supplement.py

import os.path as op
import mne
from mne.io.constants import FIFF

subjects = ('ANTS3-0Months3T', 'ANTS6-0Months3T', 'ANTS12-0Months3T')
subjects_dir = '.'

for subject in subjects:
    subject_dir = op.join(subjects_dir, subject)
    assert op.isdir(subject_dir), subject_dir
    bem_dir = op.join(subjects_dir, subject, 'bem')
    assert op.isdir(bem_dir), bem_dir

    # Fiducials
    fname = op.join(bem_dir, f'{subject}-fiducials.fif')
    if not op.isfile(fname):
        dig = mne.channels.read_dig_fif(
            op.join(subject_dir, '10-20-montage.fif')).dig[:3]
        for d, want in zip(dig, (FIFF.FIFFV_POINT_LPA,
                                 FIFF.FIFFV_POINT_NASION,
                                 FIFF.FIFFV_POINT_RPA)):
            assert d['kind'] == FIFF.FIFFV_POINT_CARDINAL
            assert d['coord_frame'] == FIFF.FIFFV_COORD_HEAD  # XXX WRONG
            d['coord_frame'] = FIFF.FIFFV_COORD_MRI
            assert d['ident'] == want
        mne.io.write_fiducials(fname, dig, FIFF.FIFFV_COORD_MRI, verbose=True)

    # -head.fif
    fname = op.join(bem_dir, f'{subject}-head.fif')
    if not op.isfile(fname):
        rr, tris = mne.read_surface(op.join(bem_dir, 'outer_skin_large.surf'))
        rr /= 1000.  # mm->m
        dec_surf = mne.bem._surfaces_to_bem(
            [dict(rr=rr, tris=tris)],
            [mne.io.constants.FIFF.FIFFV_BEM_SURF_ID_HEAD], [1], rescale=False,
            incomplete='raise', extra='')
        mne.write_bem_surfaces(fname, dec_surf)


    # -vol-5-src.fif
    fname = op.join(bem_dir, f'{subject}-vol-5-src.fif')
    fname_inner_skull = op.join(bem_dir, 'inner_skull.surf')
    if not op.isfile(fname):
        mne.write_source_spaces(fname, mne.setup_volume_source_space(
            subject, pos=5, subjects_dir=subjects_dir,
            surface=fname_inner_skull, verbose=True))

    # -oct-6-src.fif
    fname = op.join(bem_dir, f'{subject}-oct-6-src.fif')
    if not op.isfile(fname):
        mne.write_source_spaces(fname, mne.setup_source_space(
            subject, spacing='oct6', subjects_dir=subjects_dir, verbose=True))

    # -bem.fif and bem-sol.fif
    fname_bem = op.join(bem_dir, f'{subject}-5120-5120-5120-bem.fif')
    if not op.isfile(fname_bem):
        mne.write_bem_surfaces(fname_bem, mne.make_bem_model(
            subject, subjects_dir=subjects_dir,
            # ico=None,  # XXX 5 should be fine here
            verbose=True))
    fname_bem_sol = fname_bem[:-4] + '-sol.fif'
    if not op.isfile(fname_bem_sol):
        mne.write_bem_solution(fname_bem_sol, mne.make_bem_solution(
            mne.read_bem_surfaces(fname_bem), verbose=True))