mne.create_default_subject¶

mne.create_default_subject(mne_root=None, fs_home=None, update=False, subjects_dir=None)¶

Create an average brain subject for subjects without structural MRI

Create a copy of fsaverage from the Freesurfer directory in subjects_dir and add auxiliary files from the mne package.

Parameters:

mne_root : None | str The mne root directory (only needed if MNE_ROOT is not specified as environment variable). fs_home : None | str The freesurfer home directory (only needed if FREESURFER_HOME is not specified as environment variable). update : bool In cases where a copy of the fsaverage brain already exists in the subjects_dir, this option allows to only copy files that don’t already exist in the fsaverage directory. subjects_dir : None | str Override the SUBJECTS_DIR environment variable (os.environ[‘SUBJECTS_DIR’]) as destination for the new subject.

Notes

When no structural MRI is available for a subject, an average brain can be substituted. Freesurfer comes with such an average brain model, and MNE comes with some auxiliary files which make coregistration easier. create_default_subject() copies the relevant files from Freesurfer into the current subjects_dir, and also adds the auxiliary files provided by MNE.

The files provided by MNE are listed below and can be found under share/mne/mne_analyze/fsaverage in the MNE directory (see MNE manual section 7.19 Working with the average brain):

fsaverage_head.fif:

The approximate head surface triangulation for fsaverage.

fsaverage_inner_skull-bem.fif:

The approximate inner skull surface for fsaverage.

fsaverage-fiducials.fif:

The locations of the fiducial points (LPA, RPA, and nasion).

fsaverage-trans.fif:

Contains a default MEG-MRI coordinate transformation suitable for fsaverage.