def create_bem_surf(subject, subjects_dir=None, overwrite=False):
from mne.bem import make_watershed_bem
# Set file name ----------------------------------------------------------
bem_dir = op.join(subjects_dir, subject, 'bem')
src_fname = op.join(bem_dir, subject + '-oct-6-src.fif')
bem_fname = op.join(bem_dir, subject + '-5120-bem.fif')
bem_sol_fname = op.join(bem_dir, subject + '-5120-bem-sol.fif')
# Create watershed BEM surfaces
if overwrite or not op.isfile(op.join(bem_dir, subject + '-head.fif')):
make_watershed_bem(subject=subject,
subjects_dir=subjects_dir,
overwrite=True,
volume='T1',
atlas=False,
gcaatlas=False,
preflood=None,
show=False)
# Setup source space
if overwrite or not op.isfile(src_fname):
from mne import setup_source_space
files = ['lh.white', 'rh.white', 'lh.sphere', 'rh.sphere']
for fname in files:
if not op.exists(op.join(subjects_dir, subject, 'surf', fname)):
raise RuntimeError('missing: %s' % fname)
src = setup_source_space(subject=subject,
subjects_dir=subjects_dir,
spacing='oct6',
surface='white',
add_dist=True,
n_jobs=-1,
verbose=None)
src.save(src_fname, overwrite=True)
# Prepare BEM model
if overwrite or not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
# run with a single layer model (enough for MEG data)
surfs = make_bem_model(subject,
conductivity=[0.3],
subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
def anatomy_pipeline(subject, subjects_dir=None, overwrite=False):
from mne.bem import make_watershed_bem
from mne.commands.mne_make_scalp_surfaces import _run as make_scalp_surface
from mne.utils import get_config
if subjects_dir is None:
subjects_dir = get_config('SUBJECTS_DIR')
# Set file name ----------------------------------------------------------
bem_dir = op.join(subjects_dir, subject, 'bem')
src_fname = op.join(bem_dir, subject + '-oct-6-src.fif')
bem_fname = op.join(bem_dir, subject + '-5120-bem.fif')
bem_sol_fname = op.join(bem_dir, subject + '-5120-bem-sol.fif')
# 0. Create watershed BEM surfaces
if overwrite or not op.isfile(op.join(bem_dir, subject + '-head.fif')):
check_libraries()
if not check_freesurfer(subjects_dir=subjects_dir, subject=subject):
warnings.warn('%s is probably not segmented correctly, check '
'log.' % subject)
make_watershed_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=True, volume='T1', atlas=False,
gcaatlas=False, preflood=None)
# 1. Make scalp surfaces
miss_surface = False
# make_scalp is only for outer_skin
for part in ['brain', 'inner_skull', 'outer_skin', 'outer_skull']:
fname = op.join(
bem_dir, 'watershed', '%s_%s_surface' % (subject, part))
if not op.isfile(fname):
miss_surface = True
if overwrite or miss_surface:
make_scalp_surface(subjects_dir=subjects_dir, subject=subject,
force=True, overwrite=True, verbose=None)
# 2. Copy files outside watershed folder in case of bad manipulation
miss_surface_copy = False
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
fname = op.join(bem_dir, '%s.surf' % surface)
if not op.isfile(fname):
miss_surface_copy = True
if overwrite or miss_surface_copy:
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from shutil import copyfile
from_file = op.join(bem_dir,
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(bem_dir, '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
copyfile(from_file, to_file)
# 3. Setup source space
if overwrite or not op.isfile(src_fname):
from mne import setup_source_space, write_source_spaces
check_libraries()
files = ['lh.white', 'rh.white', 'lh.sphere', 'rh.sphere']
for fname in files:
if not op.exists(op.join(subjects_dir, subject, 'surf', fname)):
raise RuntimeError('missing: %s' % fname)
src = setup_source_space(subject=subject, subjects_dir=subjects_dir,
spacing='oct6', surface='white',
add_dist=True, n_jobs=-1, verbose=None)
write_source_spaces(src_fname, src)
# 4. Prepare BEM model
if overwrite or not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
check_libraries()
surfs = make_bem_model(subject=subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
def mne_anatomy(subject, subjects_dir, overwrite=False):
import warnings
# Checks that watershed hasn't already been run
for fname in [
'fiducials.fif', 'head.fif', 'head-dense.fif', 'head-medium.fif',
'head-sparse.fif', 'inner_skull.surf', 'oct-6-src.fif'
]:
fname = op.join(subjects_dir, subject, 'bem', subject + '-' + fname)
if (not overwrite) and op.exists(fname):
raise IOError('%s already exists. Set overwrite=True.' % fname)
return
# Create BEM surfaces
make_watershed_bem(subject=subject,
subjects_dir=subjects_dir,
overwrite=True,
volume='T1',
atlas=False,
gcaatlas=False,
preflood=None)
# Copy files outside watershed folder in case of bad manipulation
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from_file = op.join(subjects_dir, subject, 'bem',
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(subjects_dir, subject, 'bem', '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
