mne.bem.make_watershed_bem¶

mne.bem.make_watershed_bem(subject, subjects_dir=None, overwrite=False, volume='T1', atlas=False, gcaatlas=False, preflood=None, show=False, copy=False, T1=None, brainmask='ws.mgz', verbose=None)[source]¶

Create BEM surfaces using the FreeSurfer watershed algorithm.

Parameters

subjectstr: Subject name.
subjects_dirstr | None: The path to the FreeSurfer subjects reconstructions. It corresponds to FreeSurfer environment variable SUBJECTS_DIR.
overwritebool: Write over existing files.
volumestr: Defaults to T1.
atlasbool: Specify the –atlas option for mri_watershed.
gcaatlasbool: Specify the –brain_atlas option for mri_watershed.
prefloodint: Change the preflood height
showbool: Show surfaces to visually inspect all three BEM surfaces (recommended).

New in version 0.12.
copybool: If True (default False), use copies instead of symlinks for surfaces (if they do not already exist).

New in version 0.18.
T1bool | None: If True, pass the -T1 flag. By default (None), this takes the same value as gcaatlas.

New in version 0.19.
brainmaskstr: The filename for the brainmask output file relative to the $SUBJECTS_DIR/$SUBJECT/bem/watershed/ directory. Can be for example "../../mri/brainmask.mgz" to overwrite the brainmask obtained via recon-all -autorecon1.

New in version 0.19.
verbosebool, str, int, or None: If not None, override default verbose level (see mne.verbose() and Logging documentation for more). If used, it should be passed as a keyword-argument only.