Hugging Face's logo

MedMLX
/
totalsegmentator-mlx

Image Segmentation
MLX
Safetensors
apple-silicon
medical-imaging
segmentation
nnunet
research
Model card Files
xet
 Community
josand commited on
Commit
6c03d6f
·
verified ·
1 Parent(s): 7ea4b42

Publish TotalSegmentator v2 CT safetensors

Browse files
Files changed (42) hide show
  1. 291/conversion.json +16 -0
  2. 291/dataset.json +40 -0
  3. 291/fold_0/checkpoint_final/state.json +198 -0
  4. 291/fold_0/checkpoint_final/weights.safetensors +3 -0
  5. 291/plans.json +444 -0
  6. 292/conversion.json +16 -0
  7. 292/dataset.json +42 -0
  8. 292/fold_0/checkpoint_final/state.json +198 -0
  9. 292/fold_0/checkpoint_final/weights.safetensors +3 -0
  10. 292/plans.json +444 -0
  11. 293/conversion.json +16 -0
  12. 293/dataset.json +34 -0
  13. 293/fold_0/checkpoint_final/state.json +198 -0
  14. 293/fold_0/checkpoint_final/weights.safetensors +3 -0
  15. 293/plans.json +444 -0
  16. 294/conversion.json +16 -0
  17. 294/dataset.json +39 -0
  18. 294/fold_0/checkpoint_final/state.json +198 -0
  19. 294/fold_0/checkpoint_final/weights.safetensors +3 -0
  20. 294/plans.json +444 -0
  21. 295/conversion.json +16 -0
  22. 295/dataset.json +42 -0
  23. 295/fold_0/checkpoint_final/state.json +198 -0
  24. 295/fold_0/checkpoint_final/weights.safetensors +3 -0
  25. 295/plans.json +444 -0
  26. 297/conversion.json +16 -0
  27. 297/dataset.json +133 -0
  28. 297/fold_0/checkpoint_final/state.json +166 -0
  29. 297/fold_0/checkpoint_final/weights.safetensors +3 -0
  30. 297/plans.json +282 -0
  31. 298/conversion.json +16 -0
  32. 298/dataset.json +133 -0
  33. 298/fold_0/checkpoint_final/state.json +166 -0
  34. 298/fold_0/checkpoint_final/weights.safetensors +3 -0
  35. 298/plans.json +272 -0
  36. 300/conversion.json +20 -0
  37. 300/dataset.json +18 -0
  38. 300/fold_0/checkpoint_final/state.json +170 -0
  39. 300/fold_0/checkpoint_final/weights.safetensors +3 -0
  40. 300/plans.json +272 -0
  41. LICENSE +201 -0
  42. README.md +26 -0
291/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
291/dataset.json ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "labels": {
8
+ "background": 0,
9
+ "spleen": 1,
10
+ "kidney_right": 2,
11
+ "kidney_left": 3,
12
+ "gallbladder": 4,
13
+ "liver": 5,
14
+ "stomach": 6,
15
+ "pancreas": 7,
16
+ "adrenal_gland_right": 8,
17
+ "adrenal_gland_left": 9,
18
+ "lung_upper_lobe_left": 10,
19
+ "lung_lower_lobe_left": 11,
20
+ "lung_upper_lobe_right": 12,
21
+ "lung_middle_lobe_right": 13,
22
+ "lung_lower_lobe_right": 14,
23
+ "esophagus": 15,
24
+ "trachea": 16,
25
+ "thyroid_gland": 17,
26
+ "small_bowel": 18,
27
+ "duodenum": 19,
28
+ "colon": 20,
29
+ "urinary_bladder": 21,
30
+ "prostate": 22,
31
+ "kidney_cyst_left": 23,
32
+ "kidney_cyst_right": 24
33
+ },
34
+ "numTraining": 1559,
35
+ "channel_names": {
36
+ "0": "CT"
37
+ },
38
+ "file_ending": ".nii.gz",
39
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
40
+ }
291/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,198 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 1001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.bias",
85
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.weight",
86
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.bias",
87
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.weight",
88
+ "decoder.encoder.stages.5.0.convs.0.conv.bias",
89
+ "decoder.encoder.stages.5.0.convs.0.conv.weight",
90
+ "decoder.encoder.stages.5.0.convs.0.norm.bias",
91
+ "decoder.encoder.stages.5.0.convs.0.norm.weight",
92
