interfaces.mne.base¶
WatershedBEM¶
Wraps the executable command 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
Inputs:
[Mandatory]
subject_id: (a unicode string)
Subject ID (must have a complete Freesurfer directory)
argument: ``--subject %s``
subjects_dir: (a pathlike object or string representing an existing
directory, nipype default value: <undefined>)
Path to Freesurfer subjects directory
[Optional]
volume: ('T1' or 'aparc+aseg' or 'aseg' or 'brain' or 'orig' or
'brainmask' or 'ribbon', nipype default value: T1)
The volume from the "mri" directory to use (defaults to T1)
argument: ``--volume %s``
overwrite: (a boolean, nipype default value: True)
Overwrites the existing files
argument: ``--overwrite``
atlas_mode: (a boolean)
Use atlas mode for registration (default: no rigid alignment)
argument: ``--atlas``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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', nipype default value: {})
Environment variables
Outputs:
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)
brain_surface: (a pathlike object or string representing an existing
file)
Brain surface (in Freesurfer format)
inner_skull_surface: (a pathlike object or string representing an
existing file)
Inner skull surface (in Freesurfer format)
outer_skull_surface: (a pathlike object or string representing an
existing file)
Outer skull surface (in Freesurfer format)
outer_skin_surface: (a pathlike object or string representing an
existing file)
Outer skin surface (in Freesurfer format)
fif_file: (a pathlike object or string representing an existing file)
"fif" format file for EEG processing in MNE
cor_files: (a list of items which are a pathlike object or string
representing an existing file)
"COR" format files