def test_decimate_surface_vtk():
"""Test triangular surface decimation."""
points = np.array([[-0.00686118, -0.10369860, 0.02615170],
[-0.00713948, -0.10370162, 0.02614874],
[-0.00686208, -0.10368247, 0.02588313],
[-0.00713987, -0.10368724, 0.02587745]])
tris = np.array([[0, 1, 2], [1, 2, 3], [0, 3, 1], [1, 2, 0]])
for n_tri in [4, 3, 2]: # quadric decimation creates even numbered output.
_, this_tris = decimate_surface(points, tris, n_tri)
assert len(this_tris) == n_tri if not n_tri % 2 else 2
with pytest.raises(ValueError, match='exceeds number of original'):
decimate_surface(points, tris, len(tris) + 1)
nirvana = 5
tris = np.array([[0, 1, 2], [1, 2, 3], [0, 3, 1], [1, 2, nirvana]])
pytest.raises(ValueError, decimate_surface, points, tris, n_tri)
def test_decimate_surface():
"""Test triangular surface decimation."""
points = np.array([[-0.00686118, -0.10369860, 0.02615170],
[-0.00713948, -0.10370162, 0.02614874],
[-0.00686208, -0.10368247, 0.02588313],
[-0.00713987, -0.10368724, 0.02587745]])
tris = np.array([[0, 1, 2], [1, 2, 3], [0, 3, 1], [1, 2, 0]])
for n_tri in [4, 3, 2]: # quadric decimation creates even numbered output.
_, this_tris = decimate_surface(points, tris, n_tri)
assert_true(len(this_tris) == n_tri if not n_tri % 2 else 2)
nirvana = 5
tris = np.array([[0, 1, 2], [1, 2, 3], [0, 3, 1], [1, 2, nirvana]])
assert_raises(ValueError, decimate_surface, points, tris, n_tri)
def test_decimate_surface_sphere():
"""Test sphere mode of decimation."""
rr, tris = _tessellate_sphere(3)
assert len(rr) == 66
assert len(tris) == 128
for kind, n_tri in [('ico', 20), ('oct', 32)]:
with catch_logging() as log:
_, tris_new = decimate_surface(
rr, tris, n_tri, method='sphere', verbose=True)
log = log.getvalue()
assert 'Freesurfer' in log
assert kind in log
assert len(tris_new) == n_tri
def _run(subjects_dir, subject, force, overwrite, no_decimate, verbose=None):
this_env = copy.copy(os.environ)
subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
this_env['SUBJECTS_DIR'] = subjects_dir
this_env['SUBJECT'] = subject
if 'FREESURFER_HOME' not in this_env:
raise RuntimeError('The FreeSurfer environment needs to be set up '
'for this script')
incomplete = 'warn' if force else 'raise'
subj_path = op.join(subjects_dir, subject)
if not op.exists(subj_path):
raise RuntimeError('%s does not exist. Please check your subject '
'directory path.' % subj_path)
mri = 'T1.mgz' if op.exists(op.join(subj_path, 'mri', 'T1.mgz')) else 'T1'
logger.info('1. Creating a dense scalp tessellation with mkheadsurf...')
def check_seghead(surf_path=op.join(subj_path, 'surf')):
surf = None
for k in ['lh.seghead', 'lh.smseghead']:
this_surf = op.join(surf_path, k)
if op.exists(this_surf):
surf = this_surf
break
return surf
my_seghead = check_seghead()
if my_seghead is None:
run_subprocess(['mkheadsurf', '-subjid', subject, '-srcvol', mri],
env=this_env)
surf = check_seghead()
if surf is None:
raise RuntimeError('mkheadsurf did not produce the standard output '
'file.')
bem_dir = op.join(subjects_dir, subject, 'bem')
if not op.isdir(bem_dir):
os.mkdir(bem_dir)
dense_fname = op.join(bem_dir, '%s-head-dense.fif' % subject)
logger.info('2. Creating %s ...' % dense_fname)
_check_file(dense_fname, overwrite)
surf = mne.bem._surfaces_to_bem(
[surf], [mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1],
incomplete=incomplete)[0]
mne.write_bem_surfaces(dense_fname, surf)
levels = 'medium', 'sparse'
tris = [] if no_decimate else [30000, 2500]
if os.getenv('_MNE_TESTING_SCALP', 'false') == 'true':
tris = [len(surf['tris'])] # don't actually decimate
for ii, (n_tri, level) in enumerate(zip(tris, levels), 3):
logger.info('%i. Creating %s tessellation...' % (ii, level))
logger.info('%i.1 Decimating the dense tessellation...' % ii)
with ETSContext():
points, tris = mne.decimate_surface(points=surf['rr'],
triangles=surf['tris'],
n_triangles=n_tri)
dec_fname = dense_fname.replace('dense', level)
logger.info('%i.2 Creating %s' % (ii, dec_fname))
_check_file(dec_fname, overwrite)
dec_surf = mne.bem._surfaces_to_bem(
[dict(rr=points, tris=tris)],
[mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1], rescale=False,
incomplete=incomplete)
mne.write_bem_surfaces(dec_fname, dec_surf)
def _run(subjects_dir, subject, force, overwrite, no_decimate, verbose=None):
this_env = copy.copy(os.environ)
subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
this_env['SUBJECTS_DIR'] = subjects_dir
this_env['SUBJECT'] = subject
if 'FREESURFER_HOME' not in this_env:
raise RuntimeError('The FreeSurfer environment needs to be set up '
'for this script')
incomplete = 'warn' if force else 'raise'
subj_path = op.join(subjects_dir, subject)
if not op.exists(subj_path):
raise RuntimeError('%s does not exist. Please check your subject '
'directory path.' % subj_path)
mri = 'T1.mgz' if op.exists(op.join(subj_path, 'mri', 'T1.mgz')) else 'T1'
logger.info('1. Creating a dense scalp tessellation with mkheadsurf...')
