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mne/commands/mne_setup_forward_model.py

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+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+"""Create a BEM model for a subject.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne setup_forward_model -s 'sample'
+
+"""
+
+import os
+import sys
+
+import mne
+from mne.utils import get_subjects_dir, warn
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import _add_verbose_flag, get_optparser
+
+    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 = 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(str(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()