def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('--input', dest='input_fname',
help='Input data file name', metavar='filename')
parser.add_option('--mrk', dest='mrk_fname',
help='MEG Marker file name', metavar='filename')
parser.add_option('--elp', dest='elp_fname',
help='Headshape points file name', metavar='filename')
parser.add_option('--hsp', dest='hsp_fname',
help='Headshape file name', metavar='filename')
parser.add_option('--stim', dest='stim',
help='Colon Separated Stimulus Trigger Channels',
metavar='chs')
parser.add_option('--slope', dest='slope', help='Slope direction',
metavar='slope')
parser.add_option('--stimthresh', dest='stimthresh', default=1,
help='Threshold value for trigger channels',
metavar='value')
parser.add_option('--output', dest='out_fname',
help='Name of the resulting fiff file',
metavar='filename')
parser.add_option('--debug', dest='debug', action='store_true',
default=False,
help='Set logging level for terminal output to debug')
options, args = parser.parse_args()
if options.debug:
mne.set_log_level('debug')
input_fname = options.input_fname
if input_fname is None:
with ETSContext():
mne.gui.kit2fiff()
sys.exit(0)
hsp_fname = options.hsp_fname
elp_fname = options.elp_fname
mrk_fname = options.mrk_fname
stim = options.stim
slope = options.slope
stimthresh = options.stimthresh
out_fname = options.out_fname
if isinstance(stim, str):
stim = map(int, stim.split(':'))
raw = read_raw_kit(input_fname=input_fname, mrk=mrk_fname, elp=elp_fname,
hsp=hsp_fname, stim=stim, slope=slope,
stimthresh=stimthresh)
raw.save(out_fname)
raw.close()
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
default=None,
help="Subjects directory")
parser.add_option("-s",
"--subject",
dest="subject",
default=None,
help="Subject name")
parser.add_option("-f",
"--fiff",
dest="inst",
default=None,
help="FIFF file with digitizer data for coregistration")
parser.add_option("-t",
"--tabbed",
dest="tabbed",
action="store_true",
default=False,
help="Option for small screens: Combine "
"the data source panel and the coregistration panel "
"into a single panel with tabs.")
parser.add_option("--no-guess-mri",
dest="guess_mri_subject",
action='store_false',
default=True,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed,
inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir,
guess_mri_subject=options.guess_mri_subject)
if is_main:
sys.exit(0)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
default=None, help="Subjects directory")
parser.add_option("-s", "--subject", dest="subject", default=None,
help="Subject name")
parser.add_option("-f", "--fiff", dest="inst", default=None,
help="FIFF file with digitizer data for coregistration")
parser.add_option("-t", "--tabbed", dest="tabbed", action="store_true",
default=False, help="Option for small screens: Combine "
"the data source panel and the coregistration panel "
"into a single panel with tabs.")
parser.add_option("--no-guess-mri", dest="guess_mri_subject",
action='store_false', default=True,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
parser.add_option("--head-opacity", type=float, default=1.,
dest="head_opacity",
help="The opacity of the head surface, in the range "
"[0, 1].")
parser.add_option("--low-res-head",
action='store_true', default=False, dest="low_res_head",
help="Default to using a low-resolution head surface.")
parser.add_option('--verbose', action='store_true', dest='verbose',
help='Turn on verbose mode.')
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed, inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir,
guess_mri_subject=options.guess_mri_subject,
head_opacity=options.head_opacity,
head_high_res=not options.low_res_head,
verbose=options.verbose)
if is_main:
sys.exit(0)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
default=None,
help="Subjects directory")
parser.add_option("-s",
"--subject",
dest="subject",
default=None,
help="Subject name")
parser.add_option("-f",
"--fiff",
dest="inst",
default=None,
help="FIFF file with digitizer data for coregistration")
parser.add_option("-t",
"--tabbed",
dest="tabbed",
action="store_true",
default=False,
help="Option for small screens: Combine "
"the data source panel and the coregistration panel "
"into a single panel with tabs.")