def check_seghead(surf_path=op.join(subj_path, 'surf')):
surf = None
for k in ['lh.seghead', 'lh.smseghead']:
this_surf = op.join(surf_path, k)
if op.exists(this_surf):
surf = this_surf
break
return surf
my_seghead = check_seghead()
if my_seghead is None:
run_subprocess(['mkheadsurf', '-subjid', subject, '-srcvol', mri],
env=this_env)
surf = check_seghead()
if surf is None:
raise RuntimeError('mkheadsurf did not produce the standard output '
'file.')
dense_fname = '{0}/{1}/bem/{1}-head-dense.fif'.format(
subjects_dir, subject)
logger.info('2. Creating %s ...' % dense_fname)
_check_file(dense_fname, overwrite)
surf = mne.bem._surfaces_to_bem(
[surf], [mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1],
incomplete=incomplete)[0]
mne.write_bem_surfaces(dense_fname, surf)
levels = 'medium', 'sparse'
tris = [] if no_decimate else [30000, 2500]
if os.getenv('_MNE_TESTING_SCALP', 'false') == 'true':
tris = [len(surf['tris'])] # don't actually decimate
for ii, (n_tri, level) in enumerate(zip(tris, levels), 3):
logger.info('%i. Creating %s tessellation...' % (ii, level))
logger.info('%i.1 Decimating the dense tessellation...' % ii)
with ETSContext():
points, tris = mne.decimate_surface(points=surf['rr'],
triangles=surf['tris'],
n_triangles=n_tri)
dec_fname = dense_fname.replace('dense', level)
logger.info('%i.2 Creating %s' % (ii, dec_fname))
_check_file(dec_fname, overwrite)
dec_surf = mne.bem._surfaces_to_bem(
[dict(rr=points, tris=tris)],
[mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1],
rescale=False,
incomplete=incomplete)
mne.write_bem_surfaces(dec_fname, dec_surf)
def run(opts):
subject = opts.subject[0]
n_jobs = int(opts.n_jobs[0])
if opts.settingsjsondefaults:
json_settings_file = opts.settingsjsondefaults[0]
else:
json_settings_file = ("%s/processing_settings.json" %
os.path.dirname(os.path.realpath(__file__)))
with open(json_settings_file) as json_file:
processing_settings = json.load(json_file)
dwi_output_directory = processing_settings['dwi_output_directory']
recon_all_dir = processing_settings['recon_all_dir']
tvb_output_dir = processing_settings['tvb_output']
connectome_file_names = processing_settings['connectome_file_names']
parcellation = processing_settings["parcellation"]
if parcellation == "hcpmmp1":
borked_names = processing_settings["mrtrix_conversion"]["borked_names"]
fixed_names = processing_settings["mrtrix_conversion"]["fixed_names"]
label_info_file = processing_settings["mrtrix_conversion"]["label_info"]
parc_image = ("%s/%s/%s" %
(dwi_output_directory, subject,
processing_settings["default_file_names"]["parc_image"]))
tracts_path = ("%s/%s/%s" %
(dwi_output_directory, subject,
processing_settings["default_file_names"]["tracts"]))
weights_path = ("%s/%s/%s" %
(dwi_output_directory, subject,
processing_settings["default_file_names"]["weights"]))
tvb_output_path = "%s/sub-%s" % (tvb_output_dir, subject)
if not os.path.exists(tvb_output_path):
os.makedirs(tvb_output_path)
tvb_output = {}
tvb_output["EEG_Projection_mat"] = "%s/sub-%s_EEGProjection.mat" % (
tvb_output_path, subject)
tvb_output["EEG_Projection_npy"] = "%s/sub-%s_EEGProjection.npy" % (
tvb_output_path, subject)
tvb_output["EEG_Locations"] = "%s/sub-%s_EEG_Locations.txt" % (
tvb_output_path, subject)
tvb_output["region_mapping"] = "%s/sub-%s_region_mapping.txt" % (
tvb_output_path, subject)
tvb_output[
"region_mapping_hires"] = "%s/sub-%s_region_mapping_hires.txt" % (
tvb_output_path, subject)
# Fix labels and get centroids and area from parcellation image (voxel)
parc_img = nib.load(parc_image)
parc_data = parc_img.get_fdata()
lables, labels_sizes, label_mean_coordinates = parc_get_mean_coord(
parc_data, parc_img.affine, closest_value_voxel=True)
label_info = np.genfromtxt(label_info_file, dtype=str)
label_names = []
for label in lables:
label_names.append(label_info[:, 1][label_info[:,
0] == str(int(label))])
label_names = np.array(label_names).flatten()
if parcellation == "hcpmmp1":
for i, corr_label in enumerate(fixed_names):
if borked_names[i] in label_names:
print(borked_names[i] + "->" + corr_label)
label_names[label_names == borked_names[i]] = corr_label
