def test_make_morph_maps():
"""Test reading and creating morph maps
"""
# make a new fake subjects_dir
tempdir = _TempDir()
for subject in ('sample', 'sample_ds', 'fsaverage_ds'):
os.mkdir(op.join(tempdir, subject))
os.mkdir(op.join(tempdir, subject, 'surf'))
for hemi in ['lh', 'rh']:
args = [subject, 'surf', hemi + '.sphere.reg']
copyfile(op.join(subjects_dir, *args),
op.join(tempdir, *args))
# this should trigger the creation of morph-maps dir and create the map
mmap = read_morph_map('fsaverage_ds', 'sample_ds', tempdir)
mmap2 = read_morph_map('fsaverage_ds', 'sample_ds', subjects_dir)
assert_equal(len(mmap), len(mmap2))
for m1, m2 in zip(mmap, mmap2):
# deal with sparse matrix stuff
diff = (m1 - m2).data
assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)
# This will also trigger creation, but it's trivial
mmap = read_morph_map('sample', 'sample', subjects_dir=tempdir)
for mm in mmap:
assert_true((mm - sparse.eye(mm.shape[0], mm.shape[0])).sum() == 0)
def test_make_morph_maps():
"""Test reading and creating morph maps."""
# make a new fake subjects_dir
tempdir = _TempDir()
for subject in ('sample', 'sample_ds', 'fsaverage_ds'):
os.mkdir(op.join(tempdir, subject))
os.mkdir(op.join(tempdir, subject, 'surf'))
regs = ('reg', 'left_right') if subject == 'fsaverage_ds' else ('reg',)
for hemi in ['lh', 'rh']:
for reg in regs:
args = [subject, 'surf', hemi + '.sphere.' + reg]
copyfile(op.join(subjects_dir, *args),
op.join(tempdir, *args))
for subject_from, subject_to, xhemi in (
('fsaverage_ds', 'sample_ds', False),
('fsaverage_ds', 'fsaverage_ds', True)):
# trigger the creation of morph-maps dir and create the map
with warnings.catch_warnings(record=True):
mmap = read_morph_map(subject_from, subject_to, tempdir,
xhemi=xhemi)
mmap2 = read_morph_map(subject_from, subject_to, subjects_dir,
xhemi=xhemi)
assert_equal(len(mmap), len(mmap2))
for m1, m2 in zip(mmap, mmap2):
# deal with sparse matrix stuff
diff = (m1 - m2).data
assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)
# This will also trigger creation, but it's trivial
with warnings.catch_warnings(record=True):
mmap = read_morph_map('sample', 'sample', subjects_dir=tempdir)
for mm in mmap:
assert (mm - sparse.eye(mm.shape[0], mm.shape[0])).sum() == 0
def test_make_morph_maps():
"""Test reading and creating morph maps."""
# make a new fake subjects_dir
tempdir = _TempDir()
for subject in ('sample', 'sample_ds', 'fsaverage_ds'):
os.mkdir(op.join(tempdir, subject))
os.mkdir(op.join(tempdir, subject, 'surf'))
regs = ('reg', 'left_right') if subject == 'fsaverage_ds' else ('reg',)
for hemi in ['lh', 'rh']:
for reg in regs:
args = [subject, 'surf', hemi + '.sphere.' + reg]
copyfile(op.join(subjects_dir, *args),
op.join(tempdir, *args))
for subject_from, subject_to, xhemi in (
('fsaverage_ds', 'sample_ds', False),
('fsaverage_ds', 'fsaverage_ds', True)):
# trigger the creation of morph-maps dir and create the map
with warnings.catch_warnings(record=True):
mmap = read_morph_map(subject_from, subject_to, tempdir,
xhemi=xhemi)
mmap2 = read_morph_map(subject_from, subject_to, subjects_dir,
xhemi=xhemi)
assert_equal(len(mmap), len(mmap2))
for m1, m2 in zip(mmap, mmap2):
# deal with sparse matrix stuff
diff = (m1 - m2).data
assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)
# This will also trigger creation, but it's trivial
with warnings.catch_warnings(record=True):
mmap = read_morph_map('sample', 'sample', subjects_dir=tempdir)
for mm in mmap:
assert_true((mm - sparse.eye(mm.shape[0], mm.shape[0])).sum() == 0)
def test_make_morph_maps():
"""Test reading and creating morph maps
"""
mmap = read_morph_map('fsaverage', 'sample', subjects_dir=subjects_dir)
mmap2 = _make_morph_map('fsaverage', 'sample', subjects_dir=subjects_dir)
assert_equal(len(mmap), len(mmap2))
for m1, m2 in zip(mmap, mmap2):
# deal with sparse matrix stuff
diff = (m1 - m2).data
assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)
def test_make_morph_maps():
"""Test reading and creating morph maps
"""
mmap = read_morph_map('fsaverage', 'sample', subjects_dir=subjects_dir)
mmap2 = _make_morph_map('fsaverage', 'sample', subjects_dir=subjects_dir)
assert_equal(len(mmap), len(mmap2))
for m1, m2 in zip(mmap, mmap2):
# deal with sparse matrix stuff
diff = (m1 - m2).data
assert_allclose(diff, np.zeros_like(diff), atol=1e-3, rtol=0)
