def setup_forward_model(subjects_list, subjects_dir=None, mne_root=None):
'''Setup forward model.
Setting up of the forward model - computes Boundary Element Model geometry files.
Creates the -bem.fif, .surf and -bem-sol.fif files
If skin and/or skull surfaces intersect causing errors, it is possible to try and
shift the inner skull surface inwards or the our skin surface outwards.
The corresponding command to use would be:
mne_setup_forward_model --subject subj --ico 4 --surf --outershift 10 --scalpshift 10
mne_setup_forward_model --subject subj --ico 4 --surf --innershift 10
'''
subjects_dir = check_env_variables(subjects_dir, key='SUBJECTS_DIR')
mne_root = check_env_variables(mne_root, key='MNE_ROOT')
mne_bin_path = os.path.join(mne_root, 'bin', '')
for subj in subjects_list:
print 'Setting up BEM boundary model for %s' % (subj)
# call([mne_bin_path + 'mne_setup_forward_model', '--subject', subj, '--ico', '4',
# '--surf', '--outershift', '10', '--scalpshift', '10'])
retcode = call([mne_bin_path + 'mne_setup_forward_model', '--subject', subj, '--ico', '4', '--surf'])
if retcode != 0:
retcode_error('mne_setup_forward_model', subj)
continue
print ('Next step is to align the MRI and MEG coordinate frames using' \
'mne.coregistration.gui() resulting in a -trans.fif file.')
def make_subject_dirs(subjects_list, freesurfer_home=None):
''' Python wrapper for mksubjdirs.'''
freesurfer_home = check_env_variables(freesurfer_home, key='FREESURFER_HOME')
freesurfer_bin = os.path.join(freesurfer_home, 'bin', '')
for subj in subjects_list:
print 'Making freeesurfer directories %s' % (subj)
# Makes subject directories and dir structures
retcode = call([freesurfer_bin + 'mksubjdirs', subj])
if retcode != 0:
retcode_error('mksubjdirs', subj)
continue
def setup_mri_surfaces(subjects_list, subjects_dir=None, mne_root=None,
freesurfer_home=None, mri_convert=False,
mri_extn='mri/orig/001.mgz', nii_extn='_1x1x1mm.nii'):
'''Function to perform complete surface reconstruction and related operations.
The following commands are executed:
mksubjdirs, mri_convert, recon-all, mne_setup_mri, mne.setup_source_space,
mne_watershed_bem, mne_make_scalp_surfaces.
mri_convert is used to convert files from NIFTI (nii) to Freesurfer (mgz) format.
It is best to run the conversion via command line beforehand.
'''
from mne.commands import mne_make_scalp_surfaces
subjects_dir = check_env_variables(subjects_dir, key='SUBJECTS_DIR')
freesurfer_home = check_env_variables(freesurfer_home, key='FREESURFER_HOME')
mne_bin_path = os.path.join(mne_root, 'bin', '')
freesurfer_bin = os.path.join(freesurfer_home, 'bin', '')
print subjects_dir, freesurfer_home, mne_bin_path, freesurfer_bin
# some commands requires it, setting it here for safety
os.environ['DISPLAY'] = ':0'
for subj in subjects_list:
print 'Setting up freesurfer surfaces and source spaces for %s' % (subj)
if mri_convert:
# Convert NIFTI files to mgz format that is read by freesurfer
nii_file = os.path.join(subjects_dir, subj, subj + nii_extn)
mri_file = os.path.join(subjects_dir, subj, mri_extn)
print nii_file, mri_file
retcode = call([freesurfer_bin + 'mri_convert', nii_file, mri_file])
if retcode != 0:
retcode_error('mri_convert', subj)
continue
# Reconstruct all surfaces and basically everything else.
retcode = call([freesurfer_bin + 'recon-all', '-autorecon-all', '-subjid', subj])
if retcode != 0:
retcode_error('recon-all', subj)
continue
# Set up the MRI data for forward model.
retcode = call([mne_bin_path + 'mne_setup_mri', '--subject', subj])
if retcode != 0:
retcode_error('mne_setup_mri', subj)
continue
# $MNE_BIN_PATH/mne_setup_mri --subject $i --overwrite (if needed)
# Set up the source space - creates source space description in fif format in /bem
# setting it up as ico is useful to create labels in the future. - 06.10.14
try:
setup_source_space(subj, fname=True, spacing='ico4',
surface='white', overwrite=False,
subjects_dir=subjects_dir, n_jobs=2)
except:
retcode_error('mne.setup_source_space', subj)
continue
# Setting up of Triangulation files
retcode = call([mne_bin_path + 'mne_watershed_bem', '--subject', subj])
if retcode != 0:
retcode_error('mne_watershed_bem', subj)
continue
# $MNE_BIN_PATH/mne_watershed_bem --subject $i --overwrite (soon available in python)
# Setting up the surface files
watershed_dir = os.path.join(subjects_dir, subj, 'bem/watershed', '')
surf_dir = os.path.join(subjects_dir, subj, 'bem', '')
if not os.path.isdir(watershed_dir) or not os.path.isdir(surf_dir):
print 'BEM directories /bem/watershed or /bem/ not found.'
call(['ln', '-s', watershed_dir + subj + '_brain_surface', surf_dir + subj + '-brain.surf'])
call(['ln', '-s', watershed_dir + subj + '_inner_skull_surface', surf_dir + subj + '-inner_skull.surf'])
call(['ln', '-s', watershed_dir + subj + '_outer_skin_surface', surf_dir + subj + '-outer_skin.surf'])
call(['ln', '-s', watershed_dir + subj + '_outer_skull_surface', surf_dir + subj + '-outer_skull.surf'])
try:
mne_make_scalp_surfaces._run(subjects_dir, subj, force=True,
overwrite=True, verbose=True)
except:
retcode_error('mne_make_scalp_surfaces', subj)
continue
# refer to MNE cookbook for more details
head = os.path.join(subjects_dir, subj, 'bem/', subj + '-head.fif')
head_bkp = os.path.join(subjects_dir, subj, 'bem/', subj + '-head.fif_orig')
if os.path.isfile(head):
os.rename(head, head_orig)
head_medium = os.path.join(subjects_dir, subj, 'bem/', subj + '-head-medium.fif')
print 'linking %s as main head surface..' % (head_medium)
call(['ln', '-s', head_medium, head])
print 'Surface reconstruction routines completed for subject %s' % (subj)