region_names = label_names
cortical = np.zeros((len(region_names)))
cortical[:358] = 1
hemisphere = [1 if name[0] == "R" else 0 for name in region_names]
# process surfaces
pial_surf = [
'%s/%s/surf/lh.pial' % (recon_all_dir, subject),
'%s/%s/surf/rh.pial' % (recon_all_dir, subject)
]
if parcellation == "hcpmmp1":
annots = [
'%s/%s/label/lh.%s_HCP-MMP1.annot' %
(recon_all_dir, subject, subject),
'%s/%s/label/rh.%s_HCP-MMP1.annot' %
(recon_all_dir, subject, subject)
]
cortex_label = [
'%s/%s/label/lh.cortex.label' % (recon_all_dir, subject),
'%s/%s/label/rh.cortex.label' % (recon_all_dir, subject)
]
# make a surface output directory
output_surf_directory = "%s/surf" % tvb_output_path
if not os.path.exists(output_surf_directory):
os.makedirs(output_surf_directory)
v, f, s_info, region_map, surface_labels = subset_surface_by_cortex_label(
surfs=pial_surf,
annots=annots,
cortex_labels=cortex_label,
subset_labels=label_names,
output_surf_directory=output_surf_directory)
s_info_fs = s_info
#%%
# =============================================================================
# compute source space
# =============================================================================
# decimate surface
pial_dec = mne.decimate_surface(v, f, n_triangles=30000)
nib.freesurfer.io.write_geometry('%s/cortex_dec.srf' %
output_surf_directory,
pial_dec[0],
pial_dec[1],
volume_info=s_info_fs)
# complete decimated surface (add normals + other parameters)
pial_dict = {'rr': pial_dec[0] / 1000, 'tris': pial_dec[1]}
pial_complete = mne.surface.complete_surface_info(pial_dict)
# construct source space dictionary by hand
# use all point of the decimated surface as souce space
src = {
'rr': pial_complete['rr'],
'tris': pial_complete['tris'],
'ntri': pial_complete['ntri'],
'use_tris': pial_complete['tris'],
'np': pial_complete['np'],
'nn': pial_complete['nn'],
'inuse': np.ones(pial_complete['np']),
'nuse_tri': pial_complete['ntri'],
'nuse': pial_complete['np'],
'vertno': np.arange(0, pial_complete['np']),
'subject_his_id': subject,
'dist': None,
'dist_limit': None,
'nearest': None,
'type': 'surf',
'nearest_dist': None,
'pinfo': None,
'patch_inds': None,
'id':
101, # (FIFFV_MNE_SURF_LEFT_HEMI), # shouldn't matter, since we combined both hemispheres into one object
'coord_frame': 5
} # (FIFFV_COORD_MRI)}
src = mne.SourceSpaces([src])
#%%
# =============================================================================
# compute BEM model + EEG Locations
# =============================================================================
# following line seems to work only when calling this script via command line, when executed within spyder it gives "Command not found: mri_watershed!"
mne.bem.make_watershed_bem(subject=subject,
subjects_dir=recon_all_dir,
overwrite=True)
# This will always fail
# smooth and shrink the the inner skull surface a little bit. This prevents overlapping surface errors
v_is, f_is, s_info = nib.freesurfer.read_geometry(
"%s/%s/bem/watershed/%s_inner_skull_surface" %
(recon_all_dir, subject, subject),
read_metadata=True)
adj = create_adjac_vertex(v_is, f_is)
v_smooth, f = vectorized_surface_smooth(v_is,
f_is,
adj,
number_of_iter=10,
scalar=None,
lambda_w=0.5,
mode='laplacian',
weighted=True)
nib.freesurfer.io.write_geometry('%s/%s/bem/inner_skull.surf' %
(recon_all_dir, subject),
v_smooth,
f_is,
volume_info=s_info)
os.system(
"cp --remove-destination %s/%s/bem/watershed/%s_outer_skull_surface %s/%s/bem/outer_skull.surf"
% (recon_all_dir, subject, subject, recon_all_dir, subject))
os.system(
"cp --remove-destination %s/%s/bem/watershed/%s_outer_skin_surface %s/%s/bem/outer_skin.surf"
% (recon_all_dir, subject, subject, recon_all_dir, subject))
os.system(
"cp --remove-destination %s/%s/bem/watershed/%s_brain_surface %s/%s/bem/brain.surf"
% (recon_all_dir, subject, subject, recon_all_dir, subject))
conductivity = [0.3, 0.006, 0.3] # for three layers
try:
model = mne.make_bem_model(subject=subject,
ico=4,
conductivity=conductivity,
subjects_dir=recon_all_dir,
verbose=True)
except:
print(
"BEM model failed. Running laplacian smoothing on the inner surface (20 interations), and trying again."