def mne_anatomy(subject, subjects_dir, overwrite=False):
import warnings
# Checks that watershed hasn't already been run
for fname in [
'fiducials.fif', 'head.fif', 'head-dense.fif', 'head-medium.fif',
'head-sparse.fif', 'inner_skull.surf', 'oct-6-src.fif'
]:
fname = op.join(subjects_dir, subject, 'bem', subject + '-' + fname)
if (not overwrite) and op.exists(fname):
raise IOError('%s already exists. Set overwrite=True.' % fname)
return
# Create BEM surfaces
make_watershed_bem(subject=subject,
subjects_dir=subjects_dir,
overwrite=True,
volume='T1',
atlas=False,
gcaatlas=False,
preflood=None)
# Copy files outside watershed folder in case of bad manipulation
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from_file = op.join(subjects_dir, subject, 'bem',
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(subjects_dir, subject, 'bem', '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
# Update file
try:
os.symlink(from_file, to_file)
except OSError as e:
# if disk is not NTFS, symoblic link isn't possible
if e.strerror == 'Operation not permitted':
from shutil import copyfile
copyfile(from_file, to_file)
# Make scalp surfaces
make_scalp_surfaces(subjects_dir,
subject,
force='store_true',
overwrite='store_true',
verbose=None)
# Setup source space
src_fname = op.join(subjects_dir, subject, 'bem',
subject + 'oct-6-src.fif')
if not op.isfile(src_fname):
from mne import setup_source_space
setup_source_space(subject,
subjects_dir=subjects_dir,
fname=src_fname,
spacing='oct6',
surface='white',
overwrite=True,
add_dist=True,
n_jobs=-1,
verbose=None)
# Prepare BEM model
bem_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem.fif')
bem_sol_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem-sol.fif')
if not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
surfs = make_bem_model(subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
# Make morphs to fsaverage if has it
try:
read_morph_map(subject, 'fsaverage', subjects_dir=subjects_dir)
except IOError as e:
if 'No such file or directory' in e.strerror:
warnings.warn(e.strerror)
def mne_anatomy(subject, subjects_dir, overwrite=False):
import warnings
# Checks that watershed hasn't already been run
for fname in ['fiducials.fif', 'head.fif', 'head-dense.fif',
'head-medium.fif', 'head-sparse.fif', 'inner_skull.surf',
'oct-6-src.fif']:
fname = op.join(subjects_dir, subject, 'bem', subject + '-' + fname)
if (not overwrite) and op.exists(fname):
raise IOError('%s already exists. Set overwrite=True.' % fname)
return
# Create BEM surfaces
make_watershed_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=True, volume='T1', atlas=False,
gcaatlas=False, preflood=None)
# Copy files outside watershed folder in case of bad manipulation
for surface in ['inner_skull', 'outer_skull', 'outer_skin']:
from_file = op.join(subjects_dir, subject, 'bem',
'watershed/%s_%s_surface' % (subject, surface))
to_file = op.join(subjects_dir, subject, 'bem', '%s.surf' % surface)
if op.exists(to_file):
os.remove(to_file)
# Update file
try:
os.symlink(from_file, to_file)
except OSError as e:
# if disk is not NTFS, symoblic link isn't possible
if e.strerror == 'Operation not permitted':
from shutil import copyfile
copyfile(from_file, to_file)
# Make scalp surfaces
make_scalp_surfaces(subjects_dir, subject, force='store_true',
overwrite='store_true', verbose=None)
# Setup source space
src_fname = op.join(subjects_dir, subject, 'bem',
subject + 'oct-6-src.fif')
if not op.isfile(src_fname):
from mne import setup_source_space
setup_source_space(subject, subjects_dir=subjects_dir, fname=src_fname,
spacing='oct6', surface='white', overwrite=True,
add_dist=True, n_jobs=-1, verbose=None)
# Prepare BEM model
bem_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem.fif')
bem_sol_fname = op.join(subjects_dir, subject, 'bem',
subject + '-5120-bem-sol.fif')
if not op.exists(bem_sol_fname):
from mne.bem import (make_bem_model, write_bem_surfaces,
make_bem_solution, write_bem_solution)
surfs = make_bem_model(subject, subjects_dir=subjects_dir)
write_bem_surfaces(fname=bem_fname, surfs=surfs)
bem = make_bem_solution(surfs)
write_bem_solution(fname=bem_sol_fname, bem=bem)
# Make morphs to fsaverage if has it
try:
read_morph_map(subject, 'fsaverage', subjects_dir=subjects_dir)
except IOError as e:
if 'No such file or directory' in e.strerror:
warnings.warn(e.strerror)