The HCP anatomy data needed for MNE based source analysis Live in different places and subfolders. MNE-HCP has a convenience function that exctracts the required files and information and creates a “subjects_dir” as known from MNE and freesurfer.
The most essential contents are - freesurfer surfaces - the MRI - the headmodel - the coregistration transform
This function is your friend prior to running any source analysis.
# Author: Denis A. Engemann
# License: BSD 3 clause
import os.path as op
import hcp
storage_dir = op.expanduser('~/mne-hcp-data')
# This is where the data are after downloading from HCP
hcp_path = storage_dir + '/HCP'
# this is the new directory to be created
subjects_dir = storage_dir + '/hcp-subjects'
# it will make the subfolders 'bem', 'mir', 'surf' and 'label'
# and populate it with symbolic links if possible and write some files
# where information has to be presented in a different format to satisfy MNE.
# this is where the coregistration matrix is written as
# `105923-head_mri-transform.fif`
recordings_path = storage_dir + '/hcp-meg'
# comment out to write files on your disk
# hcp.make_mne_anatomy(
# subject='105923', hcp_path=hcp_path,
# recordings_path=recordings_path,
# subjects_dir=subjects_dir)
Total running time of the script: ( 0 minutes 0.000 seconds)