def test_scale_mri():
"""Test creating fsaverage and scaling it"""
# create fsaverage
create_default_subject(subjects_dir=tempdir)
is_mri = _is_mri_subject('fsaverage', tempdir)
assert_true(is_mri, "Creating fsaverage failed")
fid_path = os.path.join(tempdir, 'fsaverage', 'bem',
'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir)
assert_true(os.path.exists(fid_path), "Updating fsaverage")
# create source space
path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-ico-6-src.fif')
if not os.path.exists(path):
cmd = ['mne_setup_source_space', '--subject', 'fsaverage', '--ico',
'6']
env = os.environ.copy()
env['SUBJECTS_DIR'] = tempdir
run_subprocess(cmd, env=env)
# scale fsaverage
scale_mri('fsaverage', 'flachkopf', [1, .2, .8], True, subjects_dir=tempdir)
is_mri = _is_mri_subject('flachkopf', tempdir)
assert_true(is_mri, "Scaling fsaverage failed")
src_path = os.path.join(tempdir, 'flachkopf', 'bem',
'flachkopf-ico-6-src.fif')
assert_true(os.path.exists(src_path), "Source space was not scaled")
scale_labels('flachkopf', subjects_dir=tempdir)
# scale source space separately
os.remove(src_path)
scale_source_space('flachkopf', 'ico-6', subjects_dir=tempdir)
assert_true(os.path.exists(src_path), "Source space was not scaled")
def test_scale_mri():
"""Test creating fsaverage and scaling it"""
# create fsaverage
tempdir = _TempDir()
create_default_subject(subjects_dir=tempdir)
is_mri = _is_mri_subject('fsaverage', tempdir)
assert_true(is_mri, "Creating fsaverage failed")
fid_path = os.path.join(tempdir, 'fsaverage', 'bem',
'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir)
assert_true(os.path.exists(fid_path), "Updating fsaverage")
# remove redundant label files
label_temp = os.path.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-ico-0-src.fif')
src = mne.setup_source_space('fsaverage',
'ico0',
subjects_dir=tempdir,
add_dist=False)
src_path = os.path.join(tempdir, 'fsaverage', 'bem',
'fsaverage-ico-0-src.fif')
write_source_spaces(src_path, src)
# scale fsaverage
os.environ['_MNE_FEW_SURFACES'] = 'true'
scale_mri('fsaverage',
'flachkopf', [1, .2, .8],
True,
subjects_dir=tempdir)
del os.environ['_MNE_FEW_SURFACES']
is_mri = _is_mri_subject('flachkopf', tempdir)
assert_true(is_mri, "Scaling fsaverage failed")
src_path = os.path.join(tempdir, 'flachkopf', 'bem',
'flachkopf-ico-0-src.fif')
assert_true(os.path.exists(src_path), "Source space was not scaled")
scale_labels('flachkopf', subjects_dir=tempdir)
# scale source space separately
os.remove(src_path)
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
assert_true(os.path.exists(src_path), "Source space was not scaled")
# add distances to source space
src = mne.read_source_spaces(path)
mne.add_source_space_distances(src)
src.save(path, overwrite=True)
# scale with distances
os.remove(src_path)
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
assert_true(os.path.exists(src_path), "Source space was not scaled")
def test_scale_mri():
"""Test creating fsaverage and scaling it"""
# create fsaverage
tempdir = _TempDir()
create_default_subject(subjects_dir=tempdir)
is_mri = _is_mri_subject('fsaverage', tempdir)
assert_true(is_mri, "Creating fsaverage failed")
fid_path = os.path.join(tempdir, 'fsaverage', 'bem',
'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir)
assert_true(os.path.exists(fid_path), "Updating fsaverage")
# remove redundant label files
label_temp = os.path.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-ico-0-src.fif')
mne.setup_source_space('fsaverage', path, 'ico0', overwrite=True,
subjects_dir=tempdir, add_dist=False)
# scale fsaverage
os.environ['_MNE_FEW_SURFACES'] = 'true'
scale_mri('fsaverage', 'flachkopf', [1, .2, .8], True,
subjects_dir=tempdir)
del os.environ['_MNE_FEW_SURFACES']
is_mri = _is_mri_subject('flachkopf', tempdir)
assert_true(is_mri, "Scaling fsaverage failed")
src_path = os.path.join(tempdir, 'flachkopf', 'bem',
'flachkopf-ico-0-src.fif')
assert_true(os.path.exists(src_path), "Source space was not scaled")
scale_labels('flachkopf', subjects_dir=tempdir)
# scale source space separately
os.remove(src_path)
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
assert_true(os.path.exists(src_path), "Source space was not scaled")
# add distances to source space
src = mne.read_source_spaces(path)
mne.add_source_space_distances(src)
src.save(path)
# scale with distances
os.remove(src_path)
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