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.bias",
93
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.weight",
94
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.bias",
95
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.weight",
96
+ "decoder.encoder.stages.5.0.convs.1.conv.bias",
97
+ "decoder.encoder.stages.5.0.convs.1.conv.weight",
98
+ "decoder.encoder.stages.5.0.convs.1.norm.bias",
99
+ "decoder.encoder.stages.5.0.convs.1.norm.weight",
100
+ "decoder.stages.0.convs.0.all_modules.0.bias",
101
+ "decoder.stages.0.convs.0.all_modules.0.weight",
102
+ "decoder.stages.0.convs.0.all_modules.1.bias",
103
+ "decoder.stages.0.convs.0.all_modules.1.weight",
104
+ "decoder.stages.0.convs.1.all_modules.0.bias",
105
+ "decoder.stages.0.convs.1.all_modules.0.weight",
106
+ "decoder.stages.0.convs.1.all_modules.1.bias",
107
+ "decoder.stages.0.convs.1.all_modules.1.weight",
108
+ "decoder.stages.1.convs.0.all_modules.0.bias",
109
+ "decoder.stages.1.convs.0.all_modules.0.weight",
110
+ "decoder.stages.1.convs.0.all_modules.1.bias",
111
+ "decoder.stages.1.convs.0.all_modules.1.weight",
112
+ "decoder.stages.1.convs.1.all_modules.0.bias",
113
+ "decoder.stages.1.convs.1.all_modules.0.weight",
114
+ "decoder.stages.1.convs.1.all_modules.1.bias",
115
+ "decoder.stages.1.convs.1.all_modules.1.weight",
116
+ "decoder.stages.2.convs.0.all_modules.0.bias",
117
+ "decoder.stages.2.convs.0.all_modules.0.weight",
118
+ "decoder.stages.2.convs.0.all_modules.1.bias",
119
+ "decoder.stages.2.convs.0.all_modules.1.weight",
120
+ "decoder.stages.2.convs.1.all_modules.0.bias",
121
+ "decoder.stages.2.convs.1.all_modules.0.weight",
122
+ "decoder.stages.2.convs.1.all_modules.1.bias",
123
+ "decoder.stages.2.convs.1.all_modules.1.weight",
124
+ "decoder.stages.3.convs.0.all_modules.0.bias",
125
+ "decoder.stages.3.convs.0.all_modules.0.weight",
126
+ "decoder.stages.3.convs.0.all_modules.1.bias",
127
+ "decoder.stages.3.convs.0.all_modules.1.weight",
128
+ "decoder.stages.3.convs.1.all_modules.0.bias",
129
+ "decoder.stages.3.convs.1.all_modules.0.weight",
130
+ "decoder.stages.3.convs.1.all_modules.1.bias",
131
+ "decoder.stages.3.convs.1.all_modules.1.weight",
132
+ "decoder.stages.4.convs.0.all_modules.0.bias",
133
+ "decoder.stages.4.convs.0.all_modules.0.weight",
134
+ "decoder.stages.4.convs.0.all_modules.1.bias",
135
+ "decoder.stages.4.convs.0.all_modules.1.weight",
136
+ "decoder.stages.4.convs.1.all_modules.0.bias",
137
+ "decoder.stages.4.convs.1.all_modules.0.weight",
138
+ "decoder.stages.4.convs.1.all_modules.1.bias",
139
+ "decoder.stages.4.convs.1.all_modules.1.weight",
140
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
156
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
157
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
158
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
159
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
160
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
161
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
162
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
163
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
164
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
165
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
166
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
167
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
168
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
169
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
170
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
