def create_head(self):
path = mne.datasets.sample.data_path()
surf = mne.read_bem_surfaces(path +
'/subjects/sample/bem/sample-head.fif')[0]
points, triangles = surf['rr'], surf['tris']
# reduce to 30000 triangles:
points_dec, triangles_dec = decimate_surface(points,
triangles,
n_triangles=30000)
p, t = points_dec, triangles_dec
mesh_data = gl.MeshData(p, t)
mesh_item = gl.GLMeshItem(meshdata=mesh_data,
computeNormals=True,
shader='viewNormalColor',
glOptions='translucent')
mesh_item.translate(0, 0, -20)
mesh_item.rotate(90, 1, 0, 0)
mesh_item.scale(650, 650, 650)
mesh_item.setColor([0, 0, 1, 0.4])
self.view.addItem(mesh_item)
instead of e.g. EEG-cap positions.
"""
# Authors: Denis Engemann <*****@*****.**>
# Alexandre Gramfort <*****@*****.**>
#
# License: BSD (3-clause)
import mne
from mne.surface import decimate_surface
print(__doc__)
path = mne.datasets.sample.data_path()
surf = mne.read_bem_surfaces(path + '/subjects/sample/bem/sample-head.fif')[0]
points, triangles = surf['rr'], surf['tris']
# reduce to 30000 meshes equaling ${SUBJECT}-head-medium.fif output from
# mne_make_scalp_surfaces.py and mne_make_scalp_surfaces
points_dec, triangles_dec = decimate_surface(points,
triangles,
n_triangles=30000)
from mayavi import mlab # noqa
head_col = (0.95, 0.83, 0.83) # light pink
p, t = points_dec, triangles_dec
mlab.triangular_mesh(p[:, 0], p[:, 1], p[:, 2], t, color=head_col)
"""
print(__doc__)
# Authors: Denis Engemann <*****@*****.**>
# Alexandre Gramfort <*****@*****.**>
#
# License: BSD (3-clause)
import mne
from mne.surface import decimate_surface
path = mne.datasets.sample.data_path()
surf = mne.read_bem_surfaces(path + '/subjects/sample/bem/sample-head.fif')[0]
points, triangles = surf['rr'], surf['tris']
# reduce to 30000 meshes equaling ${SUBJECT}-head-medium.fif output from
# mne_make_scalp_surfaces.py and mne_make_scalp_surfaces
points_dec, triangles_dec = decimate_surface(points, triangles,
n_triangles=30000)
try:
from enthought.mayavi import mlab
except:
from mayavi import mlab
head_col = (0.95, 0.83, 0.83) # light pink
p, t = points_dec, triangles_dec
mlab.triangular_mesh(p[:, 0], p[:, 1], p[:, 2], t, color=head_col)
def process_bem(fs_subject_path, bem_path_):
"""
Main function for BEM extraction.
"""
subject_ = bem_path_.name.split("_")[0].replace("AVG", "ANTS")
epi_img_ = nib.load(str(bem_path_))
for file_name_, discard_inds in zip(
["outer_skin.surf", "outer_skull.surf", "inner_skull.surf"],
[[1, 2, 3, 4], [1, 2, 3], [1, 2]]):
epi_img_data_ = deepcopy(epi_img_.get_fdata())
correct_line_artefact(epi_img_data_)
cond = np.stack([(epi_img_data_ == i_) for i_ in discard_inds]).sum(0)
epi_img_data_[np.where(cond)] = 1
epi_img_data_[np.where(np.logical_not(cond))] = 0
vertices, simplices = measure.marching_cubes_lewiner(
epi_img_data_, spacing=(1, 1, 1), allow_degenerate=False)[:2]
path_white = fs_subject_path / subject_ / "surf" / "lh.white"
try:
volume_info_ = read_geometry(path_white, read_metadata=True)[2]
except:
print("Skipping subject {}...".format(subject_))
continue
vertices = vertices @ epi_img_.affine[:3, :
3] + epi_img_.affine[:3,
3] - volume_info_[
"cras"]
mesh_ = trimesh.Trimesh(vertices=vertices, faces=simplices)
trimesh.repair.fix_normals(mesh_, multibody=False)
smooth_mesh = trimesh.smoothing.filter_laplacian(
deepcopy(mesh_), lamb=0.8, iterations=15, volume_constraint=True)
bem_output_path_ = fs_subject_path / subject_ / "bem"
bem_output_path_.mkdir(parents=True, exist_ok=True)
vertices, faces_ = smooth_mesh.vertices, smooth_mesh.faces
# Defect corrections for the large meshes
vertices, faces_ = fix_all_defects(vertices, faces_)
# Writing a freesufer mesh file
file_name_large = file_name_.split(".")[0] + "_large.surf"
write_geometry(str(bem_output_path_ / file_name_large), vertices,
faces_)
# Writing an obj mesh file
with (bem_output_path_ /
file_name_large).with_suffix(".obj").open('w') as file_obj:
file_obj.write(
trimesh.exchange.obj.export_obj(
trimesh.Trimesh(vertices, faces_)))
# Decimating BEM surfaces
vertices, faces_ = decimate_surface(vertices,
faces_,
n_triangles=5120,
method='sphere')
# Defect correction for decimated meshes...
vertices, faces_ = fix_all_defects(vertices, faces_)
# Writing an obj mesh file
with (bem_output_path_ /
file_name_).with_suffix(".obj").open('w') as file_obj:
file_obj.write(
trimesh.exchange.obj.export_obj(
trimesh.Trimesh(vertices, faces_)))
# Writing a freesufer mesh file
print("Writing {}...".format(str(bem_output_path_ / file_name_)))
write_geometry(str(bem_output_path_ / file_name_),
vertices,
faces_,
volume_info=volume_info_)