)
v_is, f_is, s_info = nib.freesurfer.read_geometry(
"%s/%s/bem/watershed/%s_inner_skull_surface" %
(recon_all_dir, subject, subject),
read_metadata=True)
adj = create_adjac_vertex(v_is, f_is)
v_smooth, f = vectorized_surface_smooth(v_is,
f_is,
adj,
number_of_iter=20,
scalar=None,
lambda_w=0.5,
mode='laplacian',
weighted=True)
os.system("rm %s/%s/bem/inner_skull.surf" % (recon_all_dir, subject))
nib.freesurfer.io.write_geometry('%s/%s/bem/inner_skull.surf' %
(recon_all_dir, subject),
v_smooth,
f_is,
volume_info=s_info)
try:
model = mne.make_bem_model(subject=subject,
ico=4,
conductivity=conductivity,
subjects_dir=recon_all_dir,
verbose=True)
except:
print(
"BEM model failed. Running laplacian smoothing on the inner surface (40 interations), and trying again."
)
v_is, f_is, s_info = nib.freesurfer.read_geometry(
"%s/%s/bem/watershed/%s_inner_skull_surface" %
(recon_all_dir, subject, subject),
read_metadata=True)
adj = create_adjac_vertex(v_is, f_is)
v_smooth, f = vectorized_surface_smooth(v_is,
f_is,
adj,
number_of_iter=40,
scalar=None,
lambda_w=0.5,
mode='laplacian',
weighted=True)
os.system("rm %s/%s/bem/inner_skull.surf" %
(recon_all_dir, subject))
nib.freesurfer.io.write_geometry('%s/%s/bem/inner_skull.surf' %
(recon_all_dir, subject),
v_smooth,
f_is,
volume_info=s_info)
model = mne.make_bem_model(subject=subject,
ico=4,
conductivity=conductivity,
subjects_dir=recon_all_dir,
verbose=True)
bem = mne.make_bem_solution(model)
### GET AND ADJUST EEG LOCATIONS FROM DEFAULT CAP !!!!!!
# This may produce implausible results if not corrected.
# Default locations are used here to completely automize the pipeline and to not require manual input (e.g. setting the fiducials and fitting EEG locations.)
# read default cap
# mon = mne.channels.read_montage(kind="biosemi64", unit='auto', transform=True)
mon = mne.channels.make_standard_montage(kind="biosemi64")
#mon = mne.channels.read_montage(kind="easycap-M1", unit='auto', transform=False)
# create info object
ch_type = ["eeg" for i in range(len(mon.ch_names))]
# ch_type[-3:] = ["misc", "misc", "misc"] # needed for caps which include lpa, rpa and nza "channels" at the end
info = mne.create_info(ch_names=mon.ch_names,
sfreq=256,
ch_types=ch_type,
montage=mon)
# load head surface
try:
surf = mne.get_head_surf(subject=subject,
source="head",
subjects_dir=recon_all_dir)
except:
bem_dir = os.path.join(recon_all_dir, subject, 'bem')
ws_dir = os.path.join(recon_all_dir, subject, 'bem', 'watershed')
fname_head = os.path.join(bem_dir, subject + '-head.fif')
if os.path.isfile(fname_head):
os.remove(fname_head)
surf = _surfaces_to_bem(
[os.path.join(ws_dir, subject + '_outer_skin_surface')],
[FIFF.FIFFV_BEM_SURF_ID_HEAD],
sigmas=[1])
write_bem_surfaces(fname_head, surf)
surf = mne.get_head_surf(subject=subject,
source="head",
subjects_dir=recon_all_dir)
# project eeg locations onto surface and save into info
eeg_loc = np.array(
[info['chs'][i]['loc'][:3] for i in range(len(mon.ch_names))])
eegp_loc, eegp_nn = _project_onto_surface(eeg_loc,
surf,
project_rrs=True,
return_nn=True)[2:4]
for i in range(len(mon.ch_names)):
info['chs'][i]['loc'][:3] = eegp_loc[i, :]
#%%
# =============================================================================
# compute forward solution
# =============================================================================
fwd = mne.make_forward_solution(info,
trans=None,
src=src,
bem=bem,
meg=False,
eeg=True,
mindist=0.0,
n_jobs=n_jobs)
fwd_fixed = mne.convert_forward_solution(fwd,
surf_ori=True,
force_fixed=True,
