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
- subject
str
Subject name.
- subjects_dir
str
|None
The path to the FreeSurfer subjects reconstructions. It corresponds to FreeSurfer environment variable
SUBJECTS_DIR
.- overwritebool
If True (default False), overwrite the destination file if it exists.
- volume
str
Defaults to T1.
- atlasbool
Specify the –atlas option for mri_watershed.
- gcaatlasbool
Specify the –brain_atlas option for mri_watershed.
- preflood
int
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 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.
- verbosebool,
str
,int
, orNone
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.
- 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.