Hello!
I am new to mne and I have been struggling with understanding how to approach the following problem.
I have a subject that was preprocessed with Freesurfer. I have created his head model with this code:
bem.make_watershed_bem(subject,
subjects_dir=subjects_dir,
overwrite=True)
bem.make_scalp_surfaces(
subject=subject,
subjects_dir=subjects_dir,
no_decimate=False,
force=True,
overwrite=True,
)
Now I want to coregister a standard electrode montage using mne.coregistration. However, I do not have the digitization file of the subject, I want to use the standard_1020 montage from mne. How can I perform the coregistration?
I tried the following:
from mne.datasets import eegbci
import numpy as np
montage = mne.channels.make_standard_montage("standard_1020")
info = mne.create_info(
ch_names=montage.ch_names, # all channels in the montage
ch_types='eeg', # mark them as EEG sensors
sfreq=100 # arbitrary sampling frequency (Hz)
)
info.set_montage(montage)
fake_raw = mne.io.RawArray(np.zeros((len(info['ch_names']), 1)), info)
fake_raw.save('fake_raw.fif', overwrite=True)
mne.gui.coregistration(inst='fake_raw.fif', subject=subject, subjects_dir=subjects_dir)
However I am not sure it is the right approach as I am struggling in scaling the electrodes and fitting them to the mri fiducials.
Could you please confirm if I am on the right track? In what space are the locations of the mne.channels.make_standard_montage("standard_1020") ? is it compatible with the bem model generated from the free surfer output? How can I solve the problem of the electrode scaling and fitting?
Thank you in advance!
Best,
Chiara