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.
- Parameters:
- subject
str Subject name.
- subjects_dirpath-like |
None The path to the directory containing the FreeSurfer subjects reconstructions. If
None, defaults to theSUBJECTS_DIRenvironment variable.- overwrite
bool If True (default False), overwrite the destination file if it exists.
- volume
str Defaults to T1.
- atlas
bool Specify the –atlas option for mri_watershed.
- gcaatlas
bool Specify the –brain_atlas option for mri_watershed.
- preflood
int Change the preflood height.
- show
bool Show surfaces to visually inspect all three BEM surfaces (recommended).
New in version 0.12.
- copy
bool If True (default), use copies instead of symlinks for surfaces (if they do not already exist).
New in version 0.18.
Changed in version 1.1: Use copies instead of symlinks.
- T1
bool|None If True, pass the
-T1flag. By default (None), this takes the same value asgcaatlas.New in version 0.19.
- brainmask
str 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 viarecon-all -autorecon1.New in version 0.19.
- verbose
bool|str|int|None Control verbosity of the logging output. If
None, use the default verbosity level. See the logging documentation andmne.verbose()for details. Should only be passed as a keyword argument.
- subject
See also
Notes
If your BEM meshes do not look correct when viewed in
mne.viz.plot_alignment()ormne.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
