def LFcomputing(condFile, geomFile, dipoleFile, electrodesFile, savedir):
"""
condFile = 'om_demo.cond'
geomFile = 'om_demo.geom'
dipoleFile = 'cortex.dip'
squidsFile = 'meg_squids.txt'
electrodesFile = 'eeg_electrodes.txt'
"""
# Load data
geom = om.Geometry()
geom.read(geomFile, condFile)
dipoles = om.Matrix()
dipoles.load(dipoleFile)
#squids = om.Sensors()
#squids.load(squidsFile)
electrodes = om.Sensors()
electrodes.load(electrodesFile)
# Compute forward problem
gaussOrder = 3
use_adaptive_integration = True
hm = om.HeadMat(geom, gaussOrder)
hminv = hm.inverse()
dsm = om.DipSourceMat(geom, dipoles, gaussOrder, use_adaptive_integration)
#ds2mm = om.DipSource2MEGMat (dipoles, squids)
#h2mm = om.Head2MEGMat (geom, squids)
h2em = om.Head2EEGMat(geom, electrodes)
#gain_meg = om.GainMEG (hminv, dsm, h2mm, ds2mm)
gain_eeg = om.GainEEG(hminv, dsm, h2em)
gain_eeg.save(savedir)
return gain_eeg
def make_forward_solution(info,
trans_fname,
src,
bem_model,
meg=True,
eeg=True,
mindist=0.0,
ignore_ref=False,
n_jobs=1,
verbose=None):
assert not meg # XXX for now
coord_frame = 'head'
trans = mne.read_trans(trans_fname)
head_trans, meg_trans, mri_trans = _prepare_trans(info, trans, coord_frame)
dipoles = _get_dipoles(src, mri_trans, head_trans)
eeg_electrodes, ch_names = _get_sensors(info, head_trans)
geom = _get_geom_files(bem_model, mri_trans, head_trans)
assert geom.is_nested()
assert geom.selfCheck()
# OpenMEEG
gauss_order = 3
use_adaptive_integration = True
# dipole_in_cortex = True
hm = om.HeadMat(geom, gauss_order)
hm.invert()
hminv = hm
dsm = om.DipSourceMat(geom, dipoles, gauss_order, use_adaptive_integration,
"Brain")
# For EEG
eeg_picks = mne.pick_types(info, meg=False, eeg=True)
# meg_picks = mne.pick_types(info, meg=True, eeg=False)
# seeg_picks = mne.pick_types(info, meg=False, seeg=True)
if eeg and len(eeg_picks) > 0:
h2em = om.Head2EEGMat(geom, eeg_electrodes)
eeg_leadfield = om.GainEEG(hminv, dsm, h2em)
eegfwd = _make_forward(eeg_leadfield, ch_names, info, src, trans_fname)
# if meg and len(meg_picks) > 0:
# h2em = om.Head2EEGMat(geom, eeg_electrodes)
# eeg_leadfield = om.GainEEG(hminv, dsm, h2em)
# megfwd = _make_forward(eeg_leadfield, ch_names, info, src, trans_fname)
# # merge forwards
# fwd = _merge_meg_eeg_fwds(_to_forward_dict(megfwd, megnames),
# _to_forward_dict(eegfwd, eegnames),
# verbose=False)
return eegfwd
def eeg_gain(self, eeg_file=None):
"""
Call OpenMEEG's GainEEG method to calculate the final projection matrix.
Optionaly saving the matrix for later use. The OpenMEEG matrix is
converted to a Numpy array before return.
