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()
Mandatory Inputs:

  • subject_id (a 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>)

Optional Inputs:

  • args (a 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)

Outputs:

  • 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).