use_cps=True)
leadfield = fwd_fixed['sol']['data']
# write leadfield to file
sio.savemat(tvb_output["EEG_Projection_mat"],
mdict={'ProjectionMatrix': leadfield})
np.save(tvb_output["EEG_Projection_npy"], leadfield)
#%%
# =============================================================================
# save files for TVB
# =============================================================================
# get region map for source space (ie. downsampled pial), via nearest neighbour interpolation
n_vert = pial_complete['np']
region_map_lores = np.zeros((n_vert))
vert_hires = v / 1000
vert_lores = pial_complete['rr']
# serach nearest neighbour
idx = spatial.KDTree(vert_hires).query(vert_lores)[1]
region_map_lores = region_map[idx]
np.savetxt(tvb_output["region_mapping"], region_map_lores, fmt="%i")
np.savetxt(tvb_output["region_mapping_hires"], region_map, fmt="%i")
# write low res labels
write_out_labels(surface_labels=surface_labels,
vert_region_map=region_map_lores,
surface_file='%s/cortex_dec.srf' % output_surf_directory,
output_directory='%s/decimated_labels_hcpmmp1' %
output_surf_directory,
parcellation="hcpmmp1",
subject=subject)
# make annot
os.system("cp %s/cortex_dec.srf %s/%s/surf/lh.cortex_dec.srf" %
(output_surf_directory, recon_all_dir, subject))
label_files_long = " --l ".join(
glob.glob("%s/decimated_labels_hcpmmp1/*label" %
output_surf_directory))
os.system(
"mris_label2annot --s %s --ctab %s --l %s --annot-path %s/hcpmmp1_dec.annot --surf cortex_dec.srf --h lh --sd %s"
% (subject, label_info_file, label_files_long, output_surf_directory,
recon_all_dir))
os.system("rm %s/%s/surf/lh.cortex_dec.srf" % (recon_all_dir, subject))
# write BEM surfaces in RAS
write_surf_tvb(in_surf_file='%s/%s/bem/brain.surf' %
(recon_all_dir, subject),
out_surf_file="%s/bem_brain.srf" % output_surf_directory,
s_info=s_info_fs)
write_surf_tvb(
in_surf_file='%s/%s/bem/inner_skull.surf' % (recon_all_dir, subject),
out_surf_file="%s/bem_inner_skull.srf" % output_surf_directory,
s_info=s_info_fs)
write_surf_tvb(
in_surf_file='%s/%s/bem/outer_skull.surf' % (recon_all_dir, subject),
out_surf_file="%s/bem_outer_skull.srf" % output_surf_directory,
s_info=s_info_fs)
write_surf_tvb(
in_surf_file='%s/%s/bem/outer_skin.surf' % (recon_all_dir, subject),
out_surf_file="%s/bem_outer_skin.srf" % output_surf_directory,
s_info=s_info_fs)
# [leave this alone for now.]
# write cortical surface (i.e. source space) to file
cort_surf_path = tvb_output_path + "/sub-" + subject + "_Cortex/"
if not os.path.exists(cort_surf_path):
os.makedirs(cort_surf_path)
# surface vertices are in ras-tkr coordinates used by freesurfer
# for them to allign with parc_image, use affine transform to bring them into ras-scanner
p = Popen(('mri_info --tkr2scanner ' + recon_all_dir + "/" + subject +
"/mri/aparc+aseg.mgz").split(),
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
output, err = p.communicate(
b"input data that is passed to subprocess' stdin")
affine_xfm = np.array(
[i.split() for i in str(output, "utf-8").splitlines()], dtype="float")
pial_vert_converted = affine_xfm.dot(
np.concatenate((pial_complete['rr'] * 1000,
np.ones((pial_complete['rr'].shape[0], 1))),
axis=1).T)[:3, :].T
# save
np.savetxt(cort_surf_path + "triangles.txt",
pial_complete['tris'],
fmt="%i")
np.savetxt(cort_surf_path + "vertices.txt",
pial_vert_converted,
fmt="%1.6f")
np.savetxt(cort_surf_path + "normals.txt",
pial_complete['nn'],
fmt="%1.6f")
# zip files
shutil.make_archive(cort_surf_path[:-1], 'zip', cort_surf_path)
print("Cortical surface zipped !")
