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#!/usr/bin/env python
"""Set up bilateral hemisphere surface-based source space with subsampling.
Examples
--------
.. code-block:: console
$ mne setup_source_space --subject sample
.. note : Only one of --ico, --oct or --spacing options can be set at the same
time. Default to oct6.
"""
import sys
import mne
from mne.utils import _check_option
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
parser.add_option('-s', '--subject',
dest='subject',
help='Subject name (required)',
default=None)
parser.add_option('--src', dest='fname',
help='Output file name. Use a name <dir>/<name>-src.fif',
metavar='FILE', default=None)
parser.add_option('--morph',
dest='subject_to',
help='morph the source space to this subject',
default=None)
parser.add_option('--surf',
dest='surface',
help='The surface to use. (default to white)',
default='white',
type='string')
parser.add_option('--spacing',
dest='spacing',
help='Specifies the approximate grid spacing of the '
'source space in mm. (default to 7mm)',
default=None,
type='int')
parser.add_option('--ico',
dest='ico',
help='use the recursively subdivided icosahedron '
'to create the source space.',
default=None,
type='int')
parser.add_option('--oct',
dest='oct',
help='use the recursively subdivided octahedron '
'to create the source space.',
default=None,
type='int')
parser.add_option('-d', '--subjects-dir',
dest='subjects_dir',
help='Subjects directory',
default=None)
parser.add_option('-n', '--n-jobs',
dest='n_jobs',
help='The number of jobs to run in parallel '
'(default 1). Requires the joblib package. '
'Will use at most 2 jobs'
' (one for each hemisphere).',
default=1,
type='int')
parser.add_option('--add-dist',
dest='add_dist',
help='Add distances. Can be "True", "False", or "patch" '
'to only compute cortical patch statistics (like the '
'--cps option in MNE-C; requires SciPy >= 1.3)',
default='True')
parser.add_option('-o', '--overwrite',
dest='overwrite',
help='to write over existing files',
default=None, action="store_true")
_add_verbose_flag(parser)
options, args = parser.parse_args()
if options.subject is None:
parser.print_help()
sys.exit(1)
subject = options.subject
subject_to = options.subject_to
fname = options.fname
subjects_dir = options.subjects_dir
spacing = options.spacing
ico = options.ico
oct = options.oct
surface = options.surface
n_jobs = options.n_jobs
add_dist = options.add_dist
_check_option('add_dist', add_dist, ('True', 'False', 'patch'))
add_dist = {'True': True, 'False': False, 'patch': 'patch'}[add_dist]
verbose = True if options.verbose is not None else False
overwrite = True if options.overwrite is not None else False
# Parse source spacing option
spacing_options = [ico, oct, spacing]
n_options = len([x for x in spacing_options if x is not None])
if n_options > 1:
raise ValueError('Only one spacing option can be set at the same time')
elif n_options == 0:
# Default to oct6
use_spacing = 'oct6'
elif n_options == 1:
if ico is not None:
use_spacing = "ico" + str(ico)
elif oct is not None:
use_spacing = "oct" + str(oct)
elif spacing is not None:
use_spacing = spacing
# Generate filename
if fname is None:
if subject_to is None:
fname = subject + '-' + str(use_spacing) + '-src.fif'
else:
fname = (subject_to + '-' + subject + '-' +
str(use_spacing) + '-src.fif')
else:
if not (fname.endswith('_src.fif') or fname.endswith('-src.fif')):
fname = fname + "-src.fif"
# Create source space
src = mne.setup_source_space(subject=subject, spacing=use_spacing,
surface=surface, subjects_dir=subjects_dir,
n_jobs=n_jobs, add_dist=add_dist,
verbose=verbose)
# Morph source space if --morph is set
if subject_to is not None:
src = mne.morph_source_spaces(src, subject_to=subject_to,
subjects_dir=subjects_dir,
surf=surface, verbose=verbose)
# Save source space to file
src.save(fname=fname, overwrite=overwrite)
mne.utils.run_command_if_main()
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