%pylab inline

from glob import glob
from nipype.interfaces.dcm2nii import Dcm2nii
from nipype.interfaces.fsl import BET

import nipype.pipeline.engine as pe

convert = pe.Node(Dcm2nii(), name='convert_dicom')
skull_stripper = pe.Node(BET(), name = 'skull_stripper')

convert_flow = pe.Workflow(name = 'convert_and_strip')
convert_flow.connect(convert, 'converted_files', skull_stripper, 'in_file')

fl = glob('/opt/data/NIPYPE_DATA/NKI.archive.1-5.007.LiteDICOM/3466763/session_1/MPRAGE_1/*.dcm')
convert_flow.inputs.convert_dicom.source_names = fl[0] # or fl
convert_flow.base_dir = '/mnt/mydir/'

convert_flow.run()