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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()
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