interfaces.mne.base

WatershedBEM

Link to code

Wraps 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()                               

Inputs:

[Mandatory]
subject_id: (a unicode string)
        Subject ID (must have a complete Freesurfer directory)
        flag: --subject %s
subjects_dir: (an existing directory name, nipype default value: )
        Path to Freesurfer subjects directory

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
atlas_mode: (a boolean)
        Use atlas mode for registration (default: no rigid alignment)
        flag: --atlas
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
overwrite: (a boolean, nipype default value: True)
        Overwrites the existing files
        flag: --overwrite
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
volume: (u'T1' or u'aparc+aseg' or u'aseg' or u'brain' or u'orig' or
         u'brainmask' or u'ribbon', nipype default value: T1)
        The volume from the "mri" directory to use (defaults to T1)
        flag: --volume %s

Outputs:

brain_surface: (an existing file name)
        Brain surface (in Freesurfer format)
cor_files: (a list of items which are an existing file name)
        "COR" format files
fif_file: (an existing file name)
        "fif" format file for EEG processing in MNE
inner_skull_surface: (an existing file name)
        Inner skull surface (in Freesurfer format)
mesh_files: (a list of items which are an existing file name)
        Paths to the output meshes (brain, inner skull, outer skull, outer
        skin)
outer_skin_surface: (an existing file name)
        Outer skin surface (in Freesurfer format)
outer_skull_surface: (an existing file name)
        Outer skull surface (in Freesurfer format)