FreeSurfer meshes and voxels

NIfTI and GIFTI are popular neuroimaging formats for voxels and meshes. However, FreeSurfer will often generate its own internal formats. This notebook displays FreeSurfer data.

from ipyniivue import NiiVue, SliceType

nv = NiiVue(slice_type=SliceType.MULTIPLANAR)
nv.load_volumes([{"path": "../images/fs/brainmask.mgz"}])
nv.load_meshes([
        {"path": "../images/fs/rh.pial", "rgba255": [64, 22, 222, 255]},
        {"path": "../images/fs/rh.white", "rgba255": [222, 194, 0, 255]},
     ])
nv.set_clip_plane(-0.1, 270, 0)
nv.set_mesh_shader(nv.meshes[0].id, 'crosscut')
nv.set_mesh_shader(nv.meshes[1].id, 'crosscut')
nv