old_contents: import processes as procs
  
  
  def fill_and_extract_brain(t1, t2, t2_lesions):
      t1_bias_correct = procs.bias_correct(t1)
      t2_aligned_t1, t2_to_t1_transform = procs.register(t1_bias_correct, t2)
      t2_lesions_aligned_t1, _ = procs.register(
          t1_bias_correct,
          t2_lesions,
          t2_to_t1_transform,
          interpolate=False
      )
      t1_lesion_filled = procs.fill_lesions(t1_bias_correct, t2_lesions_aligned_t1)
      brain, brain_bin = procs.steps_brain_extraction(t1_lesion_filled)
      return t1_bias_correct, t1_lesion_filled, brain, brain_bin
  
  
  def mtr(t1, t2, t2_lesions, mton_short, mtoff_short, mton_long, mtoff_long):
      t1_bias_corr, _, _, brain_bin = procs.fill_and_extract_brain(t1, t2, t2_lesions)
      mton = procs.average_images(mton_short, mton_long)
      mtoff = procs.average_images(mtoff_short, mtoff_long)
      mtrmap, mtoff_midpoint, _ = procs.make_mtr_map(mton, mtoff)
      t1_aligned_mtr, t1_to_mtr_transform = procs.register(mtoff_midpoint, t1_bias_corr)
      mask_aligned_mtr, _ = procs.register(
          mtoff_midpoint,
          brain_bin,
          t1_to_mtr_transform,
          interpolate=False
      )
      procs.mask_image(mtrmap, mask_aligned_mtr)
  
new_contents: import processes as procs
  
  
  def fill_and_extract_brain(t1, t2, t2_lesions):
      t1_bias_correct = procs.bias_correct(t1)
      t2_aligned_t1, t2_to_t1_transform = procs.register(t1_bias_correct, t2)
      t2_lesions_aligned_t1, _ = procs.register(
          t1_bias_correct,
          t2_lesions,
          t2_to_t1_transform,
          interpolate=False
      )
      t1_lesion_filled = procs.fill_lesions(t1_bias_correct, t2_lesions_aligned_t1)
      brain, brain_bin = procs.steps_brain_extraction(t1_lesion_filled)
      return t1_bias_correct, t1_lesion_filled, brain, brain_bin
  
  
  def mtr(t1, t2, t2_lesions, mton_short, mtoff_short, mton_long, mtoff_long):
      t1_bias_corr, _, _, brain_bin = fill_and_extract_brain(t1, t2, t2_lesions)
      mton = procs.average_images(mton_short, mton_long)
      mtoff = procs.average_images(mtoff_short, mtoff_long)
      mtrmap, mtoff_midpoint, _ = procs.make_mtr_map(mton, mtoff)
      t1_aligned_mtr, t1_to_mtr_transform = procs.register(mtoff_midpoint, t1_bias_corr)
      mask_aligned_mtr, _ = procs.register(
          mtoff_midpoint,
          brain_bin,
          t1_to_mtr_transform,
          interpolate=False
      )
      procs.mask_image(mtrmap, mask_aligned_mtr)
  
subject: Fix call to fill_and_extract_brain - is not a member of processes module