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#!/usr/bin/env python
# Authors: Lorenzo De Santis
"""Create BEM surfaces using the watershed algorithm included with FreeSurfer.
Examples
--------
.. code-block:: console
$ mne watershed_bem -s sample
"""
import sys
import mne
from mne.bem import make_watershed_bem
from mne.utils import _check_option
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("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-o", "--overwrite", dest="overwrite",
help="Write over existing files", action="store_true")
parser.add_option("-v", "--volume", dest="volume",
help="Defaults to T1", default='T1')
parser.add_option("-a", "--atlas", dest="atlas",
help="Specify the --atlas option for mri_watershed",
default=False, action="store_true")
parser.add_option("-g", "--gcaatlas", dest="gcaatlas",
help="Specify the --brain_atlas option for "
"mri_watershed", default=False, action="store_true")
parser.add_option("-p", "--preflood", dest="preflood",
help="Change the preflood height", default=None)
parser.add_option("--copy", dest="copy",
help="Use copies instead of symlinks for surfaces",
action="store_true")
parser.add_option("-t", "--T1", dest="T1",
help="Whether or not to pass the -T1 flag "
"(can be true, false, 0, or 1). "
"By default it takes the same value as gcaatlas.",
default=None)
parser.add_option("-b", "--brainmask", dest="brainmask",
help="The filename for the brainmask output file "
"relative to the "
"$SUBJECTS_DIR/$SUBJECT/bem/watershed/ directory.",
default="ws")
_add_verbose_flag(parser)
options, args = parser.parse_args()
if options.subject is None:
parser.print_help()
sys.exit(1)
subject = options.subject
subjects_dir = options.subjects_dir
overwrite = options.overwrite
volume = options.volume
atlas = options.atlas
gcaatlas = options.gcaatlas
preflood = options.preflood
copy = options.copy
brainmask = options.brainmask
T1 = options.T1
if T1 is not None:
T1 = T1.lower()
_check_option("--T1", T1, ('true', 'false', '0', '1'))
T1 = T1 in ('true', '1')
verbose = options.verbose
make_watershed_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, volume=volume, atlas=atlas,
gcaatlas=gcaatlas, preflood=preflood, copy=copy,
T1=T1, brainmask=brainmask, verbose=verbose)
mne.utils.run_command_if_main()
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