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