Access to Big Brain cortical layer meshes

siibra provides access to cortical layer meshes obtained from Big Brain.

import siibra
from nilearn import plotting
import numpy as np
import matplotlib.pyplot as plt

Request the BigBrain cortical layer parcellation by Wagstyl et al. from siibra.

layermap = siibra.get_map(parcellation='layers', space="big brain")
layermap.regions
['cortical layer 1 left', 'cortical layer 2 left', 'cortical layer 3 left', 'cortical layer 4 left', 'cortical layer 5 left', 'cortical layer 6 left', 'non-cortical structures left', 'cortical layer 1 right', 'cortical layer 2 right', 'cortical layer 3 right', 'cortical layer 4 right', 'cortical layer 5 right', 'cortical layer 6 right', 'non-cortical structures right']

We fetch the surface mesh of a layer by specifying a unique part of its name.

l4_surf_l = layermap.fetch(region="layer 4 left", format="mesh")

We can also choose individual hemispheres, and recombine meshes. For illustration, we create a combined mesh of the white matter surface in the left hemisphere and the layer 1 surface of the right hemisphere.

wm_surf_r = layermap.fetch(region="non-cortical right", format="mesh")
mesh = siibra.commons.merge_meshes([l4_surf_l, wm_surf_r], labels=[10, 20])
plotting.view_surf(
    (mesh['verts'], mesh['faces']),
    surf_map=mesh['labels'],
    cmap='Set1', vmin=10, vmax=30, symmetric_cmap=False, colorbar=False
)