def test_make_flash_bem():
"""Test computing bem from flash images."""
tmp = _TempDir()
bemdir = op.join(subjects_dir, 'sample', 'bem')
flash_path = op.join(subjects_dir, 'sample', 'mri', 'flash')
for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
copy(op.join(bemdir, surf + '.surf'), tmp)
copy(op.join(bemdir, surf + '.tri'), tmp)
copy(op.join(bemdir, 'inner_skull_tmp.tri'), tmp)
copy(op.join(bemdir, 'outer_skin_from_testing.surf'), tmp)
# This function deletes the tri files at the end.
try:
make_flash_bem('sample', overwrite=True, subjects_dir=subjects_dir,
flash_path=flash_path)
for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
coords, faces = read_surface(op.join(bemdir, surf + '.surf'))
surf = 'outer_skin_from_testing' if surf == 'outer_skin' else surf
coords_c, faces_c = read_surface(op.join(tmp, surf + '.surf'))
assert_equal(0, faces.min())
assert_equal(coords.shape[0], faces.max() + 1)
assert_allclose(coords, coords_c)
assert_allclose(faces, faces_c)
finally:
for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
remove(op.join(bemdir, surf + '.surf')) # delete symlinks
copy(op.join(tmp, surf + '.tri'), bemdir) # return deleted tri
copy(op.join(tmp, surf + '.surf'), bemdir) # return moved surf
copy(op.join(tmp, 'inner_skull_tmp.tri'), bemdir)
copy(op.join(tmp, 'outer_skin_from_testing.surf'), bemdir)
plt.close('all')
def test_make_flash_bem(tmpdir):
"""Test computing bem from flash images."""
tmp = str(tmpdir)
bemdir = op.join(subjects_dir, 'sample', 'bem')
flash_path = op.join(subjects_dir, 'sample', 'mri', 'flash')
for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
copy(op.join(bemdir, surf + '.surf'), tmp)
copy(op.join(bemdir, surf + '.tri'), tmp)
copy(op.join(bemdir, 'inner_skull_tmp.tri'), tmp)
copy(op.join(bemdir, 'outer_skin_from_testing.surf'), tmp)
# This function deletes the tri files at the end.
try:
make_flash_bem('sample', overwrite=True, subjects_dir=subjects_dir,
flash_path=flash_path)
for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
coords, faces = read_surface(op.join(bemdir, surf + '.surf'))
surf = 'outer_skin_from_testing' if surf == 'outer_skin' else surf
coords_c, faces_c = read_surface(op.join(tmp, surf + '.surf'))
assert_equal(0, faces.min())
assert_equal(coords.shape[0], faces.max() + 1)
assert_allclose(coords, coords_c)
assert_allclose(faces, faces_c)
finally:
for surf in ('inner_skull', 'outer_skull', 'outer_skin'):
remove(op.join(bemdir, surf + '.surf')) # delete symlinks
copy(op.join(tmp, surf + '.tri'), bemdir) # return deleted tri
copy(op.join(tmp, surf + '.surf'), bemdir) # return moved surf
copy(op.join(tmp, 'inner_skull_tmp.tri'), bemdir)
copy(op.join(tmp, 'outer_skin_from_testing.surf'), bemdir)
plt.close('all')
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-3", "--noflash30", dest="noflash30",
action="store_true", default=False,
help=("Skip the 30-degree flip angle data"),)
parser.add_option("-n", "--noconvert", dest="noconvert",
action="store_true", default=False,
help=("Assume that the Flash MRI images have already "
"been converted to mgz files"))
parser.add_option("-u", "--unwarp", dest="unwarp",
action="store_true", default=False,
help=("Run grad_unwarp with -unwarp <type> option on "
"each of the converted data sets"))
parser.add_option("-o", "--overwrite", dest="overwrite",
action="store_true", default=False,
help="Write over existing .surf files in bem folder")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
parser.add_option("--copy", dest="copy",
help="Use copies instead of symlinks for surfaces",
action="store_true")
parser.add_option("-p", "--flash-path", dest="flash_path",
default=None,
help="The directory containing flash05.mgz and "
"flash30.mgz files (defaults to "
"$SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps")
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
flash30 = not options.noflash30
convert = not options.noconvert
unwarp = options.unwarp
overwrite = options.overwrite
show = options.show
flash_path = options.flash_path
copy = options.copy
if options.subject is None:
parser.print_help()
raise RuntimeError('The subject argument must be set')
convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
flash30=flash30, convert=convert, unwarp=unwarp,
verbose=True)
make_flash_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, show=show, flash_path=flash_path,
copy=copy, verbose=True)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-3", "--noflash30", dest="noflash30",
action="store_true", default=False,
help=("Skip the 30-degree flip angle data"),)