def test_scale_mri():
"""Test creating fsaverage and scaling it"""
# create fsaverage
tempdir = _TempDir()
create_default_subject(subjects_dir=tempdir)
is_mri = _is_mri_subject("fsaverage", tempdir)
assert_true(is_mri, "Creating fsaverage failed")
fid_path = os.path.join(tempdir, "fsaverage", "bem", "fsaverage-fiducials.fif")
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir)
assert_true(os.path.exists(fid_path), "Updating fsaverage")
# remove redundant label files
label_temp = os.path.join(tempdir, "fsaverage", "label", "*.label")
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
path = os.path.join(tempdir, "fsaverage", "bem", "fsaverage-ico-0-src.fif")
mne.setup_source_space("fsaverage", path, "ico0", overwrite=True, subjects_dir=tempdir, add_dist=False)
# scale fsaverage
os.environ["_MNE_FEW_SURFACES"] = "true"
scale_mri("fsaverage", "flachkopf", [1, 0.2, 0.8], True, subjects_dir=tempdir)
del os.environ["_MNE_FEW_SURFACES"]
is_mri = _is_mri_subject("flachkopf", tempdir)
assert_true(is_mri, "Scaling fsaverage failed")
src_path = os.path.join(tempdir, "flachkopf", "bem", "flachkopf-ico-0-src.fif")
assert_true(os.path.exists(src_path), "Source space was not scaled")
scale_labels("flachkopf", subjects_dir=tempdir)
# scale source space separately
os.remove(src_path)
scale_source_space("flachkopf", "ico-0", subjects_dir=tempdir)
assert_true(os.path.exists(src_path), "Source space was not scaled")
# add distances to source space
src = mne.read_source_spaces(path)
mne.add_source_space_distances(src)
src.save(path)
# scale with distances
os.remove(src_path)
scale_source_space("flachkopf", "ico-0", subjects_dir=tempdir)
def test_scale_mri():
"""Test creating fsaverage and scaling it."""
# create fsaverage using the testing "fsaverage" instead of the FreeSurfer
# one
tempdir = _TempDir()
fake_home = testing.data_path()
create_default_subject(subjects_dir=tempdir, fs_home=fake_home,
verbose=True)
assert _is_mri_subject('fsaverage', tempdir), "Creating fsaverage failed"
fid_path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir,
fs_home=fake_home)
assert op.exists(fid_path), "Updating fsaverage"
# copy MRI file from sample data (shouldn't matter that it's incorrect,
# so here choose a small one)
path_from = op.join(testing.data_path(), 'subjects', 'sample', 'mri',
'T1.mgz')
path_to = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
copyfile(path_from, path_to)
# remove redundant label files
label_temp = op.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
print('Creating surface source space')
path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-%s-src.fif')
src = mne.setup_source_space('fsaverage', 'ico0', subjects_dir=tempdir,
add_dist=False)
mri = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
print('Creating volume source space')
vsrc = mne.setup_volume_source_space(
'fsaverage', pos=50, mri=mri, subjects_dir=tempdir,
add_interpolator=False)
write_source_spaces(path % 'vol-50', vsrc)
# scale fsaverage
for scale in (.9, [1, .2, .8]):
write_source_spaces(path % 'ico-0', src, overwrite=True)
os.environ['_MNE_FEW_SURFACES'] = 'true'
with pytest.warns(None): # sometimes missing nibabel
scale_mri('fsaverage', 'flachkopf', scale, True,
subjects_dir=tempdir, verbose='debug')
del os.environ['_MNE_FEW_SURFACES']
assert _is_mri_subject('flachkopf', tempdir), "Scaling failed"
spath = op.join(tempdir, 'flachkopf', 'bem', 'flachkopf-%s-src.fif')
assert op.exists(spath % 'ico-0'), "Source space ico-0 was not scaled"
assert os.path.isfile(os.path.join(tempdir, 'flachkopf', 'surf',
'lh.sphere.reg'))
vsrc_s = mne.read_source_spaces(spath % 'vol-50')
pt = np.array([0.12, 0.41, -0.22])
assert_array_almost_equal(
apply_trans(vsrc_s[0]['src_mri_t'], pt * np.array(scale)),
apply_trans(vsrc[0]['src_mri_t'], pt))
scale_labels('flachkopf', subjects_dir=tempdir)
# add distances to source space after hacking the properties to make
# it run *much* faster
src_dist = src.copy()
for s in src_dist:
s.update(rr=s['rr'][s['vertno']], nn=s['nn'][s['vertno']],
tris=s['use_tris'])
s.update(np=len(s['rr']), ntri=len(s['tris']),
vertno=np.arange(len(s['rr'])),
inuse=np.ones(len(s['rr']), int))
mne.add_source_space_distances(src_dist)
write_source_spaces(path % 'ico-0', src_dist, overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert ssrc[0]['dist'] is not None
def test_scale_mri_xfm():
"""Test scale_mri transforms and MRI scaling."""
