1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
|
#!/usr/bin/env python
# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# simplified bsd-3 license
"""Create high-resolution head surfaces for coordinate alignment.
example usage: mne make_scalp_surfaces --overwrite --subject sample
"""
from __future__ import print_function
import os
import copy
import os.path as op
import sys
import mne
from mne.utils import run_subprocess, _TempDir, verbose, logger, ETSContext
def _check_file(fname, overwrite):
"""Helper to prevent overwrites"""
if op.isfile(fname) and not overwrite:
raise IOError('File %s exists, use --overwrite to overwrite it'
% fname)
def run():
from mne.commands.utils import 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('-f', '--force', dest='force', action='store_true',
help='Force transformation of surface into bem.')
parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
help='Print the debug messages.')
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')
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)
print(options.no_decimate)
_run(subjects_dir, subject, options.force, options.overwrite,
options.no_decimate, options.verbose)
@verbose
def _run(subjects_dir, subject, force, overwrite, no_decimate, verbose=None):
this_env = copy.copy(os.environ)
this_env['SUBJECTS_DIR'] = subjects_dir
this_env['SUBJECT'] = subject
if 'SUBJECTS_DIR' not in this_env:
raise RuntimeError('The environment variable SUBJECTS_DIR should '
'be set')
if not op.isdir(subjects_dir):
raise RuntimeError('subjects directory %s not found, specify using '
'the environment variable SUBJECTS_DIR or '
'the command line option --subjects-dir')
if 'MNE_ROOT' not in this_env:
raise RuntimeError('MNE_ROOT environment variable is not set')
if 'FREESURFER_HOME' not in this_env:
raise RuntimeError('The FreeSurfer environment needs to be set up '
'for this script')
force = '--force' if force else '--check'
subj_path = op.join(subjects_dir, subject)
if not op.exists(subj_path):
raise RuntimeError('%s does not exits. Please check your subject '
'directory path.' % subj_path)
if op.exists(op.join(subj_path, 'mri', 'T1.mgz')):
mri = 'T1.mgz'
else:
mri = 'T1'
logger.info('1. Creating a dense scalp tessellation with mkheadsurf...')
def check_seghead(surf_path=op.join(subj_path, 'surf')):
for k in ['/lh.seghead', '/lh.smseghead']:
surf = surf_path + k if op.exists(surf_path + k) else None
if surf is not None:
break
return surf
my_seghead = check_seghead()
if my_seghead is None:
run_subprocess(['mkheadsurf', '-subjid', subject, '-srcvol', mri],
env=this_env)
surf = check_seghead()
if surf is None:
raise RuntimeError('mkheadsurf did not produce the standard output '
'file.')
dense_fname = '{0}/{1}/bem/{1}-head-dense.fif'.format(subjects_dir,
subject)
logger.info('2. Creating %s ...' % dense_fname)
_check_file(dense_fname, overwrite)
run_subprocess(['mne_surf2bem', '--surf', surf, '--id', '4', force,
'--fif', dense_fname], env=this_env)
levels = 'medium', 'sparse'
my_surf = mne.read_bem_surfaces(dense_fname)[0]
tris = [] if no_decimate else [30000, 2500]
if os.getenv('_MNE_TESTING_SCALP', 'false') == 'true':
tris = [len(my_surf['tris'])] # don't actually decimate
for ii, (n_tri, level) in enumerate(zip(tris, levels), 3):
logger.info('%i. Creating %s tessellation...' % (ii, level))
logger.info('%i.1 Decimating the dense tessellation...' % ii)
with ETSContext():
points, tris = mne.decimate_surface(points=my_surf['rr'],
triangles=my_surf['tris'],
n_triangles=n_tri)
other_fname = dense_fname.replace('dense', level)
logger.info('%i.2 Creating %s' % (ii, other_fname))
_check_file(other_fname, overwrite)
tempdir = _TempDir()
surf_fname = tempdir + '/tmp-surf.surf'
# convert points to meters, make mne_analyze happy
mne.write_surface(surf_fname, points * 1e3, tris)
# XXX for some reason --check does not work here.
try:
run_subprocess(['mne_surf2bem', '--surf', surf_fname, '--id', '4',
'--force', '--fif', other_fname], env=this_env)
finally:
del tempdir
is_main = (__name__ == '__main__')
if is_main:
run()
|
