def test_flash_bem():
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(tempdir, 'sample', 'bem'))
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
files = glob.glob(op.join(mridata_path, 'flash', 'mef*.mgz'))
for infile in files:
shutil.copyfile(
infile, op.join(mridata_path_new, 'flash', op.basename(infile)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
currdir = os.getcwd()
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False,
disable_stderr=False):
mne_flash_bem.run()
os.chdir(currdir)
def test_flash_bem():
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(subject_path_new, 'bem'))
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
flash_path = op.join(mridata_path_new, 'flash')
for kind in (5, 30):
in_fname = op.join(mridata_path, 'flash', 'mef%02d.mgz' % kind)
shutil.copyfile(in_fname, op.join(flash_path, op.basename(in_fname)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
out_fnames = list()
for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
out_fnames.append(op.join(subject_path_new, 'bem', 'outer_skin.surf'))
assert not any(op.isfile(out_fname) for out_fname in out_fnames)
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False, disable_stderr=False):
mne_flash_bem.run()
# do they exist and are expected size
for out_fname in out_fnames:
_, tris = read_surface(out_fname)
assert len(tris) == 5120
def test_flash_bem(tmpdir):
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = str(tmpdir)
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(subject_path_new, 'bem'))
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
flash_path = op.join(mridata_path_new, 'flash')
for kind in (5, 30):
in_fname = op.join(mridata_path, 'flash', 'mef%02d.mgz' % kind)
shutil.copyfile(in_fname, op.join(flash_path, op.basename(in_fname)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
out_fnames = list()
for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
out_fnames.append(op.join(subject_path_new, 'bem', 'outer_skin.surf'))
assert not any(op.isfile(out_fname) for out_fname in out_fnames)
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False, disable_stderr=False):
mne_flash_bem.run()
# do they exist and are expected size
for out_fname in out_fnames:
_, tris = read_surface(out_fname)
assert len(tris) == 5120
def test_flash_bem():
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(tempdir, 'sample', 'bem'))
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
files = glob.glob(op.join(mridata_path, 'flash', 'mef*.mgz'))
for infile in files:
shutil.copyfile(infile, op.join(mridata_path_new, 'flash',
op.basename(infile)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
currdir = os.getcwd()
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False, disable_stderr=False):
mne_flash_bem.run()
os.chdir(currdir)
def test_flash_bem(tmp_path):
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Copy necessary files to tempdir
tempdir = str(tmp_path)
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(subject_path_new, 'bem'))
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
flash_path = op.join(mridata_path_new, 'flash')
for kind in (5, 30):
in_fname = op.join(mridata_path, 'flash', 'mef%02d.mgz' % kind)
shutil.copyfile(in_fname, op.join(flash_path, op.basename(in_fname)))
# 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(op.join(subject_path_new, 'bem', '%s.surf' % s))
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
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)
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)
