initial commit

mne/commands/mne_freeview_bem_surfaces.py

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+"""View the 3-Layers BEM model using Freeview.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne freeview_bem_surfaces -s sample
+
+"""
+
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import os
+import os.path as op
+import sys
+
+import mne
+from mne.utils import get_subjects_dir, run_subprocess
+
+
+def freeview_bem_surfaces(subject, subjects_dir, method=None):
+    """View 3-Layers BEM model with Freeview.
+
+    Parameters
+    ----------
+    subject : str
+        Subject name
+    subjects_dir : path-like
+        Directory containing subjects data (Freesurfer SUBJECTS_DIR)
+    method : str | None
+        Can be ``'flash'`` or ``'watershed'``, or None to use the ``bem/`` directory
+        files.
+    """
+    subjects_dir = str(get_subjects_dir(subjects_dir, raise_error=True))
+
+    if subject is None:
+        raise ValueError("subject argument is None.")
+
+    subject_dir = op.join(subjects_dir, subject)
+
+    if not op.isdir(subject_dir):
+        raise ValueError(
+            f"Wrong path: '{subject_dir}'. Check subjects-dir or subject argument."
+        )
+
+    env = os.environ.copy()
+    env["SUBJECT"] = subject
+    env["SUBJECTS_DIR"] = subjects_dir
+
+    if "FREESURFER_HOME" not in env:
+        raise RuntimeError("The FreeSurfer environment needs to be set up.")
+
+    mri_dir = op.join(subject_dir, "mri")
+    bem_dir = op.join(subject_dir, "bem")
+    mri = op.join(mri_dir, "T1.mgz")
+
+    if method == "watershed":
+        bem_dir = op.join(bem_dir, "watershed")
+        outer_skin = op.join(bem_dir, f"{subject}_outer_skin_surface")
+        outer_skull = op.join(bem_dir, f"{subject}_outer_skull_surface")
+        inner_skull = op.join(bem_dir, f"{subject}_inner_skull_surface")
+    else:
+        if method == "flash":
+            bem_dir = op.join(bem_dir, "flash")
+        outer_skin = op.join(bem_dir, "outer_skin.surf")
+        outer_skull = op.join(bem_dir, "outer_skull.surf")
+        inner_skull = op.join(bem_dir, "inner_skull.surf")
+
+    # put together the command
+    cmd = ["freeview"]
+    cmd += ["--volume", mri]
+    cmd += ["--surface", f"{inner_skull}:color=red:edgecolor=red"]
+    cmd += ["--surface", f"{outer_skull}:color=yellow:edgecolor=yellow"]
+    cmd += ["--surface", f"{outer_skin}:color=255,170,127:edgecolor=255,170,127"]
+
+    run_subprocess(cmd, env=env, stdout=sys.stdout)
+    print("[done]")
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import get_optparser
+
+    parser = get_optparser(__file__)
+
+    subject = os.environ.get("SUBJECT")
+    parser.add_option(
+        "-s", "--subject", dest="subject", help="Subject name", default=subject
+    )
+    parser.add_option(
+        "-d",
+        "--subjects-dir",
+        dest="subjects_dir",
+        help="Subjects directory",
+    )
+    parser.add_option(
+        "-m",
+        "--method",
+        dest="method",
+        help="Method used to generate the BEM model. Can be flash or watershed.",
+    )
+
+    options, args = parser.parse_args()
+
+    subject = options.subject
+    subjects_dir = options.subjects_dir
+    method = options.method
+
+    freeview_bem_surfaces(subject, subjects_dir, method)
+
+
+mne.utils.run_command_if_main()