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# -*- coding: utf-8 -*-
# Authors: Eric Larson <larson.eric.d@gmail.com>
# License: BSD Style.
import os
import os.path as op
from ..utils import _manifest_check_download, _get_path
from ...utils import verbose, get_subjects_dir, set_config
FSAVERAGE_MANIFEST_PATH = op.dirname(__file__)
@verbose
def fetch_fsaverage(subjects_dir=None, *, verbose=None):
"""Fetch and update fsaverage.
Parameters
----------
subjects_dir : str | None
The path to use as the subjects directory in the MNE-Python
config file. None will use the existing config variable (i.e.,
will not change anything), and if it does not exist, will use
``~/mne_data/MNE-fsaverage-data``.
%(verbose)s
Returns
-------
fs_dir : str
The fsaverage directory.
(essentially ``subjects_dir + '/fsaverage'``).
Notes
-----
This function is designed to provide
1. All modern (Freesurfer 6) fsaverage subject files
2. All MNE fsaverage parcellations
3. fsaverage head surface, fiducials, head<->MRI trans, 1- and 3-layer
BEMs (and surfaces)
This function will compare the contents of ``subjects_dir/fsaverage``
to the ones provided in the remote zip file. If any are missing,
the zip file is downloaded and files are updated. No files will
be overwritten.
.. versionadded:: 0.18
"""
# Code used to create the BEM (other files taken from MNE-sample-data):
#
# $ mne watershed_bem -s fsaverage -d $PWD --verbose info --copy
# $ python
# >>> bem = mne.make_bem_model('fsaverage', subjects_dir='.', verbose=True)
# >>> mne.write_bem_surfaces(
# ... 'fsaverage/bem/fsaverage-5120-5120-5120-bem.fif', bem)
# >>> sol = mne.make_bem_solution(bem, verbose=True)
# >>> mne.write_bem_solution(
# ... 'fsaverage/bem/fsaverage-5120-5120-5120-bem-sol.fif', sol)
# >>> import os
# >>> import os.path as op
# >>> names = sorted(op.join(r, f)
# ... for r, d, files in os.walk('fsaverage')
# ... for f in files)
# with open('fsaverage.txt', 'w') as fid:
# fid.write('\n'.join(names))
#
subjects_dir = _set_montage_coreg_path(subjects_dir)
subjects_dir = op.abspath(op.expanduser(subjects_dir))
fs_dir = op.join(subjects_dir, 'fsaverage')
os.makedirs(fs_dir, exist_ok=True)
_manifest_check_download(
manifest_path=op.join(FSAVERAGE_MANIFEST_PATH, 'root.txt'),
destination=op.join(subjects_dir),
url='https://osf.io/3bxqt/download?version=2',
hash_='5133fe92b7b8f03ae19219d5f46e4177',
)
_manifest_check_download(
manifest_path=op.join(FSAVERAGE_MANIFEST_PATH, 'bem.txt'),
destination=op.join(subjects_dir, 'fsaverage'),
url='https://osf.io/7ve8g/download?version=4',
hash_='b31509cdcf7908af6a83dc5ee8f49fb1',
)
return fs_dir
def _get_create_subjects_dir(subjects_dir):
subjects_dir = get_subjects_dir(subjects_dir, raise_error=False)
if subjects_dir is None:
subjects_dir = _get_path(None, 'MNE_DATA', 'montage coregistration')
subjects_dir = op.join(subjects_dir, 'MNE-fsaverage-data')
os.makedirs(subjects_dir, exist_ok=True)
return subjects_dir
def _set_montage_coreg_path(subjects_dir=None):
"""Set a subject directory suitable for montage(-only) coregistration.
Parameters
----------
subjects_dir : str | None
The path to use as the subjects directory in the MNE-Python
config file. None will use the existing config variable (i.e.,
will not change anything), and if it does not exist, will use
``~/mne_data/MNE-fsaverage-data``.
Returns
-------
subjects_dir : str
The subjects directory that was used.
See Also
--------
mne.datasets.fetch_fsaverage
mne.get_config
mne.set_config
Notes
-----
If you plan to only do EEG-montage based coregistrations with fsaverage
without any MRI warping, this function can facilitate the process.
Essentially it sets the default value for ``subjects_dir`` in MNE
functions to be ``~/mne_data/MNE-fsaverage-data`` (assuming it has
not already been set to some other value).
.. versionadded:: 0.18
"""
subjects_dir = _get_create_subjects_dir(subjects_dir)
old_subjects_dir = get_subjects_dir(None, raise_error=False)
if old_subjects_dir is None:
set_config('SUBJECTS_DIR', subjects_dir)
return subjects_dir
|
