def get_aligned_artifacts(info=None, trans=None, subject=None, subjects_dir=None,
coord_frame='mri', head_surf=None):
head_mri_t, _ = _get_trans(trans, 'head', 'mri')
dev_head_t, _ = _get_trans(info['dev_head_t'], 'meg', 'head')
head_trans = head_mri_t
mri_trans = Transform('mri', 'mri')
mri_fiducials = mne.coreg.get_mni_fiducials(subject, subjects_dir)
fid_loc = _fiducial_coords(mri_fiducials, FIFF.FIFFV_COORD_MRI)
fid_loc = apply_trans(mri_trans, fid_loc)
fid_loc = pd.DataFrame(fid_loc, index=[fid["ident"]._name.split("_")[-1] for fid in mri_fiducials],
columns=["x", "y", "z"])
if head_surf is None:
subject_dir = Path(get_subjects_dir(subjects_dir, raise_error=True)) / subject
fname = subject_dir / 'bem' / 'sample-head.fif'
head_surf = read_bem_surfaces(fname)[0]
head_surf = transform_surface_to(head_surf, coord_frame, [mri_trans, head_trans], copy=True)
eeg_picks = mne.pick_types(info, meg=False, eeg=True, ref_meg=False)
eeg_loc = np.array([info['chs'][k]['loc'][:3] for k in eeg_picks])
eeg_loc = apply_trans(head_trans, eeg_loc)
eegp_loc = _project_onto_surface(eeg_loc, head_surf, project_rrs=True, return_nn=True)[2]
eegp_loc = pd.DataFrame(eegp_loc, index=[ch["ch_name"] for ch in info['chs']], columns=["x", "y", "z"])
return eegp_loc, fid_loc, head_surf
def make_coordsys_eeg_json(dir_coordsys_eeg_json, fname_epo, subj_id, task):
import os.path as op
import json
from mne.viz._3d import _fiducial_coords
import mne
epo = mne.read_epochs(fname_epo)
coordys = {
"EEGCoordinateSystem": "T1w",
"EEGCoordinateUnits": "m",
"AnatomicalLandmarkCoordinates": {}
}
fids = _fiducial_coords(epo.info['dig'])
coordys['AnatomicalLandmarkCoordinates']['LPA'] = [
float(n) for n in fids[0]
] # has to be float and not np.float to be able to json dump
coordys['AnatomicalLandmarkCoordinates']['NAS'] = [
float(n) for n in fids[1]
]
coordys['AnatomicalLandmarkCoordinates']['RPA'] = [
float(n) for n in fids[2]
]
coordys['AnatomicalLandmarkCoordinateSystem'] = "T1w"
coordys['IntendedFor'] = '/%s/anat/%s_T1.nii' % (subj_id, subj_id)
coordys['AnatomicalLandmarkCoordinateUnits'] = "m"
fname_save = op.join(dir_coordsys_eeg_json,
'%s_task-%s_coordsystem.json' % (subj_id, task))
with open(fname_save, 'w') as f:
json.dump(coordys, f, indent=4)
def test_fiducials():
"""Test handling of fiducials."""
# Eventually the code used here should be unified with montage.py, but for
# now it uses code in odd places
for fname in (fif_fname, ctf_fif_fname):
fids, coord_frame = read_fiducials(fname)
points = _fiducial_coords(fids, coord_frame)
assert points.shape == (3, 3)
# Fids
assert_allclose(points[:, 2], 0., atol=1e-6)
assert_allclose(points[::2, 1], 0., atol=1e-6)
assert points[2, 0] > 0 # RPA
assert points[0, 0] < 0 # LPA
# Nasion
assert_allclose(points[1, 0], 0., atol=1e-6)
assert points[1, 1] > 0
def test_fiducials():
"""Test handling of fiducials."""
# Eventually the code used here should be unified with montage.py, but for
# now it uses code in odd places
for fname in (fif_fname, ctf_fif_fname):
fids, coord_frame = read_fiducials(fname)
points = _fiducial_coords(fids, coord_frame)
assert points.shape == (3, 3)
# Fids
assert_allclose(points[:, 2], 0., atol=1e-6)
assert_allclose(points[::2, 1], 0., atol=1e-6)
assert points[2, 0] > 0 # RPA
assert points[0, 0] < 0 # LPA
# Nasion
assert_allclose(points[1, 0], 0., atol=1e-6)
assert points[1, 1] > 0