171
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
172
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
173
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
174
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
175
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
176
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
177
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
178
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
179
+ "encoder.stages.4.0.convs.1.all_modules.1.weight",
180
+ "encoder.stages.5.0.convs.0.all_modules.0.bias",
181
+ "encoder.stages.5.0.convs.0.all_modules.0.weight",
182
+ "encoder.stages.5.0.convs.0.all_modules.1.bias",
183
+ "encoder.stages.5.0.convs.0.all_modules.1.weight",
184
+ "encoder.stages.5.0.convs.1.all_modules.0.bias",
185
+ "encoder.stages.5.0.convs.1.all_modules.0.weight",
186
+ "encoder.stages.5.0.convs.1.all_modules.1.bias",
187
+ "encoder.stages.5.0.convs.1.all_modules.1.weight"
188
+ ],
189
+ "identity": {
190
+ "configuration": "3d_fullres",
191
+ "fold": 0,
192
+ "trainer_name": "nnUNetTrainerNoMirroring"
193
+ },
194
+ "inference_allowed_mirroring_axes": [],
195
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
196
+ "source_nnunet_version": "v2.8.1",
197
+ "spatial_dims": 3
198
+ }
291/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0dee24d376bf4fec117cfe166d08613f2392bd7295c8b1026a81b42b379f7151
3
+ size 124866153
291/plans.json ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset291_TotalSegmentator_part1_organs_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 1.5,
6
+ 1.5,
7
+ 1.5
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 227,
11
+ 227,
12
+ 240
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 46,
30
+ "patch_size": [
31
+ 256,
32
+ 256
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 227.0,
36
+ 239.0
37
+ ],
38
+ "spacing": [
39
+ 1.5,
40
+ 1.5
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2,
56
+ 2,
57
+ 2
58
+ ],
59
+ "n_conv_per_stage_decoder": [
60
+ 2,
61
+ 2,
62
+ 2,
63
+ 2,
64
+ 2,
65
+ 2
66
+ ],
67
+ "num_pool_per_axis": [
68
+ 6,
69
+ 6
70
+ ],
71
+ "pool_op_kernel_sizes": [
72
+ [
73
+ 1,
74
+ 1
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ],
88
+ [
89
+ 2,
90
+ 2
91
+ ],
92
+ [
93
+ 2,
94
+ 2
95
+ ],
96
+ [
97
+ 2,
98
+ 2
99
+ ]
100
+ ],
101
+ "conv_kernel_sizes": [
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ],
110
+ [
111
+ 3,
112
+ 3
113
+ ],
114
+ [
115
+ 3,
116
+ 3
117
+ ],
118
+ [
119
+ 3,
120
+ 3
121
+ ],
122
+ [
123
+ 3,
124
+ 3
125
+ ],
126
+ [
127
+ 3,
128
+ 3
129
+ ]
130
+ ],
131
+ "unet_max_num_features": 512,
132
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
133
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
134
+ "resampling_fn_data_kwargs": {
135
+ "is_seg": false,
136
+ "order": 3,
137
+ "order_z": 0,
138
+ "force_separate_z": null
139
+ },
140
+ "resampling_fn_seg_kwargs": {
141
+ "is_seg": true,
142
+ "order": 1,
143
+ "order_z": 0,
144
+ "force_separate_z": null
145
+ },
146
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
147
+ "resampling_fn_probabilities_kwargs": {
148
+ "is_seg": false,
149
+ "order": 1,
150
+ "order_z": 0,
151
+ "force_separate_z": null
152
+ },
153
+ "batch_dice": true
154
+ },
155
+ "3d_lowres": {
156
+ "data_identifier": "nnUNetPlans_3d_lowres",
157
+ "preprocessor_name": "DefaultPreprocessor",
158
+ "batch_size": 2,
159
+ "patch_size": [
160
+ 128,
161
+ 128,
162
+ 128
163
+ ],
164
+ "median_image_size_in_voxels": [
165
+ 196,
166
+ 196,
167
+ 206
168
+ ],
169
