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', verbose=None)[source]

Create BEM surfaces using the FreeSurfer watershed algorithm.

Parameters
subjectstr

Subject name.

$(subjects_dir)s
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).

Notes

New in version 0.10.