# Update file
try:
os.symlink(from_file, to_file)
except OSError as e:
# if disk is not NTFS, symoblic link isn't possible
if e.strerror == 'Operation not permitted':
from shutil import copyfile
copyfile(from_file, to_file)
# Make scalp surfaces
make_scalp_surfaces(subjects_dir,
subject,
force='store_true',
overwrite='store_true',
verbose=None)
# Setup source space
src_fname = op.join(subjects_dir, subject, 'bem',
subject + 'oct-6-src.fif')
if not op.isfile(src_fname):
from mne import setup_source_space
setup_source_space(subject,
subjects_dir=subjects_dir,
fname=src_fname,
spacing='oct6',
surface='white',
overwrite=True,
add_dist=True,
n_jobs=-1,
verbose=None)
# Prepare BEM model
bem_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem.fif')
bem_sol_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem-sol.fif')
if not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
surfs = make_bem_model(subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
# Make morphs to fsaverage if has it
try:
read_morph_map(subject, 'fsaverage', subjects_dir=subjects_dir)
except IOError as e:
if 'No such file or directory' in e.strerror:
warnings.warn(e.strerror)
def mne_anatomy(subject, subjects_dir, overwrite=False):
import warnings
# Checks that watershed hasn't already been run
for fname in ['fiducials.fif', 'head.fif', 'head-dense.fif',
'head-medium.fif', 'head-sparse.fif', 'inner_skull.surf',
'oct-6-src.fif']:
fname = op.join(subjects_dir, subject, 'bem', subject + '-' + fname)
if (not overwrite) and op.exists(fname):
raise IOError('%s already exists. Set overwrite=True.' % fname)
return
# Create BEM surfaces
make_watershed_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=True, volume='T1', atlas=False,
gcaatlas=False, preflood=None)
# Copy files outside watershed folder in case of bad manipulation
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from_file = op.join(subjects_dir, subject, 'bem',
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(subjects_dir, subject, 'bem', '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
# Update file
try:
os.symlink(from_file, to_file)
except OSError as e:
# if disk is not NTFS, symoblic link isn't possible
if e.strerror == 'Operation not permitted':
from shutil import copyfile
copyfile(from_file, to_file)
# Make scalp surfaces
make_scalp_surfaces(subjects_dir, subject, force='store_true',
overwrite='store_true', verbose=None)
# Setup source space
src_fname = op.join(subjects_dir, subject, 'bem',
subject + 'oct-6-src.fif')
if not op.isfile(src_fname):
from mne import setup_source_space
setup_source_space(subject, subjects_dir=subjects_dir, fname=src_fname,
spacing='oct6', surface='white', overwrite=True,
add_dist=True, n_jobs=-1, verbose=None)
# Prepare BEM model
bem_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem.fif')
bem_sol_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem-sol.fif')
if not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
surfs = make_bem_model(subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
# Make morphs to fsaverage if has it
try:
read_morph_map(subject, 'fsaverage', subjects_dir=subjects_dir)
except IOError as e:
if 'No such file or directory' in e.strerror:
warnings.warn(e.strerror)
if True: # Runs MNE/Freesurfer BEM models
from mne.bem import (make_bem_model, write_bem_surfaces, make_bem_solution,
write_bem_solution)
for subject in bad_watershed:
bem_dir = os.path.join(subjects_dir, subject, 'bem')
bem_fname = os.path.join(bem_dir, subject + '-5120-bem.fif')
bem_sol_fname = os.path.join(bem_dir, subject + '-5120-bem-sol.fif')
# single layer
surfs = make_bem_model(subject=subject,
subjects_dir=subjects_dir,
conductivity=(.3, ))
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
from mne.viz import plot_bem
if True: # Plot subjects' BEMs and source spaces
figs = list()
for meg_subject, subject in zip(range(1, 21), subjects_id):
if subject in missing_mri + bad_mri:
continue
# Plot BEM
fig = plot_bem(subject=subject, subjects_dir=subjects_dir, show=True)
# plot source space
from mne import read_source_spaces
from surfer import Brain # noqa
from mayavi import mlab # noqa
overwrite=False)
if True: # Runs MNE/Freesurfer BEM models
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
for subject in bad_watershed:
bem_dir = os.path.join(subjects_dir, subject, 'bem')
bem_fname = os.path.join(bem_dir, subject + '-5120-bem.fif')
bem_sol_fname = os.path.join(bem_dir, subject + '-5120-bem-sol.fif')
# single layer
surfs = make_bem_model(subject=subject, subjects_dir=subjects_dir,
conductivity=(.3,))
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
from mne.viz import plot_bem
if True: # Plot subjects' BEMs and source spaces
figs = list()
for meg_subject, subject in zip(range(1, 21), subjects_id):