+ "spacing": [
170
+ 1.7389111114500002,
171
+ 1.7389111114500002,
172
+ 1.7389111114500002
173
+ ],
174
+ "normalization_schemes": [
175
+ "CTNormalization"
176
+ ],
177
+ "use_mask_for_norm": [
178
+ false
179
+ ],
180
+ "UNet_class_name": "PlainConvUNet",
181
+ "UNet_base_num_features": 32,
182
+ "n_conv_per_stage_encoder": [
183
+ 2,
184
+ 2,
185
+ 2,
186
+ 2,
187
+ 2,
188
+ 2
189
+ ],
190
+ "n_conv_per_stage_decoder": [
191
+ 2,
192
+ 2,
193
+ 2,
194
+ 2,
195
+ 2
196
+ ],
197
+ "num_pool_per_axis": [
198
+ 5,
199
+ 5,
200
+ 5
201
+ ],
202
+ "pool_op_kernel_sizes": [
203
+ [
204
+ 1,
205
+ 1,
206
+ 1
207
+ ],
208
+ [
209
+ 2,
210
+ 2,
211
+ 2
212
+ ],
213
+ [
214
+ 2,
215
+ 2,
216
+ 2
217
+ ],
218
+ [
219
+ 2,
220
+ 2,
221
+ 2
222
+ ],
223
+ [
224
+ 2,
225
+ 2,
226
+ 2
227
+ ],
228
+ [
229
+ 2,
230
+ 2,
231
+ 2
232
+ ]
233
+ ],
234
+ "conv_kernel_sizes": [
235
+ [
236
+ 3,
237
+ 3,
238
+ 3
239
+ ],
240
+ [
241
+ 3,
242
+ 3,
243
+ 3
244
+ ],
245
+ [
246
+ 3,
247
+ 3,
248
+ 3
249
+ ],
250
+ [
251
+ 3,
252
+ 3,
253
+ 3
254
+ ],
255
+ [
256
+ 3,
257
+ 3,
258
+ 3
259
+ ],
260
+ [
261
+ 3,
262
+ 3,
263
+ 3
264
+ ]
265
+ ],
266
+ "unet_max_num_features": 320,
267
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
268
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
269
+ "resampling_fn_data_kwargs": {
270
+ "is_seg": false,
271
+ "order": 3,
272
+ "order_z": 0,
273
+ "force_separate_z": null
274
+ },
275
+ "resampling_fn_seg_kwargs": {
276
+ "is_seg": true,
277
+ "order": 1,
278
+ "order_z": 0,
279
+ "force_separate_z": null
280
+ },
281
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
282
+ "resampling_fn_probabilities_kwargs": {
283
+ "is_seg": false,
284
+ "order": 1,
285
+ "order_z": 0,
286
+ "force_separate_z": null
287
+ },
288
+ "batch_dice": false,
289
+ "next_stage": "3d_cascade_fullres"
290
+ },
291
+ "3d_fullres": {
292
+ "data_identifier": "nnUNetPlans_3d_fullres",
293
+ "preprocessor_name": "DefaultPreprocessor",
294
+ "batch_size": 2,
295
+ "patch_size": [
296
+ 128,
297
+ 128,
298
+ 128
299
+ ],
300
+ "median_image_size_in_voxels": [
301
+ 227.0,
302
+ 227.0,
303
+ 239.0
304
+ ],
305
+ "spacing": [
306
+ 1.5,
307
+ 1.5,
308
+ 1.5
309
+ ],
310
+ "normalization_schemes": [
311
+ "CTNormalization"
312
+ ],
313
+ "use_mask_for_norm": [
314
+ false
315
+ ],
316
+ "UNet_class_name": "PlainConvUNet",
317
+ "UNet_base_num_features": 32,
318
+ "n_conv_per_stage_encoder": [
319
+ 2,
320
+ 2,
321
+ 2,
322
+ 2,
323
+ 2,
324
+ 2
325
+ ],
326
+ "n_conv_per_stage_decoder": [
327
+ 2,
328
+ 2,
329
+ 2,
330
+ 2,
331
+ 2
332
+ ],
333
+ "num_pool_per_axis": [
334
+ 5,
335
+ 5,
336
+ 5
337
+ ],
338
+ "pool_op_kernel_sizes": [
339
+ [
340
+ 1,
341
+ 1,
342
+ 1
343
+ ],
344
+ [
345
+ 2,
346
+ 2,
347
+ 2
348
+ ],
349
+ [
350
+ 2,
351
+ 2,
352
+ 2
353
+ ],
354
+ [
355
+ 2,
356
+ 2,
357
+ 2
358
+ ],
359
+ [
360
+ 2,
361
+ 2,
362
+ 2
363
+ ],
364
+ [
365
+ 2,
366
+ 2,
367
+ 2
368
+ ]
369
+ ],
370
+ "conv_kernel_sizes": [
371
+ [
372
+ 3,
373
+ 3,
374
+ 3
375
+ ],
376
+ [
377
+ 3,
378
+ 3,
379
+ 3
380
+ ],
381
+ [
382
+ 3,
383
+ 3,
384
+ 3
385
+ ],
386
+ [
387
+ 3,
388
+ 3,
389
+ 3
390
+ ],
391
+ [
392
+ 3,
393
+ 3,
394
+ 3
395
+ ],
396
+ [
397
+ 3,
398
+ 3,
399
+ 3
400
+ ]
401
+ ],
402
+ "unet_max_num_features": 320,
403
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
404
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
405
+ "resampling_fn_data_kwargs": {
406
+ "is_seg": false,
407
+ "order": 3,
408
+ "order_z": 0,
409
+ "force_separate_z": null
410
+ },
411
+ "resampling_fn_seg_kwargs": {