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed,
inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir)
if is_main:
sys.exit(0)
def _run(subjects_dir, subject, force, overwrite, no_decimate, verbose=None):
this_env = copy.copy(os.environ)
subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
this_env['SUBJECTS_DIR'] = subjects_dir
this_env['SUBJECT'] = subject
if 'FREESURFER_HOME' not in this_env:
raise RuntimeError('The FreeSurfer environment needs to be set up '
'for this script')
incomplete = 'warn' if force else 'raise'
subj_path = op.join(subjects_dir, subject)
if not op.exists(subj_path):
raise RuntimeError('%s does not exist. Please check your subject '
'directory path.' % subj_path)
mri = 'T1.mgz' if op.exists(op.join(subj_path, 'mri', 'T1.mgz')) else 'T1'
logger.info('1. Creating a dense scalp tessellation with mkheadsurf...')
def check_seghead(surf_path=op.join(subj_path, 'surf')):
surf = None
for k in ['lh.seghead', 'lh.smseghead']:
this_surf = op.join(surf_path, k)
if op.exists(this_surf):
surf = this_surf
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)
surf = mne.bem._surfaces_to_bem(
[surf], [mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1],
incomplete=incomplete)[0]
mne.write_bem_surfaces(dense_fname, surf)
levels = 'medium', 'sparse'
tris = [] if no_decimate else [30000, 2500]
if os.getenv('_MNE_TESTING_SCALP', 'false') == 'true':
tris = [len(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=surf['rr'],
triangles=surf['tris'],
n_triangles=n_tri)
dec_fname = dense_fname.replace('dense', level)
logger.info('%i.2 Creating %s' % (ii, dec_fname))
_check_file(dec_fname, overwrite)
dec_surf = mne.bem._surfaces_to_bem(
[dict(rr=points, tris=tris)],
[mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1],
rescale=False,
incomplete=incomplete)
mne.write_bem_surfaces(dec_fname, dec_surf)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
default=None, help="Subjects directory")
parser.add_option("-s", "--subject", dest="subject", default=None,
help="Subject name")
parser.add_option("-f", "--fiff", dest="inst", default=None,
help="FIFF file with digitizer data for coregistration")
parser.add_option("-t", "--tabbed", dest="tabbed", action="store_true",
default=False, help="Option for small screens: Combine "
"the data source panel and the coregistration panel "
"into a single panel with tabs.")
parser.add_option("--no-guess-mri", dest="guess_mri_subject",
action='store_false', default=None,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
parser.add_option("--head-opacity", type=float, default=None,
dest="head_opacity",
help="The opacity of the head surface, in the range "
"[0, 1].")
parser.add_option("--high-res-head",
action='store_true', default=False, dest="high_res_head",
help="Use a high-resolution head surface.")
parser.add_option("--low-res-head",
action='store_true', default=False, dest="low_res_head",
help="Use a low-resolution head surface.")
parser.add_option('--trans', dest='trans', default=None,
help='Head<->MRI transform FIF file ("-trans.fif")')
parser.add_option('--project-eeg', dest='project_eeg',
action='store_true', default=None,
help="Project EEG electrodes to the head surface ("
"for visualization purposes only)")
parser.add_option('--orient-to-surface',
action='store_true', default=None,
dest='orient_to_surface',
help='Orient points to the surface.')
parser.add_option('--scale-by-distance',
action='store_true', default=None,
dest='scale_by_distance',
help='Scale points by distance from the surface.')
parser.add_option('--mark-inside',
action='store_true', default=None,
dest='mark_inside',
help='Mark points inside the head using a different '
'color.')
parser.add_option('--interaction',
type=str, default=None, dest='interaction',
help='Interaction style to use, can be "trackball" or '
'"terrain".')
