98 lines
2.3 KiB
Python
98 lines
2.3 KiB
Python
# Authors: The MNE-Python contributors.
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# License: BSD-3-Clause
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# Copyright the MNE-Python contributors.
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"""Create high-resolution head surfaces for coordinate alignment.
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Examples
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--------
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.. code-block:: console
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$ mne make_scalp_surfaces --overwrite --subject sample
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"""
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import os
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import sys
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import mne
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from mne.bem import make_scalp_surfaces
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def run():
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"""Run command."""
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from mne.commands.utils import _add_verbose_flag, get_optparser
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parser = get_optparser(__file__)
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subjects_dir = mne.get_config("SUBJECTS_DIR")
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parser.add_option(
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"-o",
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"--overwrite",
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dest="overwrite",
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action="store_true",
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help="Overwrite previously computed surface",
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)
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parser.add_option(
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"-s", "--subject", dest="subject", help="The name of the subject", type="str"
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)
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parser.add_option(
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"-m",
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"--mri",
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dest="mri",
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type="str",
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default="T1.mgz",
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help="The MRI file to process using mkheadsurf.",
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)
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parser.add_option(
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"-f",
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"--force",
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dest="force",
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action="store_true",
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help="Force creation of the surface even if it has "
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"some topological defects.",
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)
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parser.add_option(
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"-t",
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"--threshold",
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dest="threshold",
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type="int",
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default=20,
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help="Threshold value to use with the MRI.",
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)
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parser.add_option(
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"-d",
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"--subjects-dir",
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dest="subjects_dir",
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help="Subjects directory",
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default=subjects_dir,
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)
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parser.add_option(
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"-n",
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"--no-decimate",
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dest="no_decimate",
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help="Disable medium and sparse decimations (dense only)",
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action="store_true",
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)
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_add_verbose_flag(parser)
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options, args = parser.parse_args()
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subject = vars(options).get("subject", os.getenv("SUBJECT"))
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subjects_dir = options.subjects_dir
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if subject is None or subjects_dir is None:
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parser.print_help()
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sys.exit(1)
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make_scalp_surfaces(
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subject=subject,
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subjects_dir=subjects_dir,
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force=options.force,
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overwrite=options.overwrite,
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no_decimate=options.no_decimate,
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threshold=options.threshold,
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mri=options.mri,
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verbose=options.verbose,
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)
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mne.utils.run_command_if_main()
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