412
+ "is_seg": true,
413
+ "order": 1,
414
+ "order_z": 0,
415
+ "force_separate_z": null
416
+ },
417
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
418
+ "resampling_fn_probabilities_kwargs": {
419
+ "is_seg": false,
420
+ "order": 1,
421
+ "order_z": 0,
422
+ "force_separate_z": null
423
+ },
424
+ "batch_dice": true
425
+ },
426
+ "3d_cascade_fullres": {
427
+ "inherits_from": "3d_fullres",
428
+ "previous_stage": "3d_lowres"
429
+ }
430
+ },
431
+ "experiment_planner_used": "ExperimentPlanner",
432
+ "label_manager": "LabelManager",
433
+ "foreground_intensity_properties_per_channel": {
434
+ "0": {
435
+ "max": 3606.0,
436
+ "mean": -370.00039267657144,
437
+ "median": -249.0,
438
+ "min": -3139.0,
439
+ "percentile_00_5": -1024.0,
440
+ "percentile_99_5": 276.0,
441
+ "std": 436.5998675471528
442
+ }
443
+ }
444
+ }
292/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
292/dataset.json ADDED
@@ -0,0 +1,42 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "labels": {
8
+ "background": 0,
9
+ "sacrum": 1,
10
+ "vertebrae_S1": 2,
11
+ "vertebrae_L5": 3,
12
+ "vertebrae_L4": 4,
13
+ "vertebrae_L3": 5,
14
+ "vertebrae_L2": 6,
15
+ "vertebrae_L1": 7,
16
+ "vertebrae_T12": 8,
17
+ "vertebrae_T11": 9,
18
+ "vertebrae_T10": 10,
19
+ "vertebrae_T9": 11,
20
+ "vertebrae_T8": 12,
21
+ "vertebrae_T7": 13,
22
+ "vertebrae_T6": 14,
23
+ "vertebrae_T5": 15,
24
+ "vertebrae_T4": 16,
25
+ "vertebrae_T3": 17,
26
+ "vertebrae_T2": 18,
27
+ "vertebrae_T1": 19,
28
+ "vertebrae_C7": 20,
29
+ "vertebrae_C6": 21,
30
+ "vertebrae_C5": 22,
31
+ "vertebrae_C4": 23,
32
+ "vertebrae_C3": 24,
33
+ "vertebrae_C2": 25,
34
+ "vertebrae_C1": 26
35
+ },
36
+ "numTraining": 1532,
37
+ "channel_names": {
38
+ "0": "CT"
39
+ },
40
+ "file_ending": ".nii.gz",
41
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
42
+ }
292/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,198 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 1001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.bias",
85
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.weight",
86
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.bias",
87
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.weight",
88
+ "decoder.encoder.stages.5.0.convs.0.conv.bias",
89
+ "decoder.encoder.stages.5.0.convs.0.conv.weight",
90
+ "decoder.encoder.stages.5.0.convs.0.norm.bias",
91
+ "decoder.encoder.stages.5.0.convs.0.norm.weight",
92
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.bias",
93
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.weight",
94
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.bias",
95
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.weight",
96
+ "decoder.encoder.stages.5.0.convs.1.conv.bias",
97
+ "decoder.encoder.stages.5.0.convs.1.conv.weight",
98
+ "decoder.encoder.stages.5.0.convs.1.norm.bias",
99
+ "decoder.encoder.stages.5.0.convs.1.norm.weight",
100
+ "decoder.stages.0.convs.0.all_modules.0.bias",
101
+ "decoder.stages.0.convs.0.all_modules.0.weight",
102
+ "decoder.stages.0.convs.0.all_modules.1.bias",
103
+ "decoder.stages.0.convs.0.all_modules.1.weight",
104
+ "decoder.stages.0.convs.1.all_modules.0.bias",
105
+ "decoder.stages.0.convs.1.all_modules.0.weight",
106
+ "decoder.stages.0.convs.1.all_modules.1.bias",
107
+ "decoder.stages.0.convs.1.all_modules.1.weight",
108
+ "decoder.stages.1.convs.0.all_modules.0.bias",
109
+ "decoder.stages.1.convs.0.all_modules.0.weight",
110
+ "decoder.stages.1.convs.0.all_modules.1.bias",
111
+ "decoder.stages.1.convs.0.all_modules.1.weight",