parser.add_option('--scale',
type=float, default=None, dest='scale',
help='Scale factor for the scene.')
parser.add_option('--simple-rendering', action='store_false',
dest='advanced_rendering',
help='Use simplified OpenGL rendering')
parser.add_option('--verbose', action='store_true', dest='verbose',
help='Turn on verbose mode.')
options, args = parser.parse_args()
if options.low_res_head:
if options.high_res_head:
raise ValueError("Can't specify --high-res-head and "
"--low-res-head at the same time.")
head_high_res = False
elif options.high_res_head:
head_high_res = True
else:
head_high_res = None
# expanduser allows ~ for --subjects-dir
subjects_dir = options.subjects_dir
if subjects_dir is not None:
subjects_dir = op.expanduser(subjects_dir)
trans = options.trans
if trans is not None:
trans = op.expanduser(trans)
try:
import faulthandler
faulthandler.enable()
except ImportError:
pass # old Python2
with ETSContext():
mne.gui.coregistration(
options.tabbed, inst=options.inst, subject=options.subject,
subjects_dir=subjects_dir,
guess_mri_subject=options.guess_mri_subject,
head_opacity=options.head_opacity, head_high_res=head_high_res,
trans=trans, scrollable=True, project_eeg=options.project_eeg,
orient_to_surface=options.orient_to_surface,
scale_by_distance=options.scale_by_distance,
mark_inside=options.mark_inside, interaction=options.interaction,
scale=options.scale,
advanced_rendering=options.advanced_rendering,
verbose=options.verbose)
if is_main:
sys.exit(0)
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 exist. 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
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
default=None,
help="Subjects directory")
parser.add_option("-s",
"--subject",
dest="subject",
default=None,
help="Subject name")
parser.add_option("-f",
"--fiff",
dest="inst",
default=None,
help="FIFF file with digitizer data for coregistration")
parser.add_option("-t",
"--tabbed",
dest="tabbed",
action="store_true",
default=False,
help="Option for small screens: Combine "
"the data source panel and the coregistration panel "
"into a single panel with tabs.")
parser.add_option("--no-guess-mri",
dest="guess_mri_subject",
action='store_false',
default=None,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
parser.add_option("--head-opacity",
type=float,
default=None,
dest="head_opacity",
help="The opacity of the head surface, in the range "
"[0, 1].")
parser.add_option("--high-res-head",
action='store_true',
default=False,
dest="high_res_head",
help="Use a high-resolution head surface.")
parser.add_option("--low-res-head",
action='store_true',
default=False,
dest="low_res_head",
help="Use a low-resolution head surface.")
parser.add_option('--trans',
dest='trans',
default=None,
help='Head<->MRI transform FIF file ("-trans.fif")')
parser.add_option('--project-eeg',
dest='project_eeg',
action='store_true',
default=False,
help="Project EEG electrodes to the head surface")
parser.add_option('--verbose',
action='store_true',
dest='verbose',
help='Turn on verbose mode.')
options, args = parser.parse_args()
if options.low_res_head:
if options.high_res_head:
raise ValueError("Can't specify --high-res-head and "
"--low-res-head at the same time.")
head_high_res = False
elif options.high_res_head:
head_high_res = True
else:
head_high_res = None
# expanduser allows ~ for --subjects-dir
subjects_dir = options.subjects_dir
if subjects_dir is not None:
subjects_dir = op.expanduser(subjects_dir)
trans = options.trans
if trans is not None:
trans = op.expanduser(trans)
with ETSContext():
mne.gui.coregistration(options.tabbed,
inst=options.inst,
subject=options.subject,
subjects_dir=subjects_dir,
guess_mri_subject=options.guess_mri_subject,
head_opacity=options.head_opacity,
head_high_res=head_high_res,
trans=trans,
scrollable=True,
project_eeg=options.project_eeg,
verbose=options.verbose)
if is_main:
sys.exit(0)