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#!/usr/bin/env python
# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
#
# simplified bsd-3 license
"""Create high-resolution head surfaces for coordinate alignment.
Examples
--------
.. code-block:: console
$ mne make_scalp_surfaces --overwrite --subject sample
"""
import os
import sys
import mne
from mne.bem import make_scalp_surfaces
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
subjects_dir = mne.get_config('SUBJECTS_DIR')
parser.add_option('-o', '--overwrite', dest='overwrite',
action='store_true',
help='Overwrite previously computed surface')
parser.add_option('-s', '--subject', dest='subject',
help='The name of the subject', type='str')
parser.add_option('-m', '--mri', dest='mri', type='str', default='T1.mgz',
help='The MRI file to process using mkheadsurf.')
parser.add_option('-f', '--force', dest='force', action='store_true',
help='Force creation of the surface even if it has '
'some topological defects.')
parser.add_option('-t', '--threshold', dest='threshold', type='int',
default=20, help='Threshold value to use with the MRI.')
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=subjects_dir)
parser.add_option("-n", "--no-decimate", dest="no_decimate",
help="Disable medium and sparse decimations "
"(dense only)", action='store_true')
_add_verbose_flag(parser)
options, args = parser.parse_args()
subject = vars(options).get('subject', os.getenv('SUBJECT'))
subjects_dir = options.subjects_dir
if subject is None or subjects_dir is None:
parser.print_help()
sys.exit(1)
make_scalp_surfaces(
subject=subject,
subjects_dir=subjects_dir,
force=options.force,
overwrite=options.overwrite,
no_decimate=options.no_decimate,
threshold=options.threshold,
mri=options.mri,
verbose=options.verbose)
mne.utils.run_command_if_main()
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