code: def initialize(self, data_collection):
      super(SkullStrip, self).initialize(data_collection)
  
      for label, data_group in list(
          data_collection.data_groups.items()
      ):
          reference_filename = data_group.data[
              data_collection.current_case
          ][self.reference_channel]
  
          self.mask_filename = self.generate_output_filename(
              reference_filename, self.mask_string
          )
  
          if type(data_group.preprocessed_case) is list:
              input_file = data_group.preprocessed_case[
                  self.reference_channel
              ]
          else:
              # What to do about affines here... Also, reroute this file to a temporary directory.
              input_file = save_numpy_2_nifti(
                  data_group.preprocessed_case[
                      ..., self.reference_channel
                  ],
                  data_group.preprocessed_affine,
                  self.generate_output_filename(reference_filename),
              )
  
          specific_command = self.command + [
              quotes(input_file),
              quotes(self.mask_filename),
              "-f",
              str(self.bet2_f),
              "-g",
              str(self.bet2_g),
              "-m",
          ]
  
          subprocess.call(" ".join(specific_command), shell=True)
          os.rename(
              self.mask_filename + "_mask.nii.gz", self.mask_filename
          )
  
      self.mask_numpy = read_image_files(
          self.mask_filename, return_affine=False
      )
  
file_path: DeepNeuro/deepneuro/preprocessing/skullstrip.py
imports: import subprocess
  import os
  import numpy
  from deepneuro.preprocessing.preprocessor import Preprocessor
  from deepneuro.utilities.conversion import read_image_files, save_numpy_2_nifti
  from deepneuro.utilities.util import add_parameter, quotes
  from deepneuro.outputs.segmentation import PatchesInference
  from deepneuro.postprocessing.label import BinarizeLabel, FillHoles, LargestComponents
  from deepneuro.models.model import load_model_with_output
label_desc: Use image node_id 2 for calling the SkullStrip obj's underlying member method code with example usage: obj.initialize(data_collection) without return types