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totalsegmentator_class_map.py
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"""
TotalSegmentator has a full resolution approach and a faster, lower resolution approach.
The full resolution approach is trained on isotropic 1.5mm CT scans, while the lower resolution
approach is trained on 3mm CT scans.
The lower resolution approach uses a single nnUNet model to predict all 104 classes.
The full resolution approach uses 5 nnUNet models, each predicting 21 classes (total of 104).
"""
CLASS_MAP_ALL = {
1: "spleen",
2: "kidney_right",
3: "kidney_left",
4: "gallbladder",
5: "liver",
6: "stomach",
7: "aorta",
8: "inferior_vena_cava",
9: "portal_vein_and_splenic_vein",
10: "pancreas",
11: "adrenal_gland_right",
12: "adrenal_gland_left",
13: "lung_upper_lobe_left",
14: "lung_lower_lobe_left",
15: "lung_upper_lobe_right",
16: "lung_middle_lobe_right",
17: "lung_lower_lobe_right",
18: "vertebrae_L5",
19: "vertebrae_L4",
20: "vertebrae_L3",
21: "vertebrae_L2",
22: "vertebrae_L1",
23: "vertebrae_T12",
24: "vertebrae_T11",
25: "vertebrae_T10",
26: "vertebrae_T9",
27: "vertebrae_T8",
28: "vertebrae_T7",
29: "vertebrae_T6",
30: "vertebrae_T5",
31: "vertebrae_T4",
32: "vertebrae_T3",
33: "vertebrae_T2",
34: "vertebrae_T1",
35: "vertebrae_C7",
36: "vertebrae_C6",
37: "vertebrae_C5",
38: "vertebrae_C4",
39: "vertebrae_C3",
40: "vertebrae_C2",
41: "vertebrae_C1",
42: "esophagus",
43: "trachea",
44: "heart_myocardium",
45: "heart_atrium_left",
46: "heart_ventricle_left",
47: "heart_atrium_right",
48: "heart_ventricle_right",
49: "pulmonary_artery",
50: "brain",
51: "iliac_artery_left",
52: "iliac_artery_right",
53: "iliac_vena_left",
54: "iliac_vena_right",
55: "small_bowel",
56: "duodenum",
57: "colon",
58: "rib_left_1",
59: "rib_left_2",
60: "rib_left_3",
61: "rib_left_4",
62: "rib_left_5",
63: "rib_left_6",
64: "rib_left_7",
65: "rib_left_8",
66: "rib_left_9",
67: "rib_left_10",
68: "rib_left_11",
69: "rib_left_12",
70: "rib_right_1",
71: "rib_right_2",
72: "rib_right_3",
73: "rib_right_4",
74: "rib_right_5",
75: "rib_right_6",
76: "rib_right_7",
77: "rib_right_8",
78: "rib_right_9",
79: "rib_right_10",
80: "rib_right_11",
81: "rib_right_12",
82: "humerus_left",
83: "humerus_right",
84: "scapula_left",
85: "scapula_right",
86: "clavicula_left",
87: "clavicula_right",
88: "femur_left",
89: "femur_right",
90: "hip_left",
91: "hip_right",
92: "sacrum",
93: "face",
94: "gluteus_maximus_left",
95: "gluteus_maximus_right",
96: "gluteus_medius_left",
97: "gluteus_medius_right",
98: "gluteus_minimus_left",
99: "gluteus_minimus_right",
100: "autochthon_left",
101: "autochthon_right",
102: "iliopsoas_left",
103: "iliopsoas_right",
104: "urinary_bladder"
}
CLASS_MAP_5_PARTS = {
# 17 classes
"organs": {
1: "spleen",
2: "kidney_right",
3: "kidney_left",
4: "gallbladder",
5: "liver",
6: "stomach",
7: "aorta",
8: "inferior_vena_cava",
9: "portal_vein_and_splenic_vein",
10: "pancreas",
11: "adrenal_gland_right",
12: "adrenal_gland_left",
13: "lung_upper_lobe_left",
14: "lung_lower_lobe_left",
15: "lung_upper_lobe_right",
16: "lung_middle_lobe_right",
17: "lung_lower_lobe_right"
},
# 24 classes
"vertebrae": {
1: "vertebrae_L5",
2: "vertebrae_L4",
3: "vertebrae_L3",
4: "vertebrae_L2",
5: "vertebrae_L1",
6: "vertebrae_T12",
7: "vertebrae_T11",
8: "vertebrae_T10",
9: "vertebrae_T9",
10: "vertebrae_T8",
11: "vertebrae_T7",
12: "vertebrae_T6",
13: "vertebrae_T5",
14: "vertebrae_T4",
15: "vertebrae_T3",
16: "vertebrae_T2",
17: "vertebrae_T1",
18: "vertebrae_C7",
19: "vertebrae_C6",
20: "vertebrae_C5",
21: "vertebrae_C4",
22: "vertebrae_C3",
23: "vertebrae_C2",
24: "vertebrae_C1"
},
# 18
"cardiac": {
1: "esophagus",
2: "trachea",
3: "heart_myocardium",
4: "heart_atrium_left",
5: "heart_ventricle_left",
6: "heart_atrium_right",
7: "heart_ventricle_right",
8: "pulmonary_artery",
9: "brain",
10: "iliac_artery_left",
11: "iliac_artery_right",
12: "iliac_vena_left",
13: "iliac_vena_right",
14: "small_bowel",
15: "duodenum",
16: "colon",
17: "urinary_bladder",
18: "face"
},
# 21
"muscles": {
1: "humerus_left",
2: "humerus_right",
3: "scapula_left",
4: "scapula_right",
5: "clavicula_left",
6: "clavicula_right",
7: "femur_left",
8: "femur_right",
9: "hip_left",
10: "hip_right",
11: "sacrum",
12: "gluteus_maximus_left",
13: "gluteus_maximus_right",
14: "gluteus_medius_left",
15: "gluteus_medius_right",
16: "gluteus_minimus_left",
17: "gluteus_minimus_right",
18: "autochthon_left",
19: "autochthon_right",
20: "iliopsoas_left",
21: "iliopsoas_right"
},
# 24 classes
# 12. ribs start from vertebrae T12
# Small subset of population (roughly 8%) have 13. rib below 12. rib
# (would start from L1 then)
# -> this has label rib_12
# Even smaller subset (roughly 1%) has extra rib above 1. rib ("Halsrippe")
# (the extra rib would start from C7)
# -> this has label rib_1
#
# Quite often only 11 ribs (12. ribs probably so small that not found). Those
# cases often wrongly segmented.
"ribs": {
1: "rib_left_1",
2: "rib_left_2",
3: "rib_left_3",
4: "rib_left_4",
5: "rib_left_5",
6: "rib_left_6",
7: "rib_left_7",
8: "rib_left_8",
9: "rib_left_9",
10: "rib_left_10",
11: "rib_left_11",
12: "rib_left_12",
13: "rib_right_1",
14: "rib_right_2",
15: "rib_right_3",
16: "rib_right_4",
17: "rib_right_5",
18: "rib_right_6",
19: "rib_right_7",
20: "rib_right_8",
21: "rib_right_9",
22: "rib_right_10",
23: "rib_right_11",
24: "rib_right_12"
}
}