threshold0.15
Opacity1.0
Quality160
View & appearance
▸🔪 Slice view
Controls the 🔪 Slices view (top bar). Load a stat .nii in Overlay to see a heatmap; click a slice or drag the X/Y/Z sliders to navigate.
MNI template
▸✨ Appearance
Figure brain size1.00×
▸🎨 Color & opacity
All opacity1.00
Opacity · colored
Opacity · gray
Color cutoff
▸🧊 Surface & shading
🫧 Mesh smoothing4
Wire thickness
Pattern scale
Pattern strength
Pattern tilt0°
▸✒ Outlines & depth
Outline width2
Edge width (px)1.5
Edge strength1.0
SSAO strength1.0
SSAO radius1.0
▸🪟 Glass & shell
Shell opacity0.10
▸💡 Lighting & glow
Brightness0.98
Ambient0.70
Key light0.70
Drag a glowing handle in the 3D view to move that light.
Vividness
Rim glow
Aura reach1.35
Aura intensity0.85
Aura pulse0.0
▸◯ Regions
Connectivity
▸🧬 Connectivity
▸🧵 WM tracts
Fade cortex (3D)0.75
Tract opacity0.85
Fiber density70
Tract line1.5
Slab ± mm6
Mask ± mm4
Tract smoothing4
▸🧬 Connectivity edges
Min strength40
Line thickness1.0×
Pulse speed0.8
▸🏹 Arc arrows
Pick source → target in 3D
Arc thickness1.6
Arc height35
Cap size9
click an arc to label it
Timeseries & longitudinal
▸📈 Timecourse (4D)
Load a 4D overlay (e.g. rs-fMRI), then click regions in the brain to plot each region's mean signal across time. The cursor tracks the ▶ player.
No 4D overlay loaded.
▸🌱 Seed connectivity (4D)
With a 4D overlay loaded, pick a seed region — brainWhiz correlates its timecourse with every region and colours the brain by Pearson r (live seed-based functional connectivity).
No 4D overlay loaded.
|r| threshold0.30
▸🗓 Sessions (longitudinal)
Add a map per timepoint (lesion, thickness, %-signal…), scrub across sessions to colour the brain, and plot a region's change over time — overlay a behavioral CSV (day,score) to relate imaging to recovery.
Timepoint—
Tools
▸🎬 Projector
Opacity0.85
Scale X1.0
Scale Y1.0
Offset X0.00
Offset Y0.00
Rotation0°
Rim boost0.0
Wrap spin0.0
1×
Decal size22
Decal rotation0°
Decal outline0
Tap a stamp to select it, then adjust size / rotation / shape / outline.
▸🥔 PotatoHead
Build a head from a T1 (drop a whole-head/skull-stripped .nii on BUILD MESH), then
paint realistic face features onto the surface and try to re-identify the person —
demonstrating the MRI-face privacy risk (cf. Schwarz et al., NEJM 2019).
Pick a feature, then click the head to paint it on. Tap a placed feature to select & edit it.
Size
Width
Rotation
Hair:
Output & motion
▸🎥 View & motion
Axis width
Letter size
Letters explode out
💥 Explosion0%
Explosion distance1.5×
🔍 Mouse zoom1.0×
Rotate speed1.0×
Explosion speed1.0×
▸🖼 Figure
Build multi-panel figures with 🗔 Panels (top bar): drop views into a grid, label them,
and export PNG or a portable .bwz recipe. Save the whole look as a Preset (top bar).
🔗 Living figure — export the current 3D view as one self-contained .html a reader can
rotate / zoom / explode. Drop it into a paper's supplementary, a webpage, or an iframe.
▸🧾 AutoMethods
Auto-writes a Methods / figure-caption paragraph describing the atlas, underlay and overlays currently loaded — paste it into a paper. Regenerates as you load scans.
Software ref is exact; atlas refs are the canonical source for the bundled atlases — verify against the atlas's official citation before submission.
▸🎬 Keyframe director
Set up a view, add a keyframe, change the view, add another… then Preview or Record MP4.
Keyframes capture camera, explode, overlay opacity, 4D frame & a caption; the flythrough is
smoothly interpolated and captions are baked into the video.
2.5s
🎨 Look & feel
28🔍%
×
Selected item:
Drag to move · handles to resize/rotate · double-click text to edit · Del removes · Ctrl/⌘ C/V copy-paste · paste an image from the clipboard
🗔 Figure panels
Gridor
×
Click a tile to drop the current view in. Save a .bwz to share/recreate the whole figure.
drag rotate · scroll zoom · right-drag pan · click region = info
