VolumePlot: Whole-brain contacts

Use VolumePlot to see contacts in the context of the whole brain. Here, translucent fsaverage pial surfaces provide the anatomical background.

1. Draw the background

Fetch both hemispheres to build the translucent background. VolumePlot draws these surfaces, rather than image voxels.

from anatplot import VolumePlot, datasets

surfaces = datasets.fetch_surfaces(
    template="fsaverage",
    surface="pial",
    density="10k",
)

plot = VolumePlot(
    left=surfaces["left"],
    right=surfaces["right"],
)
fig = plot.to_figure()

2. Add contacts

Next, add contacts on both sides of the brain, using red and blue to distinguish the two groups.

# Coordinates in the fsaverage surface's RAS millimetre frame.
xyz = [
    [-28, -18, -12],
    [-28, -22, -12],
    [-28, -26, -12],
    [28, -18, -12],
    [28, -22, -12],
    [28, -26, -12],
]
plot.add_contacts(
    xyz,
    radius=2.0,
    color=["crimson", "crimson", "crimson", "royalblue", "royalblue", "royalblue"],
)
fig = plot.to_figure()

VolumePlot keeps the supplied coordinates rather than projecting them onto the surface. If contacts lie outside the view, call plot.plotter.reset_camera() before to_figure() to fit the whole scene.

3. Save and share

Finally, save the contact figure as a PNG and export the scene as interactive HTML.

fig.savefig("brain.png", dpi=300)
plot.export_html("brain.html")
plot.close()