bems_brainsuite_fsl.py

gistfile1.txt

# convert MGZ->NII
#
# $ bet T1.nii stripped.nii.gz -n -A -v -e
#
import numpy as np
import nibabel as nib
import pyvista as pv
import mne

img = nib.load('T1.mgz')
xfm = img.header.get_vox2ras_tkr()
bet_map = dict(
    brain='',
    outer_skin='_outskin',
    inner_skull='_inskull',
    outer_skull='_outskull',
)
for fs_name, bet_name in bet_map.items():
    continue # XXX
    mesh = pv.read(f'stripped{bet_name}_mesh.vtk')
    rr = np.array(mesh.points)
    rr = mne.transforms.apply_trans(xfm, rr)
    tris = mesh.faces.reshape(5120, 4)[:, 1:]
    mne.write_surface(f'bet_{fs_name}.surf', rr, tris)

# Nearly instantaneous but not great:
#
# $ bse -i T1.nii --mask T1_brain.nii
# $ skullfinder -i T1.nii -m T1_brain.nii -o T1_labeled.nii -s subject --finalOpening
#
bs_map = dict(
    brain='brain',
    inner_skull='inner_skull',
    # These are swapped, which is weird
    outer_skull='scalp',
    outer_skin='outer_skull',
)
ras_xfm = np.array(
    [[-1, 0, 0, 256], [0, 0, -1, 256], [0, 1, 0, 0], [0, 0, 0, 1]])
xfm = img.header.get_vox2ras_tkr() @ ras_xfm
for fs_name, bs_name in bs_map.items():
    with open(f'subject.{bs_name}.dfs', 'rb') as fid:
        header_type = fid.read(12).decode().split('\x00')[0]
        assert header_type in ('DFS_LE v2.0', 'DFS_BE v2.0'), repr(header_type)
        bo = dict(L='<', B='>')[header_type[4]]
        header_size, meta_off, subj_off, n_tris, n_verts = \
            np.fromfile(fid, f'{bo}i4', 5)
        fid.seek(header_size + meta_off + subj_off)
        tris = np.fromfile(fid, f'{bo}i4', 3 * n_tris).reshape(n_tris, 3)
        rr = np.fromfile(fid, f'{bo}f4', 3 * n_verts).reshape(n_verts, 3)
    rr = mne.transforms.apply_trans(xfm, rr)
    mne.write_surface(f'bs_{fs_name}.surf', rr, tris, overwrite=True)