# MNE Source Model (Part 2)

In this example, we read a con file. And save these data in a epoch file
and a evoked file.

%matplotlib qt

data_path = '/Users/kevinhsu/Documents/D/000_experiment/project_cospro/PG_meg_data/001_temp'
confile = data_path + '/de_EM.con'
raw = mne.io.kit.read_raw_kit(confile, stim = [192, 193, 194], slope = '+')
picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=False)
raw.load_data()
raw.pick(picks)
noise_cov = mne.compute_raw_covariance(raw, tmin=0, tmax=None)

Morph

morph = mne.compute_source_morph(stc, subject_from=subject,
                                     subject_to='fsaverage',
                                     subjects_dir=subjects_dir, spacing=4)
stc_fsaverage = morph.apply(stc)

Grand averaging (STC)

import numpy as np
# average two stc object

# from "stc1_fsaverage" and "stc2_fsaverage", get "data" array
# average two "data" array, keep mean of stc in "data" object
data = np.average([stc1_fsaverage.data, stc2_fsaverage.data], axis=0)

# create an stc object using "data" and parameters of "stc1_fsaverage"
stc = mne.SourceEstimate(data, stc1_fsaverage.vertices,
                               stc1_fsaverage.tmin,
                         stc1_fsaverage.tstep,
                         stc1_fsaverage.subject)

# create BEM files
mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s CTCHANG --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s CYHONG --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s CYLIN --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s EstherS --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s YHLAI --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s YNCHANG --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s YRLIN --overwrite

mne watershed_bem -d /Users/kevinhsu/Documents/D/000_experiment/compounding_VR/subjects -s YYWANG --overwrite

# Install Freesurfer
https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall
1. Installing XQuartz
2. Download freesurfer installation file
3. Setup and Configuration
4.