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)

Create BEM surfaces using the FreeSurfer watershed algorithm.

Parameters

subjectstr

Subject name.

subjects_dirstr | pathlib.Path | 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

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 | 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.

See also

mne.viz.plot_bem

Notes

If your BEM meshes do not look correct when viewed in mne.viz.plot_alignment() or mne.viz.plot_bem(), consider potential solutions from the FAQ.

New in version 0.10.

Examples using mne.bem.make_watershed_bem

Working with CTF data: the Brainstorm auditory dataset

Head model and forward computation

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