def _run_interface(self, runtime):
sbj_id = self.inputs.sbj_id
sbj_dir = self.inputs.sbj_dir
raw_info = self.inputs.raw_info
aseg = self.inputs.aseg
is_blind = self.inputs.is_blind
spacing = self.inputs.spacing
aseg_labels = self.inputs.aseg_labels
self.fwd_filename = self._get_fwd_filename(raw_info, aseg,
spacing, is_blind)
# check if we have just created the fwd matrix
if not op.isfile(self.fwd_filename):
bem = create_bem_sol(sbj_dir, sbj_id) # bem solution
src = create_src_space(sbj_dir, sbj_id, spacing, is_blind) # src space
if aseg:
src = create_mixed_source_space(sbj_dir, sbj_id, spacing,
aseg_labels, src)
n = sum(src[i]['nuse'] for i in range(len(src)))
print('il src space contiene %d spaces e %d vertici'
% (len(src), n))
trans_fname = is_trans(raw_info)
# TODO: ha senso una funzione con un solo cmd?
compute_fwd_sol(raw_info, trans_fname, src, bem, self.fwd_filename)
else:
print '\n*** FWD file %s exists!!!\n' % self.fwd_filename
return runtime
def compute_LF_matrix(sbj_id, sbj_dir, raw_info, aseg, spacing, labels):
import os.path as op
import mne
from mne.bem import make_watershed_bem
from mne.report import Report
from nipype.utils.filemanip import split_filename as split_f
from neuropype_ephy.compute_fwd_problem import create_mixed_source_space
report = Report()
bem_dir = op.join(sbj_dir, sbj_id, 'bem')
surf_name = 'inner_skull.surf'
sbj_inner_skull_fname = op.join(bem_dir, sbj_id + '-' + surf_name)
inner_skull_fname = op.join(bem_dir, surf_name)
data_path, raw_fname, ext = split_f(raw_info['filename'])
if aseg:
fwd_filename = op.join(data_path, '%s-%s-aseg-fwd.fif'
% (raw_fname, spacing))
else:
fwd_filename = op.join(data_path, '%s-%s-fwd.fif'
% (raw_fname, spacing))
# check if we have just created the fwd matrix
if not op.isfile(fwd_filename):
# check if bem-sol was created, if not creates the bem sol using C MNE
bem_fname = op.join(bem_dir, '%s-5120-bem-sol.fif' % sbj_id)
model_fname = op.join(bem_dir, '%s-5120-bem.fif' % sbj_id)
if not op.isfile(bem_fname):
# chek if inner_skull surf exists, if not BEM computation is
# performed by MNE python functions mne.bem.make_watershed_bem
if not (op.isfile(sbj_inner_skull_fname) or
op.isfile(inner_skull_fname)):
print sbj_inner_skull_fname + '---> FILE NOT FOUND!!! ---> BEM is computed'
make_watershed_bem(sbj_id, sbj_dir, overwrite=True)
else:
print '*** inner skull surface exists!!!'
# Create a BEM model for a subject
surfaces = mne.make_bem_model(sbj_id, ico=4, conductivity=[0.3],
subjects_dir=sbj_dir)
# Write BEM surfaces to a fiff file
mne.write_bem_surfaces(model_fname, surfaces)
# Create a BEM solution using the linear collocation approach
bem = mne.make_bem_solution(surfaces)
mne.write_bem_solution(bem_fname, bem)
print '*** BEM solution file %s written ***' % bem_fname
# add BEM figures to a Report
report.add_bem_to_section(subject=sbj_id, subjects_dir=sbj_dir)
report_filename = op.join(bem_dir, "BEM_report.html")
print report_filename
report.save(report_filename, open_browser=False, overwrite=True)
else:
bem = bem_fname
print '*** BEM solution file %s exists!!!' % bem_fname
# check if source space exists, if not it creates using mne-python fun
# we have to create the cortical surface source space even when aseg is
# True
src_fname = op.join(bem_dir, '%s-%s-src.fif' % (sbj_id, spacing))
if not op.isfile(src_fname):
src = mne.setup_source_space(sbj_id, subjects_dir=sbj_dir,
fname=True,
spacing=spacing.replace('-', ''),
add_dist=False, overwrite=True,
n_jobs=2)
print '*** source space file %s written ***' % src_fname
else:
print '*** source space file %s exists!!!' % src_fname
src = mne.read_source_spaces(src_fname)
if aseg:
src = create_mixed_source_space(sbj_dir, sbj_id, spacing,
labels, src)
n = sum(src[i]['nuse'] for i in range(len(src)))
print('il src space contiene %d spaces e %d vertici' % (len(src), n))
# check if the co-registration file was created
# if not raise an runtime error
trans_fname = op.join(data_path, '%s-trans.fif' % raw_fname)
if not op.isfile(trans_fname):
raise RuntimeError('coregistration file %s NOT found!!!'
% trans_fname)
# if all is ok creates the fwd matrix
mne.make_forward_solution(raw_info, trans_fname, src, bem,
fwd_filename,
mindist=5.0, # ignore sources <= 0mm from inner skull
meg=True, eeg=False,
n_jobs=2,
overwrite=True)
else:
print '*** FWD file %s exists!!!' % fwd_filename
return fwd_filename