"""
LOG.info("Computing GainEEG...")
eeg_gain = om.GainEEG(self.om_inverse_head, self.om_source_matrix,
self.om_head2sensor)
LOG.info("eeg_gain: %d x %d" % (eeg_gain.nlin(), eeg_gain.ncol()))
if eeg_file is not None:
LOG.info("Saving eeg_gain as %s..." % eeg_file)
eeg_gain.save(
os.path.join(OM_STORAGE_DIR, eeg_file + OM_SAVE_SUFFIX))
return om.asarray(eeg_gain)
gauss_order = 3
use_adaptive_integration = True
dipole_in_cortex = True
hm = om.HeadMat(geom, gauss_order)
#hm.invert() # invert hm inplace (no copy)
#hminv = hm
hminv = hm.inverse() # invert hm with a copy
ssm = om.SurfSourceMat(geom, mesh)
ss2mm = om.SurfSource2MEGMat(mesh, sensors)
dsm = om.DipSourceMat(geom, dipoles, gauss_order, use_adaptive_integration, "")
ds2mm = om.DipSource2MEGMat(dipoles, sensors)
h2mm = om.Head2MEGMat(geom, sensors)
h2em = om.Head2EEGMat(geom, patches)
gain_meg_surf = om.GainMEG(hminv, ssm, h2mm, ss2mm)
gain_eeg_surf = om.GainEEG(hminv, ssm, h2em)
gain_meg_dip = om.GainMEG(hminv, dsm, h2mm, ds2mm)
gain_adjoint_meg_dip = om.GainMEGadjoint(geom, dipoles, hm, h2mm, ds2mm)
gain_eeg_dip = om.GainEEG(hminv, dsm, h2em)
gain_adjoint_eeg_dip = om.GainEEGadjoint(geom, dipoles, hm, h2em)
gain_adjoint_eeg_meg_dip = om.GainEEGMEGadjoint(geom, dipoles, hm, h2em, h2mm,
ds2mm)
print "hm : %d x %d" % (hm.nlin(), hm.ncol())
print "hminv : %d x %d" % (hminv.nlin(), hminv.ncol())
print "ssm : %d x %d" % (ssm.nlin(), ssm.ncol())
print "ss2mm : %d x %d" % (ss2mm.nlin(), ss2mm.ncol())
print "dsm : %d x %d" % (ssm.nlin(), ssm.ncol())
print "ds2mm : %d x %d" % (ss2mm.nlin(), ss2mm.ncol())
print "h2mm : %d x %d" % (h2mm.nlin(), h2mm.ncol())
print "h2em : %d x %d" % (h2mm.nlin(), h2mm.ncol())
# For ECoG
h2ecogm = om.Head2ECoGMat(geom, ecog_electrodes, "Cortex")
# For MEG
ds2mm = om.DipSource2MEGMat(dipoles, meg_sensors)
h2mm = om.Head2MEGMat(geom, meg_sensors)
# For EIT
eitsm = om.EITSourceMat(geom, eit_electrodes, gauss_order)
'''
'''
# For Internal Potential
iphm = om.Surf2VolMat(geom, int_electrodes)
ipsm = om.DipSource2InternalPotMat(geom, dipoles, int_electrodes)
'''
eeg_leadfield = om.GainEEG(hminv, dsm, h2em)
# eeg_leadfield_adjoint = om.GainEEGadjoint(geom,dipoles,hm, h2em)
print("hminv : %d x %d" % (hminv.nlin(), hminv.ncol()))
print("dsm : %d x %d" % (dsm.nlin(), dsm.ncol()))
print("h2em : %d x %d" % (h2em.nlin(), h2em.ncol()))
print("h2ecogm : %d x %d" % (h2ecogm.nlin(), h2ecogm.ncol()))
print("ds2mm : %d x %d" % (ds2mm.nlin(), ds2mm.ncol()))
print("h2mm : %d x %d" % (h2mm.nlin(), h2mm.ncol()))
print("eeg_leadfield : %d x %d" %
(eeg_leadfield.nlin(), eeg_leadfield.ncol()))
print("ecog_leadfield : %d x %d" %
(ecog_leadfield.nlin(), ecog_leadfield.ncol()))
print("meg_leadfield : %d x %d" %
(meg_leadfield.nlin(), meg_leadfield.ncol()))