ShapeKit/config.yaml at main · BodyMaps/ShapeKit · GitHub

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# folder name to contain all the organ files in a case
subfolder_name: segmentations

# mapping dict, remember to change
class_map:
  1: aorta
  2: gall_bladder
  3: kidney_left
  4: kidney_right
  5: liver
  6: pancreas
  7: postcava
  8: spleen
  9: stomach
  10: adrenal_gland_left
  11: adrenal_gland_right
  12: bladder
  13: celiac_trunk
  14: colon
  15: duodenum
  16: esophagus
  17: femur_left
  18: femur_right
  19: hepatic_vessel
  20: intestine
  21: lung_left
  22: lung_right
  23: portal_vein_and_splenic_vein
  24: prostate
  25: rectum
  26: vertebrae_L5
  27: vertebrae_L4
  28: vertebrae_L3
  29: vertebrae_L2
  30: vertebrae_L1
  31: vertebrae_T12
  32: vertebrae_T11
  33: vertebrae_T10
  34: vertebrae_T9
  35: vertebrae_T8
  36: vertebrae_T7
  37: vertebrae_T6
  38: vertebrae_T5
  39: vertebrae_T4
  40: vertebrae_T3
  41: vertebrae_T2
  42: vertebrae_T1
  43: vertebrae_C7
  44: vertebrae_C6
  45: vertebrae_C5
  46: vertebrae_C4
  47: vertebrae_C3
  48: vertebrae_C2
  49: vertebrae_C1

# plug-and-play like Lego! choose organs for processing
target_organs:
  - adrenal_gland
  - aorta
  - bladder
  - colon
  - duodenum
  - femur
  - intestine
  - kidney
  - liver
  - lung
  - pancreas
  - postcava
  - prostate
  - spleen
  - stomach
  - vertebrae


# list of false positive suspects
organ_adjacency_map:
  lung_left: [postcava]
  lung_right: [postcava]
  liver: [kidney_right, pancreas]
  pancreas: [liver, stomach, colon, intestine]
  spleen: [liver]
  kidney_left: [liver]
  stomach: [pancreas, intestine, colon]
  aorta: [postcava]
  postcava: [aorta]
  colon: [intestine, lung_left, lung_right]

# affine reference, default as liver
affine_reference_file_name: liver.nii.gz

if_save_combined_label: True