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Hello,
I'm starting to play around with mne-hcp
I'm picking code in the examples of mne-hcp to create in each subjec:
mne_anatomy. fine
bem_model and _solution. fine
head_mri_t. fine
check that everything is in place with mne.viz.plot_alignment, and I get
this:
https://drive.google.com/open?id=17altWLQIfyZMxUcvnsxgzJp9zN0qcET0
I understand that the head_mri_t is not applied to the helmet. is that
correct? how impactfull is that for upcoming computations? how can I fix it?
Many thanks,
Max
This is my code:
import os.path as op
import glob
import mne
import hcp
storage_dir =
op.expanduser('~/owncloud/Lab/Projects/SOLID_MEEG/data/HCPunzipped')
subjects_dir =
op.expanduser('~/owncloud/Lab/Projects/SOLID_MEEG/data/HCPsubjects')
recordings_dir =
op.expanduser('~/owncloud/Lab/Projects/SOLID_MEEG/data/HCPmeg')
subjects = glob.glob(op.join(storage_dir,'[0-9][0-9][0-9][0-9][0-9][0-9]'))
src_fsaverage = mne.setup_source_space(
subject='fsaverage',
subjects_dir='/network/lustre/iss01/cenir/software/meeg/freesurfer/subjects',
add_dist=False,
spacing='oct6')
for subject in subjects:
hcp_params = dict(
hcp_path=storage_dir,
subject=subject,
data_type='rest')
run_index = 0
hcp.make_mne_anatomy(
subject, subjects_dir = subjects_dir,
hcp_path = storage_dir,
recordings_path = recordings_dir)
bems = mne.make_bem_model(subject, conductivity=(0.3,),
subjects_dir=subjects_dir,
ico=None) # ico = None for morphed SP.
mne.write_bem_surfaces(op.join(subjects_dir,subject,'bem',subject+'-bem.fif'),bems)
bem_sol = mne.make_bem_solution(bems)
bem_sol['surfs'][0]['coord_frame'] = 5
mne.write_bem_solution(op.join(subjects_dir,subject,'bem',subject+'-bem-sol.fif'),bem_sol)
head_mri_t = mne.read_trans(
op.join(recordings_dir, subject,
'{}-head_mri-trans.fif'.format(subject)))
mne.write_trans(op.join(subjects_dir,subject,'bem',subject+'-trans.fif'),head_mri_t)
info = hcp.read_info(run_index=run_index, **hcp_params)
picks = mne.pick_types(info, meg=True, ref_meg=False)
info = mne.pick_info(info, picks)
mne.viz.plot_alignment(info,head_mri_t,subject=subject,subjects_dir=subjects_dir,surfaces=('inner_skull','white'))
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