Fetch and update :ref:`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
(subjects_dir=None, *, verbose=None)
| 12 | |
| 13 | @verbose |
| 14 | def fetch_fsaverage(subjects_dir=None, *, verbose=None): |
| 15 | """Fetch and update :ref:`fsaverage <fsaverage_background>`. |
| 16 | |
| 17 | Parameters |
| 18 | ---------- |
| 19 | subjects_dir : str | None |
| 20 | The path to use as the subjects directory in the MNE-Python |
| 21 | config file. None will use the existing config variable (i.e., |
| 22 | will not change anything), and if it does not exist, will use |
| 23 | ``~/mne_data/MNE-fsaverage-data``. |
| 24 | %(verbose)s |
| 25 | |
| 26 | Returns |
| 27 | ------- |
| 28 | fs_dir : Path |
| 29 | The fsaverage directory. |
| 30 | (essentially ``subjects_dir / 'fsaverage'``). |
| 31 | |
| 32 | .. versionchanged:: 1.8 |
| 33 | A :class:`pathlib.Path` object is returned instead of a string. |
| 34 | |
| 35 | Notes |
| 36 | ----- |
| 37 | This function is designed to provide |
| 38 | |
| 39 | 1. All modern (Freesurfer 6) fsaverage subject files |
| 40 | 2. All MNE fsaverage parcellations |
| 41 | 3. fsaverage head surface, fiducials, head<->MRI trans, 1- and 3-layer |
| 42 | BEMs (and surfaces) |
| 43 | |
| 44 | This function will compare the contents of ``subjects_dir/fsaverage`` |
| 45 | to the ones provided in the remote zip file. If any are missing, |
| 46 | the zip file is downloaded and files are updated. No files will |
| 47 | be overwritten. |
| 48 | |
| 49 | .. versionadded:: 0.18 |
| 50 | """ |
| 51 | # Code used to create the BEM (other files taken from MNE-sample-data): |
| 52 | # |
| 53 | # $ mne watershed_bem -s fsaverage -d $PWD --verbose info --copy |
| 54 | # $ python |
| 55 | # >>> bem = mne.make_bem_model('fsaverage', subjects_dir='.', verbose=True) |
| 56 | # >>> mne.write_bem_surfaces( |
| 57 | # ... 'fsaverage/bem/fsaverage-5120-5120-5120-bem.fif', bem) |
| 58 | # >>> sol = mne.make_bem_solution(bem, verbose=True) |
| 59 | # >>> mne.write_bem_solution( |
| 60 | # ... 'fsaverage/bem/fsaverage-5120-5120-5120-bem-sol.fif', sol) |
| 61 | # >>> import os |
| 62 | # >>> import os.path as op |
| 63 | # >>> names = sorted(op.join(r, f) |
| 64 | # ... for r, d, files in os.walk('fsaverage') |
| 65 | # ... for f in files) |
| 66 | # with open('fsaverage.txt', 'w') as fid: |
| 67 | # fid.write('\n'.join(names)) |
| 68 | # |
| 69 | subjects_dir = _set_montage_coreg_path(subjects_dir) |
| 70 | subjects_dir = subjects_dir.expanduser().absolute() |
| 71 | fs_dir = subjects_dir / "fsaverage" |
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