[Mne_analysis] hcp-mne head_mri trans

[Maximilien Chaumon]

        External Email - Use Caution        

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'))
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190111/4f31ab71/attachment-0001.html