if subject in missing_mri + bad_mri:
continue
# Plot BEM
fig = plot_bem(subject=subject, subjects_dir=subjects_dir, show=True)
# plot source space
from mne import read_source_spaces
from surfer import Brain # noqa
from mayavi import mlab # noqa
def create_bem_surf(subject,
subjects_dir=None,
overwrite=False): # from jr.meg # noqa
# from mne.bem import make_watershed_bem
# from mne.commands.mne_make_scalp_surfaces import _run as make_scalp_surface
from mne.utils import get_config
if subjects_dir is None:
subjects_dir = get_config('SUBJECTS_DIR')
# Set file name ----------------------------------------------------------
bem_dir = op.join(subjects_dir, subject, 'bem')
src_fname = op.join(bem_dir, subject + '-oct-6-src.fif')
bem_fname = op.join(bem_dir, subject + '-5120-bem.fif')
bem_sol_fname = op.join(bem_dir, subject + '-5120-bem-sol.fif')
# Skip make_watershed_bem and make_scalp_surface because it is
# already done from bash shell (freesurfer command)
miss_surface_copy = False
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
fname = op.join(bem_dir, '%s.surf' % surface)
if not op.isfile(fname):
miss_surface_copy = True
if overwrite or miss_surface_copy:
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from shutil import copyfile
from_file = op.join(bem_dir,
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(bem_dir, '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
copyfile(from_file, to_file)
# 3. Setup source space
if overwrite or not op.isfile(src_fname):
from mne import setup_source_space
check_libraries()
files = ['lh.white', 'rh.white', 'lh.sphere', 'rh.sphere']
for fname in files:
if not op.exists(op.join(subjects_dir, subject, 'surf', fname)):
raise RuntimeError('missing: %s' % fname)
setup_source_space(subject=subject,
subjects_dir=subjects_dir,
fname=src_fname,
spacing='oct6',
surface='white',
overwrite=True,
add_dist=True,
n_jobs=-1,
verbose=None)
# 4. Prepare BEM model
if overwrite or not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
check_libraries()
# run with a single layer model (enough for MEG data)
surfs = make_bem_model(subject,
conductivity=[0.3],
subjects_dir=subjects_dir)
# surfs = make_bem_model(subject=subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
def anatomy_pipeline(subject, subjects_dir=None, overwrite=False):
from mne.bem import make_watershed_bem
from mne.commands.mne_make_scalp_surfaces import _run as make_scalp_surface
from mne.utils import get_config
if subjects_dir is None:
subjects_dir = get_config('SUBJECTS_DIR')
# Set file name ----------------------------------------------------------
bem_dir = op.join(subjects_dir, subject, 'bem')
src_fname = op.join(bem_dir, subject + '-oct-6-src.fif')
bem_fname = op.join(bem_dir, subject + '-5120-bem.fif')
bem_sol_fname = op.join(bem_dir, subject + '-5120-bem-sol.fif')
# 0. Create watershed BEM surfaces
if overwrite or not op.isfile(op.join(bem_dir, subject + '-head.fif')):
check_libraries()
if not check_freesurfer(subjects_dir=subjects_dir, subject=subject):
warnings.warn('%s is probably not segmented correctly, check '
'log.' % subject)
make_watershed_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=True, volume='T1', atlas=False,
gcaatlas=False, preflood=None)
# 1. Make scalp surfaces
miss_surface = False
# make_scalp is only for outer_skin
for part in ['brain', 'inner_skull', 'outer_skin', 'outer_skull']:
fname = op.join(
bem_dir, 'watershed', '%s_%s_surface' % (subject, part))
if not op.isfile(fname):
miss_surface = True
if overwrite or miss_surface:
make_scalp_surface(subjects_dir=subjects_dir, subject=subject,
force=True, overwrite=True, verbose=None)
# 2. Copy files outside watershed folder in case of bad manipulation
miss_surface_copy = False
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
fname = op.join(bem_dir, '%s.surf' % surface)
if not op.isfile(fname):
miss_surface_copy = True
if overwrite or miss_surface_copy:
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from shutil import copyfile
from_file = op.join(bem_dir,
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(bem_dir, '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
copyfile(from_file, to_file)
# 3. Setup source space
if overwrite or not op.isfile(src_fname):
from mne import setup_source_space
check_libraries()
files = ['lh.white', 'rh.white', 'lh.sphere', 'rh.sphere']
for fname in files:
if not op.exists(op.join(subjects_dir, subject, 'surf', fname)):
raise RuntimeError('missing: %s' % fname)
setup_source_space(subject=subject, subjects_dir=subjects_dir,
fname=src_fname,
spacing='oct6', surface='white', overwrite=True,
add_dist=True, n_jobs=-1, verbose=None)
# 4. Prepare BEM model
if overwrite or not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
check_libraries()
surfs = make_bem_model(subject=subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)