shutil.rmtree(cort_surf_path)
# write BEM surfaces too file
names = [
"inner_skull_surface", "outer_skull_surface", "outer_skin_surface"
] # "brain_surface",
for name in names:
# make dir
bem_path = tvb_output_path + "/sub-" + subject + "_" + name + "/"
if not os.path.exists(bem_path):
os.makedirs(bem_path)
bem_surf = mne.read_surface(recon_all_dir + "/" + subject +
"/bem/watershed/" + subject + "_" + name)
bem_dict = {'rr': bem_surf[0], 'tris': bem_surf[1]}
bem_complete = mne.surface.complete_surface_info(bem_dict)
bem_vert_converted = affine_xfm.dot(
np.concatenate(
(bem_complete['rr'], np.ones(
(bem_complete['rr'].shape[0], 1))),
axis=1).T)[:3, :].T
# save files
np.savetxt(bem_path + "triangles.txt", bem_complete['tris'], fmt="%i")
np.savetxt(bem_path + "vertices.txt", bem_vert_converted, fmt="%1.6f")
np.savetxt(bem_path + "normals.txt", bem_complete['nn'], fmt="%1.6f")
# zip folder
shutil.make_archive(bem_path[:-1], 'zip', bem_path)
shutil.rmtree(bem_path)
print("BEM surfaces saved !")
# save eeg_locations, are in ras-tkr coordinates used by freesurfer
# for them to allign with parc_image, use affine transform to bring them into ras-scanner
eegp_loc_converted = affine_xfm.dot(
np.concatenate((eegp_loc * 1000, np.ones((eegp_loc.shape[0], 1))),
axis=1).T)[:3, :].T
f = open(tvb_output["EEG_Locations"], "w")
for i in range(len(eegp_loc_converted)):
f.write(mon.ch_names[i] + " " + "%.6f" % eegp_loc_converted[i, 0] +
" " + "%.6f" % eegp_loc_converted[i, 1] + " " +
"%.6f" % eegp_loc_converted[i, 2] + "\n")
f.close()
v_eeg, f_eeg = eeg_sensors_to_surface(eeg_coordinates=eegp_loc_converted,
unit_size=4,
generate=False)
nib.freesurfer.io.write_geometry(
'%s/eeg_biosemi64.srf' % (output_surf_directory), v_eeg, f_eeg)
print("EEG locations saved !")
# create and save connectome.zip
tvb_connectome_path = tvb_output_path + "/sub-" + subject + "_Connectome/"
if not os.path.exists(tvb_connectome_path):
os.makedirs(tvb_connectome_path)
# 1 weights, set diagonal to zero and make it symmetric
weights = np.genfromtxt(weights_path)
weights[np.diag_indices_from(weights)] = 0
i_lower = np.tril_indices_from(weights, -1)
weights[i_lower] = weights.T[i_lower]
n_regions = weights.shape[0]
np.savetxt(tvb_connectome_path + connectome_file_names['weights'],
weights,
delimiter="\t")
print("Weights saved !")
# 2 tracts, set diagonal to zero and make it symmetric
tracts = np.genfromtxt(tracts_path)
tracts[np.diag_indices_from(tracts)] = 0
i_lower = np.tril_indices_from(tracts, -1)
tracts[i_lower] = tracts.T[i_lower]
np.savetxt(tvb_connectome_path + connectome_file_names['tract_lengths'],
tracts,
delimiter="\t")
print("Tracts saved !")
#3. centers
with open(tvb_connectome_path + connectome_file_names['centres'],
"a") as roicentres:
for i, roi in enumerate(label_names):
roicentres.write(
"%s\t%1.6f\t%1.6f\t%1.6f\n" %
(roi, label_mean_coordinates[i, 0],
label_mean_coordinates[i, 1], label_mean_coordinates[i, 2]))
voxel_area = parc_img.header['pixdim'][1] * parc_img.header['pixdim'][
1] * parc_img.header['pixdim'][1]
print("Centers saved !")
# 4 orientation
# First get all Vertex-Normals corresponding to the Vertices of a Region
# Now compute mean Vector and Normalize the Vector
# for subcortical regions set [0,0,1]
orientation = np.zeros((n_regions, 3))
v_smooth, f, _ = nib.freesurfer.read_geometry('%s/cortex_smooth.srf' %
output_surf_directory,
read_metadata=True)
n = compute_normals(v_smooth, f)
for i in range(n_regions):
if cortical[i] == 1: # cortical regions
nn = n[region_map == int(i + 1), :]
orientation[i, :] = nn.mean(axis=0) / np.linalg.norm(
nn.mean(axis=0))
elif not cortical[i] == 1: # subcortical regions
# select normal vertices of a region, average and normalize them
orientation[i, :] = np.array([0, 0, 1])
np.savetxt(tvb_connectome_path +
connectome_file_names['average_orientations'],
orientation,
fmt="%f")
print("Orientations saved !")
# 5 area
area = get_surface_area(surface_file='%s/cortex_smooth.srf' %
output_surf_directory,
region_map=region_map,
verbose=True)
np.savetxt(tvb_connectome_path + connectome_file_names['areas'],
area,
fmt='%1.6f')
print("Area saved !")