# scale fsaverage
tempdir = _TempDir()
os.environ['_MNE_FEW_SURFACES'] = 'true'
fake_home = testing.data_path()
# add fsaverage
create_default_subject(subjects_dir=tempdir, fs_home=fake_home,
verbose=True)
# add sample (with few files)
sample_dir = op.join(tempdir, 'sample')
os.mkdir(sample_dir)
os.mkdir(op.join(sample_dir, 'bem'))
for dirname in ('mri', 'surf'):
copytree(op.join(fake_home, 'subjects', 'sample', dirname),
op.join(sample_dir, dirname))
subject_to = 'flachkopf'
spacing = 'oct2'
for subject_from in ('fsaverage', 'sample'):
if subject_from == 'fsaverage':
scale = 1. # single dim
else:
scale = [0.9, 2, .8] # separate
src_from_fname = op.join(tempdir, subject_from, 'bem',
'%s-%s-src.fif' % (subject_from, spacing))
src_from = mne.setup_source_space(
subject_from, spacing, subjects_dir=tempdir, add_dist=False)
write_source_spaces(src_from_fname, src_from)
print(src_from_fname)
vertices_from = np.concatenate([s['vertno'] for s in src_from])
assert len(vertices_from) == 36
hemis = ([0] * len(src_from[0]['vertno']) +
[1] * len(src_from[0]['vertno']))
mni_from = mne.vertex_to_mni(vertices_from, hemis, subject_from,
subjects_dir=tempdir)
if subject_from == 'fsaverage': # identity transform
source_rr = np.concatenate([s['rr'][s['vertno']]
for s in src_from]) * 1e3
assert_allclose(mni_from, source_rr)
if subject_from == 'fsaverage':
overwrite = skip_fiducials = False
else:
with pytest.raises(IOError, match='No fiducials file'):
scale_mri(subject_from, subject_to, scale,
subjects_dir=tempdir)
skip_fiducials = True
with pytest.raises(IOError, match='already exists'):
scale_mri(subject_from, subject_to, scale,
subjects_dir=tempdir, skip_fiducials=skip_fiducials)
overwrite = True
scale_mri(subject_from, subject_to, scale, subjects_dir=tempdir,
verbose='debug', overwrite=overwrite,
skip_fiducials=skip_fiducials)
if subject_from == 'fsaverage':
assert _is_mri_subject(subject_to, tempdir), "Scaling failed"
src_to_fname = op.join(tempdir, subject_to, 'bem',
'%s-%s-src.fif' % (subject_to, spacing))
assert op.exists(src_to_fname), "Source space was not scaled"
# Check MRI scaling
fname_mri = op.join(tempdir, subject_to, 'mri', 'T1.mgz')
assert op.exists(fname_mri), "MRI was not scaled"
# Check MNI transform
src = mne.read_source_spaces(src_to_fname)
vertices = np.concatenate([s['vertno'] for s in src])
assert_array_equal(vertices, vertices_from)
mni = mne.vertex_to_mni(vertices, hemis, subject_to,
subjects_dir=tempdir)
assert_allclose(mni, mni_from, atol=1e-3) # 0.001 mm
del os.environ['_MNE_FEW_SURFACES']
def test_scale_mri(tmp_path, few_surfaces, scale):
"""Test creating fsaverage and scaling it."""
