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#!/usr/bin/env python
# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# simplified bsd-3 license
"""
Create high-resolution head surfaces for coordinate alignment.
example usage: mne make_scalp_surfaces --overwrite --subject sample
"""
from __future__ import print_function
import os
import os.path as op
import sys
import mne
if __name__ == '__main__':
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('-o', '--overwrite', dest='overwrite',
action='store_true',
help='Overwrite previously computed surface')
parser.add_option('-s', '--subject', dest='subject',
help='The name of the subject', type='str')
parser.add_option('-f', '--force', dest='force', action='store_true',
help='Force transformation of surface into bem.')
parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
help='Print the debug messages.')
options, args = parser.parse_args()
env = os.environ
subject = vars(options).get('subject', env.get('SUBJECT'))
if subject is None:
parser.print_help()
sys.exit(1)
overwrite = options.overwrite
verbose = options.verbose
force = '--force' if options.force else '--check'
from mne.commands.utils import get_status_output
def my_run_cmd(cmd, err_msg):
sig, out, error = get_status_output(cmd)
if verbose:
print(out, error)
if sig != 0:
print(err_msg)
sys.exit(1)
if not 'SUBJECTS_DIR' in env:
print('The environment variable SUBJECTS_DIR should be set')
sys.exit(1)
if not op.isabs(env['SUBJECTS_DIR']):
env['SUBJECTS_DIR'] = op.abspath(env['SUBJECTS_DIR'])
subj_dir = env['SUBJECTS_DIR']
if not 'MNE_ROOT' in env:
print('MNE_ROOT environment variable is not set')
sys.exit(1)
if not 'FREESURFER_HOME' in env:
print('The FreeSurfer environment needs to be set up for this script')
sys.exit(1)
subj_path = op.join(subj_dir, subject)
if not op.exists(subj_path):
print(('%s does not exits. Please check your subject directory '
'path.' % subj_path))
sys.exit(1)
if op.exists(op.join(subj_path, 'mri', 'T1.mgz')):
mri = 'T1.mgz'
else:
mri = 'T1'
print('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:
cmd = 'mkheadsurf -subjid %s -srcvol %s >/dev/null' % (subject, mri)
my_run_cmd(cmd, 'mkheadsurf failed')
else:
print('%s/surf/%s already there' % (subj_path, my_seghead))
if not overwrite:
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)
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