old_contents: from processes import (
      register, fill_lesions, average_images, make_mtr_map, mask_image,
      steps_brain_extraction, bias_correct
  )
  
  
  def fill_and_extract_brain(t1, t2, t2_lesions):
      t1_bias_correct = bias_correct(t1)
      t2_aligned_t1, t2_to_t1_transform = register(t1_bias_correct, t2)
      t2_lesions_aligned_t1, _ = register(
          t1_bias_correct,
          t2_lesions,
          t2_to_t1_transform,
          interpolate=False
      )
      t1_lesion_filled = fill_lesions(t1_bias_correct, t2_lesions_aligned_t1)
      brain, brain_bin = 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 = average_images(mton_short, mton_long)
      mtoff = average_images(mtoff_short, mtoff_long)
      mtrmap, mtoff_midpoint, _ = make_mtr_map(mton, mtoff)
      t1_aligned_mtr, t1_to_mtr_transform = register(mtoff_midpoint, t1_bias_corr)
      mask_aligned_mtr, _ = register(
          mtoff_midpoint,
          brain_bin,
          t1_to_mtr_transform,
          interpolate=False
      )
      mask_image(mtrmap, mask_aligned_mtr)
      return mtrmap_brain
  
new_contents: from processes import (
      register, fill_lesions, average_images, make_mtr_map, mask_image,
      steps_brain_extraction, bias_correct
  )
  
  
  def fill_and_extract_brain(t1, t2, t2_lesions):
      t1_bias_correct = bias_correct(t1)
      t2_aligned_t1, t2_to_t1_transform = register(t1_bias_correct, t2)
      t2_lesions_aligned_t1, _ = register(
          t1_bias_correct,
          t2_lesions,
          t2_to_t1_transform,
          interpolate=False
      )
      t1_lesion_filled = fill_lesions(t1_bias_correct, t2_lesions_aligned_t1)
      brain, brain_bin = 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 = average_images(mton_short, mton_long)
      mtoff = average_images(mtoff_short, mtoff_long)
      mtrmap, mtoff_midpoint, _ = make_mtr_map(mton, mtoff)
      t1_aligned_mtr, t1_to_mtr_transform = register(mtoff_midpoint, t1_bias_corr)
      mask_aligned_mtr, _ = register(
          mtoff_midpoint,
          brain_bin,
          t1_to_mtr_transform,
          interpolate=False
      )
      mask_image(mtrmap, mask_aligned_mtr)
  
subject: Stop returning MTR mapped brain from mtr pipeline