# create fsaverage using the testing "fsaverage" instead of the FreeSurfer
# one
tempdir = str(tmp_path)
fake_home = testing.data_path()
create_default_subject(subjects_dir=tempdir,
fs_home=fake_home,
verbose=True)
assert _is_mri_subject('fsaverage', tempdir), "Creating fsaverage failed"
fid_path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True,
subjects_dir=tempdir,
fs_home=fake_home)
assert op.exists(fid_path), "Updating fsaverage"
# copy MRI file from sample data (shouldn't matter that it's incorrect,
# so here choose a small one)
path_from = op.join(testing.data_path(), 'subjects', 'sample', 'mri',
'T1.mgz')
path_to = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
copyfile(path_from, path_to)
# remove redundant label files
label_temp = op.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
print('Creating surface source space')
path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-%s-src.fif')
src = mne.setup_source_space('fsaverage',
'ico0',
subjects_dir=tempdir,
add_dist=False)
mri = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
print('Creating volume source space')
vsrc = mne.setup_volume_source_space('fsaverage',
pos=50,
mri=mri,
subjects_dir=tempdir,
add_interpolator=False)
write_source_spaces(path % 'vol-50', vsrc)
# scale fsaverage
write_source_spaces(path % 'ico-0', src, overwrite=True)
with pytest.warns(None): # sometimes missing nibabel
scale_mri('fsaverage',
'flachkopf',
scale,
True,
subjects_dir=tempdir,
verbose='debug')
assert _is_mri_subject('flachkopf', tempdir), "Scaling failed"
spath = op.join(tempdir, 'flachkopf', 'bem', 'flachkopf-%s-src.fif')
assert op.exists(spath % 'ico-0'), "Source space ico-0 was not scaled"
assert os.path.isfile(
os.path.join(tempdir, 'flachkopf', 'surf', 'lh.sphere.reg'))
vsrc_s = mne.read_source_spaces(spath % 'vol-50')
for vox in ([0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1], [1, 2, 3]):
idx = np.ravel_multi_index(vox, vsrc[0]['shape'], order='F')
err_msg = f'idx={idx} @ {vox}, scale={scale}'
assert_allclose(apply_trans(vsrc[0]['src_mri_t'], vox),
vsrc[0]['rr'][idx],
err_msg=err_msg)
assert_allclose(apply_trans(vsrc_s[0]['src_mri_t'], vox),
vsrc_s[0]['rr'][idx],
err_msg=err_msg)
scale_labels('flachkopf', subjects_dir=tempdir)
# add distances to source space after hacking the properties to make
# it run *much* faster
src_dist = src.copy()
for s in src_dist:
s.update(rr=s['rr'][s['vertno']],
nn=s['nn'][s['vertno']],
tris=s['use_tris'])
s.update(np=len(s['rr']),
ntri=len(s['tris']),
vertno=np.arange(len(s['rr'])),
inuse=np.ones(len(s['rr']), int))
mne.add_source_space_distances(src_dist)
write_source_spaces(path % 'ico-0', src_dist, overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert ssrc[0]['dist'] is not None
assert ssrc[0]['nearest'] is not None
# check patch info computation (only if SciPy is new enough to be fast)
if check_version('scipy', '1.3'):
for s in src_dist:
for key in ('dist', 'dist_limit'):
s[key] = None
write_source_spaces(path % 'ico-0', src_dist, overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert ssrc[0]['dist'] is None
assert ssrc[0]['nearest'] is not None
def test_scale_mri_xfm(tmp_path, few_surfaces):
"""Test scale_mri transforms and MRI scaling."""
