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# -*- coding: utf-8 -*-
"""
.. _tut-eeg-fsaverage-source-modeling:
========================================
EEG forward operator with a template MRI
========================================
This tutorial explains how to compute the forward operator from EEG data
using the standard template MRI subject ``fsaverage``.
.. caution:: Source reconstruction without an individual T1 MRI from the
subject will be less accurate. Do not over interpret activity
locations which can be off by multiple centimeters.
Adult template MRI (fsaverage)
------------------------------
First we show how ``fsaverage`` can be used as a surrogate subject.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Joan Massich <mailsik@gmail.com>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import os.path as op
import numpy as np
import mne
from mne.datasets import eegbci
from mne.datasets import fetch_fsaverage
# Download fsaverage files
fs_dir = fetch_fsaverage(verbose=True)
subjects_dir = op.dirname(fs_dir)
# The files live in:
subject = 'fsaverage'
trans = 'fsaverage' # MNE has a built-in fsaverage transformation
src = op.join(fs_dir, 'bem', 'fsaverage-ico-5-src.fif')
bem = op.join(fs_dir, 'bem', 'fsaverage-5120-5120-5120-bem-sol.fif')
##############################################################################
# Load the data
# ^^^^^^^^^^^^^
#
# We use here EEG data from the BCI dataset.
#
# .. note:: See :ref:`plot_montage` to view all the standard EEG montages
# available in MNE-Python.
raw_fname, = eegbci.load_data(subject=1, runs=[6])
raw = mne.io.read_raw_edf(raw_fname, preload=True)
# Clean channel names to be able to use a standard 1005 montage
new_names = dict(
(ch_name,
ch_name.rstrip('.').upper().replace('Z', 'z').replace('FP', 'Fp'))
for ch_name in raw.ch_names)
raw.rename_channels(new_names)
# Read and set the EEG electrode locations, which are already in fsaverage's
# space (MNI space) for standard_1020:
montage = mne.channels.make_standard_montage('standard_1005')
raw.set_montage(montage)
raw.set_eeg_reference(projection=True) # needed for inverse modeling
# Check that the locations of EEG electrodes is correct with respect to MRI
mne.viz.plot_alignment(
raw.info, src=src, eeg=['original', 'projected'], trans=trans,
show_axes=True, mri_fiducials=True, dig='fiducials')
##############################################################################
# Setup source space and compute forward
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
fwd = mne.make_forward_solution(raw.info, trans=trans, src=src,
bem=bem, eeg=True, mindist=5.0, n_jobs=None)
print(fwd)
##############################################################################
# From here on, standard inverse imaging methods can be used!
#
# Infant MRI surrogates
# ---------------------
# We don't have a sample infant dataset for MNE, so let's fake a 10-20 one:
ch_names = \
'Fz Cz Pz Oz Fp1 Fp2 F3 F4 F7 F8 C3 C4 T7 T8 P3 P4 P7 P8 O1 O2'.split()
data = np.random.RandomState(0).randn(len(ch_names), 1000)
info = mne.create_info(ch_names, 1000., 'eeg')
raw = mne.io.RawArray(data, info)
##############################################################################
# Get an infant MRI template
# ^^^^^^^^^^^^^^^^^^^^^^^^^^
# To use an infant head model for M/EEG data, you can use
# :func:`mne.datasets.fetch_infant_template` to download an infant template:
subject = mne.datasets.fetch_infant_template('6mo', subjects_dir, verbose=True)
##############################################################################
# It comes with several helpful built-in files, including a 10-20 montage
# in the MRI coordinate frame, which can be used to compute the
# MRI<->head transform ``trans``:
fname_1020 = op.join(subjects_dir, subject, 'montages', '10-20-montage.fif')
mon = mne.channels.read_dig_fif(fname_1020)
mon.rename_channels(
{f'EEG{ii:03d}': ch_name for ii, ch_name in enumerate(ch_names, 1)})
trans = mne.channels.compute_native_head_t(mon)
raw.set_montage(mon)
print(trans)
##############################################################################
# There are also BEM and source spaces:
bem_dir = op.join(subjects_dir, subject, 'bem')
fname_src = op.join(bem_dir, f'{subject}-oct-6-src.fif')
src = mne.read_source_spaces(fname_src)
print(src)
fname_bem = op.join(bem_dir, f'{subject}-5120-5120-5120-bem-sol.fif')
bem = mne.read_bem_solution(fname_bem)
##############################################################################
# You can ensure everything is as expected by plotting the result:
fig = mne.viz.plot_alignment(
raw.info, subject=subject, subjects_dir=subjects_dir, trans=trans,
src=src, bem=bem, coord_frame='mri', mri_fiducials=True, show_axes=True,
surfaces=('white', 'outer_skin', 'inner_skull', 'outer_skull'))
mne.viz.set_3d_view(fig, 25, 70, focalpoint=[0, -0.005, 0.01])
##############################################################################
# From here, standard forward and inverse operators can be computed
#
# If you have digitized head positions or MEG data, consider using
# :ref:`mne coreg` to warp a suitable infant template MRI to your
# digitization information.
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