interfaces.mne.base¶
WatershedBEM¶
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 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 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 value of type 'str' and
with values which are a value of type 'str', 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: ('stream' or 'allatonce' or 'file' or '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: ('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)
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)