# scale fsaverage
tempdir = str(tmp_path)
fake_home = testing.data_path()
# add fsaverage
create_default_subject(subjects_dir=tempdir,
fs_home=fake_home,
verbose=True)
# add sample (with few files)
sample_dir = op.join(tempdir, 'sample')
os.mkdir(sample_dir)
os.mkdir(op.join(sample_dir, 'bem'))
for dirname in ('mri', 'surf'):
copytree(op.join(fake_home, 'subjects', 'sample', dirname),
op.join(sample_dir, dirname))
subject_to = 'flachkopf'
spacing = 'oct2'
for subject_from in ('fsaverage', 'sample'):
if subject_from == 'fsaverage':
scale = 1. # single dim
else:
scale = [0.9, 2, .8] # separate
src_from_fname = op.join(tempdir, subject_from, 'bem',
'%s-%s-src.fif' % (subject_from, spacing))
src_from = mne.setup_source_space(subject_from,
spacing,
subjects_dir=tempdir,
add_dist=False)
write_source_spaces(src_from_fname, src_from)
vertices_from = np.concatenate([s['vertno'] for s in src_from])
assert len(vertices_from) == 36
hemis = ([0] * len(src_from[0]['vertno']) +
[1] * len(src_from[0]['vertno']))
mni_from = mne.vertex_to_mni(vertices_from,
hemis,
subject_from,
subjects_dir=tempdir)
if subject_from == 'fsaverage': # identity transform
source_rr = np.concatenate(
[s['rr'][s['vertno']] for s in src_from]) * 1e3
assert_allclose(mni_from, source_rr)
if subject_from == 'fsaverage':
overwrite = skip_fiducials = False
else:
with pytest.raises(IOError, match='No fiducials file'):
scale_mri(subject_from,
subject_to,
scale,
subjects_dir=tempdir)
skip_fiducials = True
with pytest.raises(IOError, match='already exists'):
scale_mri(subject_from,
subject_to,
scale,
subjects_dir=tempdir,
skip_fiducials=skip_fiducials)
overwrite = True
if subject_from == 'sample': # support for not needing all surf files
os.remove(op.join(sample_dir, 'surf', 'lh.curv'))
scale_mri(subject_from,
subject_to,
scale,
subjects_dir=tempdir,
verbose='debug',
overwrite=overwrite,
skip_fiducials=skip_fiducials)
if subject_from == 'fsaverage':
assert _is_mri_subject(subject_to, tempdir), "Scaling failed"
src_to_fname = op.join(tempdir, subject_to, 'bem',
'%s-%s-src.fif' % (subject_to, spacing))
assert op.exists(src_to_fname), "Source space was not scaled"
# Check MRI scaling
fname_mri = op.join(tempdir, subject_to, 'mri', 'T1.mgz')
assert op.exists(fname_mri), "MRI was not scaled"
# Check MNI transform
src = mne.read_source_spaces(src_to_fname)
vertices = np.concatenate([s['vertno'] for s in src])
assert_array_equal(vertices, vertices_from)
mni = mne.vertex_to_mni(vertices,
hemis,
subject_to,
subjects_dir=tempdir)
assert_allclose(mni, mni_from, atol=1e-3) # 0.001 mm
def test_scale_mri():
"""Test creating fsaverage and scaling it"""
# create fsaverage
tempdir = _TempDir()
create_default_subject(subjects_dir=tempdir)
assert_true(_is_mri_subject('fsaverage', tempdir),
"Creating fsaverage failed")
fid_path = os.path.join(tempdir, 'fsaverage', 'bem',
'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir)
assert_true(os.path.exists(fid_path), "Updating fsaverage")
# copy MRI file from sample data
path = os.path.join('%s', 'fsaverage', 'mri', 'orig.mgz')
sample_sdir = os.path.join(mne.datasets.sample.data_path(), 'subjects')
copyfile(path % sample_sdir, path % tempdir)
# remove redundant label files
label_temp = os.path.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-%s-src.fif')
src = mne.setup_source_space('fsaverage', 'ico0', subjects_dir=tempdir,
add_dist=False)
write_source_spaces(path % 'ico-0', src)
mri = os.path.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
vsrc = mne.setup_volume_source_space('fsaverage', pos=50, mri=mri,
subjects_dir=tempdir,
add_interpolator=False)
write_source_spaces(path % 'vol-50', vsrc)
# scale fsaverage
os.environ['_MNE_FEW_SURFACES'] = 'true'
scale = np.array([1, .2, .8])
scale_mri('fsaverage', 'flachkopf', scale, True, subjects_dir=tempdir)
del os.environ['_MNE_FEW_SURFACES']
assert_true(_is_mri_subject('flachkopf', tempdir),
"Scaling fsaverage failed")
spath = os.path.join(tempdir, 'flachkopf', 'bem', 'flachkopf-%s-src.fif')
assert_true(os.path.exists(spath % 'ico-0'),
"Source space ico-0 was not scaled")
vsrc_s = mne.read_source_spaces(spath % 'vol-50')
pt = np.array([0.12, 0.41, -0.22])
assert_array_almost_equal(apply_trans(vsrc_s[0]['src_mri_t'], pt * scale),
apply_trans(vsrc[0]['src_mri_t'], pt))
scale_labels('flachkopf', subjects_dir=tempdir)
# add distances to source space
mne.add_source_space_distances(src)
src.save(path % 'ico-0', overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert_is_not(ssrc[0]['dist'], None)
def test_scale_mri():
"""Test creating fsaverage and scaling it."""
