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=True, T1=None, brainmask='ws.mgz', verbose=None)[source]#

Create BEM surfaces using the FreeSurfer watershed algorithm.

See Using the watershed algorithm for additional information.

Parameters:

subjectstr: Subject name.
subjects_dirpath-like | None: The path to the directory containing the FreeSurfer subjects reconstructions. If None, defaults to the SUBJECTS_DIR environment variable.
overwritebool: If True (default False), overwrite the destination file if it exists.
volumestr: The name of the MRI volume (without file extension) that will be used as input to mri_watershed. The volume is expected to be full-head (non-skull-stripped), as the watershed algorithm relies on tissue intensity gradients to estimate the inner skull, outer skull, and outer skin surfaces. Defaults to "T1", corresponding to $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz in a typical FreeSurfer subject directory. This volume is typically produced by the recon-all pipeline after the intensity normalization step.
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 v0.12.
copybool: If True (default), use copies instead of symlinks for surfaces (if they do not already exist).

New in v0.18.

Changed in version 1.1: Use copies instead of symlinks.
T1bool | None: If True, pass the -T1 flag. By default (None), this takes the same value as gcaatlas.

New in v0.19.
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 v0.19.
verbosebool | str | int | None: Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.