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mne/commands/mne_make_scalp_surfaces.py

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+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+"""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 _add_verbose_flag, get_optparser
+
+    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()