# create fsaverage using the testing "fsaverage" instead of the FreeSurfer
# one
tempdir = _TempDir()
fake_home = testing.data_path()
create_default_subject(subjects_dir=tempdir, fs_home=fake_home,
verbose=True)
assert _is_mri_subject('fsaverage', tempdir), "Creating fsaverage failed"
fid_path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir,
fs_home=fake_home)
assert op.exists(fid_path), "Updating fsaverage"
# copy MRI file from sample data (shouldn't matter that it's incorrect,
# so here choose a small one)
path_from = op.join(testing.data_path(), 'subjects', 'sample', 'mri',
'T1.mgz')
path_to = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
copyfile(path_from, path_to)
# remove redundant label files
label_temp = op.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
print('Creating surface source space')
path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-%s-src.fif')
src = mne.setup_source_space('fsaverage', 'ico0', subjects_dir=tempdir,
add_dist=False)
write_source_spaces(path % 'ico-0', src)
mri = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
print('Creating volume source space')
vsrc = mne.setup_volume_source_space(
'fsaverage', pos=50, mri=mri, subjects_dir=tempdir,
add_interpolator=False)
write_source_spaces(path % 'vol-50', vsrc)
# scale fsaverage
os.environ['_MNE_FEW_SURFACES'] = 'true'
scale = np.array([1, .2, .8])
scale_mri('fsaverage', 'flachkopf', scale, True, subjects_dir=tempdir,
verbose='debug')
del os.environ['_MNE_FEW_SURFACES']
assert _is_mri_subject('flachkopf', tempdir), "Scaling fsaverage failed"
spath = op.join(tempdir, 'flachkopf', 'bem', 'flachkopf-%s-src.fif')
assert op.exists(spath % 'ico-0'), "Source space ico-0 was not scaled"
assert os.path.isfile(os.path.join(tempdir, 'flachkopf', 'surf',
'lh.sphere.reg'))
vsrc_s = mne.read_source_spaces(spath % 'vol-50')
pt = np.array([0.12, 0.41, -0.22])
assert_array_almost_equal(apply_trans(vsrc_s[0]['src_mri_t'], pt * scale),
apply_trans(vsrc[0]['src_mri_t'], pt))
scale_labels('flachkopf', subjects_dir=tempdir)
# add distances to source space
mne.add_source_space_distances(src)
src.save(path % 'ico-0', overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert ssrc[0]['dist'] is not None
def test_scale_mri_xfm(tmp_path, few_surfaces, subjects_dir_tmp_few):
"""Test scale_mri transforms and MRI scaling."""