# 6 cortical
# connectivity cortical/non-cortical region flags; text file containing one boolean value on each line
# (as 0 or 1 value) being 1 when corresponding region is cortical.
# due to error in configuring projection matrix in EEG, see monitors.py, class Projection, def config_for_sim
# this would need to get fixed, otherwise I don't know how to define the cortical variable or the lead field matrix
# therefor for now declare all regions as cortical
np.savetxt(tvb_connectome_path + connectome_file_names['cortical'],
cortical,
fmt="%i")
print("Cortical saved !")
# 7 hemisphere
# text file containing one boolean value on each line
# (as 0 or 1 value) being 1 when corresponding region is in the right hemisphere and 0 when in left hemisphere.
np.savetxt(tvb_connectome_path + connectome_file_names['hemispheres'],
hemisphere,
fmt="%i")
print("Hemisphere saved !")
# zip all files
shutil.make_archive(tvb_connectome_path[:-1], 'zip', tvb_connectome_path)
print("Connectome zipped !")
shutil.rmtree(tvb_connectome_path)
print("TVBconverter has finished !")
surf = check_seghead()
if surf is None:
print('mkheadsurf did not produce the standard output file.')
sys.exit(1)
fif = '{0}/{1}/bem/{1}-head-dense.fif'.format(subj_dir, subject)
print('2. Creating %s ...' % fif)
cmd = 'mne_surf2bem --surf %s --id 4 %s --fif %s' % (surf, force, fif)
my_run_cmd(cmd, 'Failed to create %s, see above' % fif)
levels = 'medium', 'sparse'
for ii, (n_tri, level) in enumerate(zip([30000, 2500], levels), 3):
my_surf = mne.read_bem_surfaces(fif)[0]
print('%i. Creating medium grade tessellation...' % ii)
print('%i.1 Decimating the dense tessellation...' % ii)
points, tris = mne.decimate_surface(points=my_surf['rr'],
triangles=my_surf['tris'],
n_triangles=n_tri)
out_fif = fif.replace('dense', level)
print('%i.2 Creating %s' % (ii, out_fif))
surf_fname = '/tmp/tmp-surf.surf'
# convert points to meters, make mne_analyze happy
mne.write_surface(surf_fname, points * 1e3, tris)
# XXX for some reason --check does not work here.
cmd = 'mne_surf2bem --surf %s --id 4 --force --fif %s'
cmd %= (surf_fname, out_fif)
my_run_cmd(cmd, 'Failed to create %s, see above' % out_fif)
os.remove(surf_fname)
sys.exit(0)
surf = check_seghead()
if surf is None:
print 'mkheadsurf did not produce the standard output file.'
sys.exit(1)
fif = '{0}/{1}/bem/{1}-head-dense.fif'.format(subj_dir, subject)
print '2. Creating %s ...' % fif
cmd = 'mne_surf2bem --surf %s --id 4 %s --fif %s' % (surf, force, fif)
my_run_cmd(cmd, 'Failed to create %s, see above' % fif)
levels = 'medium', 'sparse'
for ii, (n_tri, level) in enumerate(zip([30000, 2500], levels), 3):
my_surf = mne.read_bem_surfaces(fif)[0]
print '%i. Creating medium grade tessellation...' % ii
print '%i.1 Decimating the dense tessellation...' % ii
points, tris = mne.decimate_surface(points=my_surf['rr'],
triangles=my_surf['tris'],
n_triangles=n_tri)
out_fif = fif.replace('dense', level)
print '%i.2 Creating %s' % (ii, out_fif)
surf_fname = '/tmp/tmp-surf.surf'
# convert points to meters, make mne_analyze happy
mne.write_surface(surf_fname, points * 1e3, tris)
# XXX for some reason --check does not work here.
cmd = 'mne_surf2bem --surf %s --id 4 --force --fif %s'
cmd %= (surf_fname, out_fif)
my_run_cmd(cmd, 'Failed to create %s, see above' % out_fif)
os.remove(surf_fname)
sys.exit(0)
def _run(subjects_dir, subject, force, overwrite, verbose=None):
this_env = copy.copy(os.environ)
this_env['SUBJECTS_DIR'] = subjects_dir
this_env['SUBJECT'] = subject
if 'SUBJECTS_DIR' not in this_env:
raise RuntimeError('The environment variable SUBJECTS_DIR should '
'be set')
if not op.isdir(subjects_dir):
raise RuntimeError('subjects directory %s not found, specify using '
'the environment variable SUBJECTS_DIR or '
'the command line option --subjects-dir')
if 'MNE_ROOT' not in this_env:
raise RuntimeError('MNE_ROOT environment variable is not set')
if 'FREESURFER_HOME' not in this_env:
raise RuntimeError('The FreeSurfer environment needs to be set up '
'for this script')
force = '--force' if force else '--check'
subj_path = op.join(subjects_dir, subject)
if not op.exists(subj_path):
raise RuntimeError('%s does not exits. Please check your subject '
'directory path.' % subj_path)
if op.exists(op.join(subj_path, 'mri', 'T1.mgz')):
mri = 'T1.mgz'
else:
mri = 'T1'
logger.info('1. Creating a dense scalp tessellation with mkheadsurf...')
