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()                               # doctest: +SKIP
subject_id : a unicode string
Subject ID (must have a complete Freesurfer directory). Maps to a command-line argument: --subject %s.
subjects_dir : a pathlike object or string representing an existing directory
Path to Freesurfer subjects directory. (Nipype default value: <undefined>)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
atlas_mode : a boolean
Use atlas mode for registration (default: no rigid alignment). Maps to a command-line argument: --atlas.
environ : a 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: {})
overwrite : a 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_surface : a pathlike object or string representing an existing file
Brain surface (in Freesurfer format).
cor_files : a list of items which are a pathlike object or string representing an existing file
“COR” format files.
fif_file : a pathlike object or string representing an existing file
“fif” format file for EEG processing in MNE.
inner_skull_surface : a pathlike object or string representing an existing file
Inner skull surface (in Freesurfer format).
mesh_files : a 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_surface : a pathlike object or string representing an existing file
Outer skin surface (in Freesurfer format).
outer_skull_surface : a pathlike object or string representing an existing file
Outer skull surface (in Freesurfer format).