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#!/usr/bin/env python
"""Create a BEM model for a subject.
Examples
--------
.. code-block:: console
$ mne setup_forward_model -s 'sample'
"""
import sys
import os
import mne
from mne.utils import get_subjects_dir, warn
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
parser.add_option("-s", "--subject",
dest="subject",
help="Subject name (required)",
default=None)
parser.add_option("--model",
dest="model",
help="Output file name. Use a name <dir>/<name>-bem.fif",
default=None,
type='string')
parser.add_option('--ico',
dest='ico',
help='The surface ico downsampling to use, e.g. '
' 5=20484, 4=5120, 3=1280. If None, no subsampling'
' is applied.',
default=None,
type='int')
parser.add_option('--brainc',
dest='brainc',
help='Defines the brain compartment conductivity. '
'The default value is 0.3 S/m.',
default=0.3,
type='float')
parser.add_option('--skullc',
dest='skullc',
help='Defines the skull compartment conductivity. '
'The default value is 0.006 S/m.',
default=None,
type='float')
parser.add_option('--scalpc',
dest='scalpc',
help='Defines the scalp compartment conductivity. '
'The default value is 0.3 S/m.',
default=None,
type='float')
parser.add_option('--homog',
dest='homog',
help='Use a single compartment model (brain only) '
'instead a three layer one (scalp, skull, and '
' brain). If this flag is specified, the options '
'--skullc and --scalpc are irrelevant.',
default=None, action="store_true")
parser.add_option('-d', '--subjects-dir',
dest='subjects_dir',
help='Subjects directory',
default=None)
_add_verbose_flag(parser)
options, args = parser.parse_args()
if options.subject is None:
parser.print_help()
sys.exit(1)
subject = options.subject
fname = options.model
subjects_dir = options.subjects_dir
ico = options.ico
brainc = options.brainc
skullc = options.skullc
scalpc = options.scalpc
homog = True if options.homog is not None else False
verbose = True if options.verbose is not None else False
# Parse conductivity option
if homog is True:
if skullc is not None:
warn('Trying to set the skull conductivity for a single layer '
'model. To use a 3 layer model, do not set the --homog flag.')
if scalpc is not None:
warn('Trying to set the scalp conductivity for a single layer '
'model. To use a 3 layer model, do not set the --homog flag.')
# Single layer
conductivity = [brainc]
else:
if skullc is None:
skullc = 0.006
if scalpc is None:
scalpc = 0.3
conductivity = [brainc, skullc, scalpc]
# Create source space
bem_model = mne.make_bem_model(subject,
ico=ico,
conductivity=conductivity,
subjects_dir=subjects_dir,
verbose=verbose)
# Generate filename
if fname is None:
n_faces = list(str(len(surface['tris'])) for surface in bem_model)
fname = subject + '-' + '-'.join(n_faces) + '-bem.fif'
else:
if not (fname.endswith('-bem.fif') or fname.endswith('_bem.fif')):
fname = fname + "-bem.fif"
# Save to subject's directory
subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
fname = os.path.join(subjects_dir, subject, "bem", fname)
# Save source space to file
mne.write_bem_surfaces(fname, bem_model)
# Compute the solution
sol_fname = os.path.splitext(fname)[0] + '-sol.fif'
bem_sol = mne.make_bem_solution(bem_model, verbose=verbose)
mne.write_bem_solution(sol_fname, bem_sol)
mne.utils.run_command_if_main()
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