112
+ "decoder.stages.1.convs.1.all_modules.0.bias",
113
+ "decoder.stages.1.convs.1.all_modules.0.weight",
114
+ "decoder.stages.1.convs.1.all_modules.1.bias",
115
+ "decoder.stages.1.convs.1.all_modules.1.weight",
116
+ "decoder.stages.2.convs.0.all_modules.0.bias",
117
+ "decoder.stages.2.convs.0.all_modules.0.weight",
118
+ "decoder.stages.2.convs.0.all_modules.1.bias",
119
+ "decoder.stages.2.convs.0.all_modules.1.weight",
120
+ "decoder.stages.2.convs.1.all_modules.0.bias",
121
+ "decoder.stages.2.convs.1.all_modules.0.weight",
122
+ "decoder.stages.2.convs.1.all_modules.1.bias",
123
+ "decoder.stages.2.convs.1.all_modules.1.weight",
124
+ "decoder.stages.3.convs.0.all_modules.0.bias",
125
+ "decoder.stages.3.convs.0.all_modules.0.weight",
126
+ "decoder.stages.3.convs.0.all_modules.1.bias",
127
+ "decoder.stages.3.convs.0.all_modules.1.weight",
128
+ "decoder.stages.3.convs.1.all_modules.0.bias",
129
+ "decoder.stages.3.convs.1.all_modules.0.weight",
130
+ "decoder.stages.3.convs.1.all_modules.1.bias",
131
+ "decoder.stages.3.convs.1.all_modules.1.weight",
132
+ "decoder.stages.4.convs.0.all_modules.0.bias",
133
+ "decoder.stages.4.convs.0.all_modules.0.weight",
134
+ "decoder.stages.4.convs.0.all_modules.1.bias",
135
+ "decoder.stages.4.convs.0.all_modules.1.weight",
136
+ "decoder.stages.4.convs.1.all_modules.0.bias",
137
+ "decoder.stages.4.convs.1.all_modules.0.weight",
138
+ "decoder.stages.4.convs.1.all_modules.1.bias",
139
+ "decoder.stages.4.convs.1.all_modules.1.weight",
140
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
156
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
157
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
158
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
159
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
160
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
161
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
162
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
163
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
164
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
165
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
166
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
167
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
168
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
169
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
170
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
171
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
172
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
173
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
174
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
175
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
176
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
177
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
178
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
179
+ "encoder.stages.4.0.convs.1.all_modules.1.weight",
180
+ "encoder.stages.5.0.convs.0.all_modules.0.bias",
181
+ "encoder.stages.5.0.convs.0.all_modules.0.weight",
182
+ "encoder.stages.5.0.convs.0.all_modules.1.bias",
183
+ "encoder.stages.5.0.convs.0.all_modules.1.weight",
184
+ "encoder.stages.5.0.convs.1.all_modules.0.bias",
185
+ "encoder.stages.5.0.convs.1.all_modules.0.weight",
186
+ "encoder.stages.5.0.convs.1.all_modules.1.bias",
187
+ "encoder.stages.5.0.convs.1.all_modules.1.weight"
188
+ ],
189
+ "identity": {
190
+ "configuration": "3d_fullres",
191
+ "fold": 0,
192
+ "trainer_name": "nnUNetTrainerNoMirroring"
193
+ },
194
