nipype.interfaces.mne.base module

WatershedBEM

Link to code

Bases: FSCommand

Wrapped executable: mne watershed_bem.

Uses mne_watershed_bem to get information from dicom directories

Examples

>>> from nipype.interfaces.mne import WatershedBEM
>>> bem = WatershedBEM()
>>> bem.inputs.subject_id = 'subj1'
>>> bem.inputs.subjects_dir = '.'
>>> bem.cmdline
'mne watershed_bem --overwrite --subject subj1 --volume T1'
>>> bem.run()  
subject_ida unicode string

Subject ID (must have a complete Freesurfer directory). Maps to a command-line argument: --subject %s.

subjects_dira pathlike object or string representing an existing directory

Path to Freesurfer subjects directory. (Nipype default value: <undefined>)

argsa unicode string

Additional parameters to the command. Maps to a command-line argument: %s.

atlas_modea boolean

Use atlas mode for registration (default: no rigid alignment). Maps to a command-line argument: --atlas.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

overwritea boolean

Overwrites the existing files. Maps to a command-line argument: --overwrite. (Nipype default value: True)

volume‘T1’ or ‘aparc+aseg’ or ‘aseg’ or ‘brain’ or ‘orig’ or ‘brainmask’ or ‘ribbon’

The volume from the “mri” directory to use (defaults to T1). Maps to a command-line argument: --volume %s. (Nipype default value: T1)

brain_surfacea pathlike object or string representing an existing file

Brain surface (in Freesurfer format).

cor_filesa list of items which are a pathlike object or string representing an existing file

“COR” format files.

fif_filea pathlike object or string representing an existing file

“fif” format file for EEG processing in MNE.

inner_skull_surfacea pathlike object or string representing an existing file

Inner skull surface (in Freesurfer format).

mesh_filesa list of items which are a pathlike object or string representing an existing file

Paths to the output meshes (brain, inner skull, outer skull, outer skin).

outer_skin_surfacea pathlike object or string representing an existing file

Outer skin surface (in Freesurfer format).

outer_skull_surfacea pathlike object or string representing an existing file

Outer skull surface (in Freesurfer format).