# scale fsaverage
tempdir = str(subjects_dir_tmp_few)
sample_dir = subjects_dir_tmp_few / 'sample'
subject_to = 'flachkopf'
spacing = 'oct2'
for subject_from in ('fsaverage', 'sample'):
if subject_from == 'fsaverage':
scale = 1. # single dim
else:
scale = [0.9, 2, .8] # separate
src_from_fname = op.join(tempdir, subject_from, 'bem',
'%s-%s-src.fif' % (subject_from, spacing))
src_from = mne.setup_source_space(subject_from,
spacing,
subjects_dir=tempdir,
add_dist=False)
write_source_spaces(src_from_fname, src_from)
vertices_from = np.concatenate([s['vertno'] for s in src_from])
assert len(vertices_from) == 36
hemis = ([0] * len(src_from[0]['vertno']) +
[1] * len(src_from[0]['vertno']))
mni_from = mne.vertex_to_mni(vertices_from,
hemis,
subject_from,
subjects_dir=tempdir)
if subject_from == 'fsaverage': # identity transform
source_rr = np.concatenate(
[s['rr'][s['vertno']] for s in src_from]) * 1e3
assert_allclose(mni_from, source_rr)
if subject_from == 'fsaverage':
overwrite = skip_fiducials = False
else:
with pytest.raises(IOError, match='No fiducials file'):
scale_mri(subject_from,
subject_to,
scale,
subjects_dir=tempdir)
skip_fiducials = True
with pytest.raises(IOError, match='already exists'):
scale_mri(subject_from,
subject_to,
scale,
subjects_dir=tempdir,
skip_fiducials=skip_fiducials)
overwrite = True
if subject_from == 'sample': # support for not needing all surf files
os.remove(op.join(sample_dir, 'surf', 'lh.curv'))
scale_mri(subject_from,
subject_to,
scale,
subjects_dir=tempdir,
verbose='debug',
overwrite=overwrite,
skip_fiducials=skip_fiducials)
if subject_from == 'fsaverage':
assert _is_mri_subject(subject_to, tempdir), "Scaling failed"
src_to_fname = op.join(tempdir, subject_to, 'bem',
'%s-%s-src.fif' % (subject_to, spacing))
assert op.exists(src_to_fname), "Source space was not scaled"
# Check MRI scaling
fname_mri = op.join(tempdir, subject_to, 'mri', 'T1.mgz')
assert op.exists(fname_mri), "MRI was not scaled"
# Check MNI transform
src = mne.read_source_spaces(src_to_fname)
vertices = np.concatenate([s['vertno'] for s in src])
assert_array_equal(vertices, vertices_from)
mni = mne.vertex_to_mni(vertices,
hemis,
subject_to,
subjects_dir=tempdir)
assert_allclose(mni, mni_from, atol=1e-3) # 0.001 mm
# Check head_to_mni (the `trans` here does not really matter)
trans = rotation(0.001, 0.002, 0.003) @ translation(0.01, 0.02, 0.03)
trans = Transform('head', 'mri', trans)
pos_head_from = np.random.RandomState(0).randn(4, 3)
pos_mni_from = mne.head_to_mni(pos_head_from, subject_from, trans,
tempdir)
pos_mri_from = apply_trans(trans, pos_head_from)
pos_mri = pos_mri_from * scale
pos_head = apply_trans(invert_transform(trans), pos_mri)
pos_mni = mne.head_to_mni(pos_head, subject_to, trans, tempdir)
assert_allclose(pos_mni, pos_mni_from, atol=1e-3)
def test_scale_mri():
"""Test creating fsaverage and scaling it"""
# create fsaverage
tempdir = _TempDir()
create_default_subject(subjects_dir=tempdir)
assert_true(_is_mri_subject('fsaverage', tempdir),
"Creating fsaverage failed")
fid_path = os.path.join(tempdir, 'fsaverage', 'bem',
'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir)
assert_true(os.path.exists(fid_path), "Updating fsaverage")
# copy MRI file from sample data
path = os.path.join('%s', 'fsaverage', 'mri', 'orig.mgz')
sample_sdir = os.path.join(mne.datasets.sample.data_path(), 'subjects')
copyfile(path % sample_sdir, path % tempdir)
# remove redundant label files
label_temp = os.path.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-%s-src.fif')
src = mne.setup_source_space('fsaverage',
'ico0',
subjects_dir=tempdir,
add_dist=False)
write_source_spaces(path % 'ico-0', src)
mri = os.path.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
vsrc = mne.setup_volume_source_space('fsaverage',
pos=50,
mri=mri,
subjects_dir=tempdir,
add_interpolator=False)
write_source_spaces(path % 'vol-50', vsrc)
# scale fsaverage
os.environ['_MNE_FEW_SURFACES'] = 'true'
scale = np.array([1, .2, .8])
scale_mri('fsaverage', 'flachkopf', scale, True, subjects_dir=tempdir)
del os.environ['_MNE_FEW_SURFACES']
assert_true(_is_mri_subject('flachkopf', tempdir),
"Scaling fsaverage failed")
spath = os.path.join(tempdir, 'flachkopf', 'bem', 'flachkopf-%s-src.fif')
assert_true(os.path.exists(spath % 'ico-0'),
"Source space ico-0 was not scaled")
vsrc_s = mne.read_source_spaces(spath % 'vol-50')
pt = np.array([0.12, 0.41, -0.22])
assert_array_almost_equal(apply_trans(vsrc_s[0]['src_mri_t'], pt * scale),
apply_trans(vsrc[0]['src_mri_t'], pt))
scale_labels('flachkopf', subjects_dir=tempdir)
# add distances to source space
mne.add_source_space_distances(src)
src.save(path % 'ico-0', overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert_is_not(ssrc[0]['dist'], None)
def test_scale_mri(tmpdir, few_surfaces):
"""Test creating fsaverage and scaling it."""
