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 test_flash_bem(tmp_path):
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Copy necessary files to tempdir
tempdir = Path(str(tmp_path))
mridata_path = Path(subjects_dir) / 'sample' / 'mri'
subject_path_new = tempdir / 'sample'
mridata_path_new = subject_path_new / 'mri'
flash_path = mridata_path_new / 'flash'
flash_path.mkdir(parents=True, exist_ok=True)
bem_path = mridata_path_new / 'bem'
bem_path.mkdir(parents=True, exist_ok=True)
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
shutil.copyfile(op.join(mridata_path, 'brain.mgz'),
op.join(mridata_path_new, 'brain.mgz'))
# Copy the available mri/flash/mef*.mgz files from the dataset
for kind in (5, 30):
in_fname = mridata_path / "flash" / f'mef{kind:02d}.mgz'
in_fname_echo = flash_path / f'mef{kind:02d}_001.mgz'
shutil.copyfile(in_fname, flash_path / in_fname_echo.name)
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
for s in ('outer_skin', 'outer_skull', 'inner_skull'):
assert not op.isfile(subject_path_new / 'bem' / f'{s}.surf')
# First test without flash30
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n', '-r', '-3'),
disable_stdout=False,
disable_stderr=False):
mne_flash_bem.run()
for s in ('outer_skin', 'outer_skull', 'inner_skull'):
surf_path = subject_path_new / 'bem' / f'{s}.surf'
assert surf_path.exists()
surf_path.unlink() # cleanup
shutil.rmtree(flash_path / "parameter_maps") # remove old files
# Test synthesize flash5 with MEF flash5 and flash30 default locations
flash5_img = convert_flash_mris(subject="sample",
subjects_dir=tempdir,
convert=False,
unwarp=False)
assert flash5_img == (flash_path / "parameter_maps" / "flash5.mgz")
assert flash5_img.exists()
shutil.rmtree(flash_path / "parameter_maps") # remove old files
# Test with flash5 and flash30
shutil.rmtree(flash_path) # first remove old files
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n', '-3',
str(mridata_path / "flash" / 'mef30.mgz'), '-5',
str(mridata_path / "flash" / 'mef05.mgz')),
disable_stdout=False,
disable_stderr=False):
mne_flash_bem.run()
kwargs = dict(rtol=1e-5, atol=1e-5)
for s in ('outer_skin', 'outer_skull', 'inner_skull'):
rr, tris = read_surface(op.join(subject_path_new, 'bem',
'%s.surf' % s))
assert_equal(len(tris), 5120)
assert_equal(tris.min(), 0)
assert_equal(rr.shape[0], tris.max() + 1)
# compare to the testing flash surfaces
rr_c, tris_c = read_surface(
op.join(subjects_dir, 'sample', 'bem', '%s.surf' % s))
assert_allclose(rr, rr_c, **kwargs)
assert_allclose(tris, tris_c, **kwargs)