parser.add_option("-n", "--noconvert", dest="noconvert",
action="store_true", default=False,
help=("Assume that the Flash MRI images have already "
"been converted to mgz files"))
parser.add_option("-u", "--unwarp", dest="unwarp",
action="store_true", default=False,
help=("Run grad_unwarp with -unwarp <type> option on "
"each of the converted data sets"))
parser.add_option("-o", "--overwrite", dest="overwrite",
action="store_true", default=False,
help="Write over existing .surf files in bem folder")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
parser.add_option("-p", "--flash-path", dest="flash_path",
default=None,
help="The directory containing flash05.mgz and "
"flash30.mgz files (defaults to "
"$SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps")
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
flash30 = not options.noflash30
convert = not options.noconvert
unwarp = options.unwarp
overwrite = options.overwrite
show = options.show
flash_path = options.flash_path
if options.subject is None:
parser.print_help()
raise RuntimeError('The subject argument must be set')
convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
flash30=flash30, convert=convert, unwarp=unwarp,
verbose=True)
make_flash_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, show=show, flash_path=flash_path,
verbose=True)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-3", "--noflash30", dest="noflash30",
action="store_true", default=False,
help=("Skip the 30-degree flip angle data"),)
parser.add_option("-n", "--noconvert", dest="noconvert",
action="store_true", default=False,
help=("Assume that the Flash MRI images have already "
"been converted to mgz files"))
parser.add_option("-u", "--unwarp", dest="unwarp",
action="store_true", default=False,
help=("Run grad_unwarp with -unwarp <type> option on "
"each of the converted data sets"))
parser.add_option("-o", "--overwrite", dest="overwrite",
action="store_true", default=False,
help="Write over existing .surf files in bem folder")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
flash30 = not options.noflash30
convert = not options.noconvert
unwarp = options.unwarp
overwrite = options.overwrite
show = options.show
if options.subject is None:
parser.print_help()
raise RuntimeError('The subject argument must be set')
convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
flash30=flash30, convert=convert, unwarp=unwarp)
make_flash_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, show=show, flash_path='.')
def run_forward(subject, session=None):
print("Processing subject: %s" % subject)
# Construct the search path for the data file. `sub` is mandatory
subject_path = op.join('sub-{}'.format(subject))
# `session` is optional
if session is not None:
subject_path = op.join(subject_path, 'ses-{}'.format(session))
subject_path = op.join(subject_path, config.kind)
bids_basename = make_bids_basename(subject=subject,
session=session,
task=config.task,
acquisition=config.acq,
run=None,
processing=config.proc,
recording=config.rec,
space=config.space)
fpath_deriv = op.join(config.bids_root, 'derivatives',
config.PIPELINE_NAME, subject_path)
fname_evoked = \
op.join(fpath_deriv, bids_basename + '-ave.fif')
print("Input: ", fname_evoked)
fname_trans = \
op.join(fpath_deriv, 'sub-{}'.format(subject) + '-trans.fif')
fname_fwd = \
op.join(fpath_deriv, bids_basename + '-fwd.fif')
print("Output: ", fname_fwd)
# Find the raw data file
# XXX : maybe simplify
bids_basename = make_bids_basename(subject=subject,
session=session,
task=config.task,
acquisition=config.acq,
run=config.runs[0],
processing=config.proc,
recording=config.rec,
space=config.space)
data_dir = op.join(config.bids_root, subject_path)
search_str = op.join(data_dir, bids_basename) + '_' + config.kind + '*'
fnames = sorted(glob.glob(search_str))
fnames = [f for f in fnames if op.splitext(f)[1] in mne_bids_readers]
if len(fnames) >= 1:
bids_fname = fnames[0]
elif len(fnames) == 0:
raise ValueError('Could not find input data file matching: '
'"{}"'.format(search_str))
bids_fname = op.basename(bids_fname)
mne.gui.coregistration()
trans = get_head_mri_trans(bids_fname=bids_fname,
bids_root=config.bids_root)
mne.write_trans(fname_trans, trans)
# create the boundary element model (BEM) once
from mne.bem import make_watershed_bem, make_flash_bem
if 'eeg' in config.ch_types or config.kind == 'eeg':
make_flash_bem(subject, subjects_dir=subjects_dir, overwrite=True)
else:
mne.bem.make_watershed_bem(subject,
subjects_dir=subjects_dir,
overwrite=True)
