Tract viewer Methods Ideas

Mesh modeling

Thalamus and nucleus accumbens only. No cortex, no tracts, no other nuclei. Switch proposals to compare. The live tract viewer keeps the unfilled atlas meshes and now also shows the Paint lids.

Loading meshes…

Drag to orbit. Scroll to zoom. Hard-refresh this page. To judge the C-hole: Front faces, Keep right, Left, then switch Right lid or Hull and lid. Keep right +2 mm keeps a strip of midline. Cap the cut adds a flat wall on the kept side.

Show Thalamus Nucleus accumbens

Mesh proposal (both structures). Live tract viewer stays original.

Paint is Original plus the hand-painted midline patches. Right lid puts tissue on x≥0 so Keep right + Front faces still sees a wall. Thick lid is ±3 voxels. Hull and lid is Fill cave plus that right-side wall. Cap lid / thin bridge / shrink dent remain the earlier slivers.

Overlay original as wire Cyan wire is the unfilled mesh. Use this to see whether the proposal actually moved.

Ghost (viewer) Ghost, one surface Solid Wire

Ghost (viewer) is 28% glass over the plate paper. A bowl still looks like a hole in that shade, including Fill cave. Ghost, one surface writes depth and uses a high opacity so the nearest wall reads as tissue. Solid is opaque. This page opens on Solid.

Front faces Both faces

Opacity 0.28 Cap the cut Plane at the midline (x = 0). Largest hole only. Extra fill toward caudal (−y) so the posterior lip is not left open. Midline plane Show all opening markers

Midline paint

Two translucent surfaces on x = 0. Left-drag draws or erases. Right-drag orbits. Scroll zooms.

Paint on the midline

Thalamus Accumbens

Draw Erase

Brush 2.0 mm

Download saves midline-paint.json (both colors plus world bounds). Put it at meshes/modeling/midline-paint.json (or meshes/modeling/paint/) and bake with python3 scripts/bake_midline_paint.py.

Which opening (thalamus)

Pick every opening you mean. “The hole” is not enough — these look different from different views.

Front V-notch

Dent between the two hills, front view, superior midline.

How to describe the change

Name the view first: Front, top, left, or oblique. The same mesh shows a V, a U, or a cave depending on the camera.
Say look-into versus look-through versus dent: A dent is a notch in the outline. A cave is inner walls you look into. A tunnel would go through; these meshes are not tunnels (they are genus 0).
Say whether two lobes should remain: A thin bridge keeps left and right readable. Filling the cave makes one blob.
Say what must not happen: The failed edit roofed the third ventricle and opened larger inferior windows. Tick “no new windows” if that is still forbidden.
Paste the spec: Copy the spec box into chat. That is enough to start the next edit. Do not only write “close the hole”.