# create fsaverage using the testing "fsaverage" instead of the FreeSurfer
# one
tempdir = str(tmpdir)
fake_home = testing.data_path()
create_default_subject(subjects_dir=tempdir, fs_home=fake_home,
verbose=True)
assert _is_mri_subject('fsaverage', tempdir), "Creating fsaverage failed"
fid_path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-fiducials.fif')
os.remove(fid_path)
create_default_subject(update=True, subjects_dir=tempdir,
fs_home=fake_home)
assert op.exists(fid_path), "Updating fsaverage"
# copy MRI file from sample data (shouldn't matter that it's incorrect,
# so here choose a small one)
path_from = op.join(testing.data_path(), 'subjects', 'sample', 'mri',
'T1.mgz')
path_to = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
copyfile(path_from, path_to)
# remove redundant label files
label_temp = op.join(tempdir, 'fsaverage', 'label', '*.label')
label_paths = glob(label_temp)
for label_path in label_paths[1:]:
os.remove(label_path)
# create source space
print('Creating surface source space')
path = op.join(tempdir, 'fsaverage', 'bem', 'fsaverage-%s-src.fif')
src = mne.setup_source_space('fsaverage', 'ico0', subjects_dir=tempdir,
add_dist=False)
mri = op.join(tempdir, 'fsaverage', 'mri', 'orig.mgz')
print('Creating volume source space')
vsrc = mne.setup_volume_source_space(
'fsaverage', pos=50, mri=mri, subjects_dir=tempdir,
add_interpolator=False)
write_source_spaces(path % 'vol-50', vsrc)
# scale fsaverage
for scale in (.9, [1, .2, .8]):
write_source_spaces(path % 'ico-0', src, overwrite=True)
with pytest.warns(None): # sometimes missing nibabel
scale_mri('fsaverage', 'flachkopf', scale, True,
subjects_dir=tempdir, verbose='debug')
assert _is_mri_subject('flachkopf', tempdir), "Scaling failed"
spath = op.join(tempdir, 'flachkopf', 'bem', 'flachkopf-%s-src.fif')
assert op.exists(spath % 'ico-0'), "Source space ico-0 was not scaled"
assert os.path.isfile(os.path.join(tempdir, 'flachkopf', 'surf',
'lh.sphere.reg'))
vsrc_s = mne.read_source_spaces(spath % 'vol-50')
pt = np.array([0.12, 0.41, -0.22])
assert_array_almost_equal(
apply_trans(vsrc_s[0]['src_mri_t'], pt * np.array(scale)),
apply_trans(vsrc[0]['src_mri_t'], pt))
scale_labels('flachkopf', subjects_dir=tempdir)
# add distances to source space after hacking the properties to make
# it run *much* faster
src_dist = src.copy()
for s in src_dist:
s.update(rr=s['rr'][s['vertno']], nn=s['nn'][s['vertno']],
tris=s['use_tris'])
s.update(np=len(s['rr']), ntri=len(s['tris']),
vertno=np.arange(len(s['rr'])),
inuse=np.ones(len(s['rr']), int))
mne.add_source_space_distances(src_dist)
write_source_spaces(path % 'ico-0', src_dist, overwrite=True)
# scale with distances
os.remove(spath % 'ico-0')
scale_source_space('flachkopf', 'ico-0', subjects_dir=tempdir)
ssrc = mne.read_source_spaces(spath % 'ico-0')
assert ssrc[0]['dist'] is not None