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#!/usr/bin/env python
"""View the 3-Layers BEM model using Freeview.
You can do for example:
$ mne freeview_bem_surfaces -s sample
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
import sys
import os
import os.path as op
from mne.utils import run_subprocess, get_subjects_dir
def freeview_bem_surfaces(subject, subjects_dir, method):
"""View 3-Layers BEM model with Freeview.
Parameters
----------
subject : string
Subject name
subjects_dir : string
Directory containing subjects data (Freesurfer SUBJECTS_DIR)
method : string
Can be 'flash' or 'watershed'.
"""
subjects_dir = 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("Wrong path: '{}'. Check subjects-dir or"
"subject argument.".format(subject_dir))
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, '%s_outer_skin_surface' % subject)
outer_skull = op.join(bem_dir, '%s_outer_skull_surface' % subject)
inner_skull = op.join(bem_dir, '%s_inner_skull_surface' % subject)
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", "%s:color=red:edgecolor=red" % inner_skull]
cmd += ["--surface", "%s:color=yellow:edgecolor=yellow" % outer_skull]
cmd += ["--surface",
"%s:color=255,170,127:edgecolor=255,170,127" % outer_skin]
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')
subjects_dir = get_subjects_dir()
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=subject)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=subjects_dir)
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)
is_main = (__name__ == '__main__')
if is_main:
run()
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