def check_seghead(surf_path=op.join(subj_path, 'surf')):
for k in ['/lh.seghead', '/lh.smseghead']:
surf = surf_path + k if op.exists(surf_path + k) else None
if surf is not None:
break
return surf
my_seghead = check_seghead()
if my_seghead is None:
run_subprocess(['mkheadsurf', '-subjid', subject, '-srcvol', mri],
env=this_env)
surf = check_seghead()
if surf is None:
raise RuntimeError('mkheadsurf did not produce the standard output '
'file.')
dense_fname = '{0}/{1}/bem/{1}-head-dense.fif'.format(subjects_dir,
subject)
logger.info('2. Creating %s ...' % dense_fname)
_check_file(dense_fname, overwrite)
run_subprocess(['mne_surf2bem', '--surf', surf, '--id', '4', force,
'--fif', dense_fname], env=this_env)
levels = 'medium', 'sparse'
my_surf = mne.read_bem_surfaces(dense_fname)[0]
tris = [30000, 2500]
if os.getenv('_MNE_TESTING_SCALP', 'false') == 'true':
tris = [len(my_surf['tris'])] # don't actually decimate
for ii, (n_tri, level) in enumerate(zip(tris, levels), 3):
logger.info('%i. Creating %s tessellation...' % (ii, level))
logger.info('%i.1 Decimating the dense tessellation...' % ii)
points, tris = mne.decimate_surface(points=my_surf['rr'],
triangles=my_surf['tris'],
n_triangles=n_tri)
other_fname = dense_fname.replace('dense', level)
logger.info('%i.2 Creating %s' % (ii, other_fname))
_check_file(other_fname, overwrite)
tempdir = _TempDir()
surf_fname = tempdir + '/tmp-surf.surf'
# convert points to meters, make mne_analyze happy
mne.write_surface(surf_fname, points * 1e3, tris)
# XXX for some reason --check does not work here.
try:
run_subprocess(['mne_surf2bem', '--surf', surf_fname, '--id', '4',
'--force', '--fif', other_fname], env=this_env)
finally:
del tempdir
hemisphere = np.zeros((n_regions))
index_hemisphere = np.unique(
gii_r.darrays[0].data
)[1:] - 1 # skip the 0 for "subcortical" vertices and remove by 1 because region start counting at 0
hemisphere[index_hemisphere] = 1
# all labels appearing in region_map correspond to cortical regions
cortical = np.zeros((n_regions))
cortical[np.unique(region_map)] = 1
#%%
# =============================================================================
# compute source space
# =============================================================================
# decimate surface
pial_dec = mne.decimate_surface(pial_vertices, pial_tris, n_triangles=30000)
# complete decimated surface (add normals + other parameters)
pial_dict = {'rr': pial_dec[0], 'tris': pial_dec[1]}
pial_complete = mne.surface.complete_surface_info(pial_dict)
# construct source space dictionary by hand
# use all point of the decimated surface as souce space
src = {
'rr': pial_complete['rr'],
'tris': pial_complete['tris'],
'ntri': pial_complete['ntri'],
'use_tris': pial_complete['tris'],
'np': pial_complete['np'],
'nn': pial_complete['nn'],
'inuse': np.ones(pial_complete['np']),
print("Use the --overwrite option to replace exisiting surfaces.")
sys.exit()
surf = check_seghead()
if surf is None:
print("mkheadsurf did not produce the standard output file.")
sys.exit(1)
fif = "{0}/{1}/bem/{1}-head-dense.fif".format(subj_dir, subject)
print("2. Creating %s ..." % fif)
cmd = "mne_surf2bem --surf %s --id 4 %s --fif %s" % (surf, force, fif)
my_run_cmd(cmd, "Failed to create %s, see above" % fif)
levels = "medium", "sparse"
for ii, (n_tri, level) in enumerate(zip([30000, 2500], levels), 3):
my_surf = mne.read_bem_surfaces(fif)[0]
print("%i. Creating medium grade tessellation..." % ii)
print("%i.1 Decimating the dense tessellation..." % ii)
points, tris = mne.decimate_surface(points=my_surf["rr"], triangles=my_surf["tris"], n_triangles=n_tri)
out_fif = fif.replace("dense", level)
print("%i.2 Creating %s" % (ii, out_fif))
surf_fname = "/tmp/tmp-surf.surf"
# convert points to meters, make mne_analyze happy
mne.write_surface(surf_fname, points * 1e3, tris)
# XXX for some reason --check does not work here.
cmd = "mne_surf2bem --surf %s --id 4 --force --fif %s"
cmd %= (surf_fname, out_fif)
my_run_cmd(cmd, "Failed to create %s, see above" % out_fif)
os.remove(surf_fname)
sys.exit(0)