preprocessing_cfg_aisd.yml

# GENERAL CONFIGS
general_config:
  datapath: '<PATH_TO_THE_DATA>'
  datasets: 'aisd'
  case_selection: ['all']  # Check
  data_csv_path: '<PATH_TO_THE_PROJECT>/data/dataset.csv'
  command_line: False
  steps:
    - read_and_write_sitk
    - resample
    - super_resolution
    - skull_stripping
    - tissue_segmentation
    - registration
    - intensity_clipping
    - brain_region_crop
    - difference_image
    - cleaning

# RESAMPLING CONFIGS
resample:
  resolution: [1., 1., 1.]
  tolerance: [0.05, 0.05]
  size: null
  interpolator: 'linear'
  gaussian_smooth: True
  force: True
  modalities:
    - ncct
    - dwi
    - msk
  suffix: res

# SUPER RESOLUTION CONFIGS
super_resolution:
  apply_over_resampled: False
  resampled_suffix: res
  check_resolution: True
  modalities:
    - ncct
  suffix: sr
  gpu: False
  force: True

# SKULL STRIPPING CONFIGS
skull_stripping:
  save_brain_mask: True
  brain_mask_suffix: bm
  save_skull_stripped: True
  skull_striped_suffix: ss
  alternative_suffix: alt
  check_resolution: True
  gpu: False
  force: True
  success_metric:
    - convexity
  convexity_threshold: 0.25
  ncct:
    over_image: sr
    method: synth-strip
    border: 0
    alternative_method: hd-bet
    mode: 'fast'
    tta: False
  dwi:
    over_image: res
    method: synth-strip
    border: 1
    alternative_method: hd-bet
    mode: 'fast'
    tta: False
  skull_strip_imgs:
    ncct-res: ncct-sr-bm

# TISSUE SEGMENTATION CONFIGS
tissue_segmentation:
  over_image:
    ncct: ncct-sr
    dwi: dwi-res
  suffix: tseg
  gpu: False
  save_simplified: True
  simplified_sufix: stseg
  get_qc_df: True
  force: True
  check_resolution: True

# REGISTRATION CONFIGS
registration:
  verbose: False
  apply_over_resampled: True
  resampled_suffix: res
  fixed_img: ncct-res-ss
  alternative_fixed_img: null
  moving_img: dwi-res-ss
  suffix: reg
  force: True
  method:
    name: elastix
    config:
      parameter_maps:
        - Par0010/Par0010affine.txt
      use_brain_masks: False
      brain_mask_suffix: bm
      write_img: False
  images_to_propagate:
    - dwi-res
  masks_to_propagate:
    # - msk-res
    # - msk
  final_skull_stripping:
    ncct-res: ncct-sr-bm
    dwi-res-reg: ncct-sr-bm
    # msk-res-reg: ncct-sr-bm
  success_metric:
    mutual_info:
      mri_img: dwi-res-reg-ss
      ncct_img: ncct-res-ss
      threshold: null
  check_resolution: True

# INTENSITY CLIPPING
intensity_clipping:
  ncct-res-ss:
    min: -100
    max: 400
  suffix: ic
  force: True

# BRAIN REGION CROPPING
brain_region_crop:
  margin: 3
  brain_mask: ncct-sr-bm
  over_img:
    - ncct-res-ss-ic
    - adc-res-reg-ss
    - msk-res
    - msk-res-reg-ss
    - ncct-sr-bm
    - ncct-sr-stseg
  suffix: c
  force: True
  bboxes_info_path: '<PATH_TO_THE_PROJECT>/experiments/crop_brain_vols/temporal_files'
  bboxes_info_file: 'bbxes_info_aisd.json'

# DIFFERENCE IMAGE GENERATION
difference_image:
  verbose: True
  apply_over_img: ncct-res-ss-ic-c
  brain_mask: ncct-sr-bm-c
  mni_template_path: '<PATH_TO_DATA>/source_data/mni_ct/atlas-ss.nii.gz'
  diff_suffix: diff
  save_contralateral_img: True
  cntrlt_suffix: flip
  save_original_size: True
  force: True
  parameter_maps:
    - Par0010/Par0010affine.txt
  register_vascular_map: True
  mni_vascular_map_path: '<PATH_TO_THE_DATA>/source_data/vascular_territories/mni_vascular_territories.nii.gz'
  mni_vascular_map_t1_path: '<PATH_TO_THE_DATA>/source_data/vascular_territories/caa_t1_mni_ss.nii.gz'
  bboxes_info_path: '<PATH_TO_THE_PROJECT>/experiments/crop_brain_vols/bbox_info.json'

# CLEANING 
cleaning:
  clean_datasets_path: '<PATH_TO_THE_DATA>/clean'
  cleaning_matching:
    # ADC
    adc: 'adc'
    adc-res-reg-ss: 'adc-pp'
    adc-res-reg-ss-c: 'adc-pp-c'
    # DWI
    dwi: 'dwi'
    dwi-res-reg-ss: 'dwi-pp'
    dwi-res-reg-ss-c: 'dwi-pp-c'
    # GT
    msk: 'msk'
    msk-res: 'msk-pp'
    msk-res-c: 'msk-pp-c'
    msk-tilt-res: 'msk-pp'
    msk-tilt-res-c: 'msk-pp-c'
    # msk-res-reg-ss: 'msk-pp'
    # msk-res-reg-ss-c: 'msk-pp-c'
    # msk-tilt-res-reg-ss: 'msk-pp'
    # msk-tilt-res-reg-ss-c: 'msk-pp-c'
    # NCCT
    ncct: 'ncct'
    ncct-ss: 'ncct-pp'
    ncct-res-ss-ic: 'ncct-pp'
    ncct-res-ss-ic-c: 'ncct-pp-c'
    # NCCT-TILT
    ncct-tilt: 'ncct'
    ncct-tilt-ss: 'ncct-pp'
    ncct-tilt-res-ss-ic: 'ncct-pp'
    ncct-tilt-res-ss-ic-c: 'ncct-pp-c'
    # CONTRALATERAL IMAGES
    ncct-res-ss-ic-c-flip: 'ncct-pp-flip-c'
    ncct-res-ss-ic-flip: 'ncct-pp-flip'
    ncct-sr-bm-c-flip: 'bm-flip-c'
    ncct-sr-bm-flip: 'bm-flip'
    ncct-tilt-res-ss-ic-c-flip: 'ncct-pp-flip-c'
    ncct-tilt-res-ss-ic-flip: 'ncct-pp-flip'
    ncct-tilt-sr-bm-c-flip: 'bm-flip-c'
    ncct-tilt-sr-bm-flip: 'bm-flip'
    # STSEG
    ncct-sr-stseg: 'stseg'
    ncct-sr-stseg-c: 'stseg-c'
    ncct-tilt-sr-stseg: 'stseg'
    ncct-tilt-sr-stseg-c: 'stseg-c'
    # VASC MAPS
    vm-pp: 'vm-pp'
    vm-pp-c: 'vm-pp-c'
    # BRAIN MASK
    ncct-sr-bm: 'bm'
    ncct-sr-bm-c: 'bm-c'
    ncct-tilt-sr-bm: 'bm'
    ncct-tilt-sr-bm-c: 'bm-c'
    # DIFF IMAGE
    diff-pp: 'diff-pp'
    diff-pp-c: 'diff-pp-c'