+ "inference_allowed_mirroring_axes": [],
195
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
196
+ "source_nnunet_version": "v2.8.1",
197
+ "spatial_dims": 3
198
+ }
292/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:c3a81d9838c89d5b9de723bf39616807d3837e72d8ea0965cce63c31e2ed38ba
3
+ size 124872593
292/plans.json ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset292_TotalSegmentator_part2_vertebrae_1532subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 1.5,
6
+ 1.5,
7
+ 1.5
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 225,
11
+ 227,
12
+ 239
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 46,
30
+ "patch_size": [
31
+ 256,
32
+ 256
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 227.0,
36
+ 239.0
37
+ ],
38
+ "spacing": [
39
+ 1.5,
40
+ 1.5
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2,
56
+ 2,
57
+ 2
58
+ ],
59
+ "n_conv_per_stage_decoder": [
60
+ 2,
61
+ 2,
62
+ 2,
63
+ 2,
64
+ 2,
65
+ 2
66
+ ],
67
+ "num_pool_per_axis": [
68
+ 6,
69
+ 6
70
+ ],
71
+ "pool_op_kernel_sizes": [
72
+ [
73
+ 1,
74
+ 1
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ],
88
+ [
89
+ 2,
90
+ 2
91
+ ],
92
+ [
93
+ 2,
94
+ 2
95
+ ],
96
+ [
97
+ 2,
98
+ 2
99
+ ]
100
+ ],
101
+ "conv_kernel_sizes": [
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ],
110
+ [
111
+ 3,
112
+ 3
113
+ ],
114
+ [
115
+ 3,
116
+ 3
117
+ ],
118
+ [
119
+ 3,
120
+ 3
121
+ ],
122
+ [
123
+ 3,
124
+ 3
125
+ ],
126
+ [
127
+ 3,
128
+ 3
129
+ ]
130
+ ],
131
+ "unet_max_num_features": 512,
132
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
133
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
134
+ "resampling_fn_data_kwargs": {
135
+ "is_seg": false,
136
+ "order": 3,
137
+ "order_z": 0,
138
+ "force_separate_z": null
139
+ },
140
+ "resampling_fn_seg_kwargs": {
141
+ "is_seg": true,
142
+ "order": 1,
143
+ "order_z": 0,
144
+ "force_separate_z": null
145
+ },
146
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
147
+ "resampling_fn_probabilities_kwargs": {
148
+ "is_seg": false,
149
+ "order": 1,
150
+ "order_z": 0,
151
+ "force_separate_z": null
152
+ },
153
+ "batch_dice": true
154
+ },
155
+ "3d_lowres": {
156
+ "data_identifier": "nnUNetPlans_3d_lowres",
157
+ "preprocessor_name": "DefaultPreprocessor",
158
+ "batch_size": 2,
159
+ "patch_size": [
160
+ 128,
161
+ 128,
162
+ 128
163
+ ],
164
+ "median_image_size_in_voxels": [
165
+ 194,
166
+ 196,
167
+ 206
168
+ ],
169
+ "spacing": [
170
+ 1.7389111114500002,
171
+ 1.7389111114500002,
172
+ 1.7389111114500002
173
+ ],
174
+ "normalization_schemes": [
175
+ "CTNormalization"
176
+ ],
177
+ "use_mask_for_norm": [
178
+ false
179
+ ],
180
+ "UNet_class_name": "PlainConvUNet",
181
+ "UNet_base_num_features": 32,
182
+ "n_conv_per_stage_encoder": [
183
+ 2,
184
+ 2,
185
+ 2,
186
+ 2,
187
+ 2,
188
+ 2
189
+ ],
190
+ "n_conv_per_stage_decoder": [
191
+ 2,
192
+ 2,
193
+ 2,
194
+ 2,
195
+ 2
196
+ ],
197
+ "num_pool_per_axis": [
198
+ 5,
199
+ 5,
200
+ 5
201
+ ],
202
+ "pool_op_kernel_sizes": [
203
+ [
204
+ 1,
205
+ 1,
206
+ 1
207
+ ],
208
+ [
209
+ 2,
210
+ 2,
211
+ 2
212
+ ],
213
+ [
214
+ 2,
215
+ 2,
216
+ 2
217
+ ],
218
+ [
219
+ 2,
220
+ 2,
221
+ 2
222
+ ],
223
+ [
224
+ 2,
225
+ 2,
226
+ 2
227
+ ],
228
+ [
229
+ 2,
230
+ 2,
231
+ 2
232
+ ]
233
+ ],
234
+ "conv_kernel_sizes": [
235
+ [
236
+ 3,
237
+ 3,
238
+ 3
239
+ ],
240
+ [
241
+ 3,
242
+ 3,
243
+ 3
244
+ ],
245
+ [
246
+ 3,
247
+ 3,
248
+ 3
249
+ ],
250
+ [
251
+ 3,
252
+ 3,
253
+ 3
254
+ ],
255
+ [
256
+ 3,
257
+ 3,
258
+ 3
259
+ ],
260
+ [
261
+ 3,
262
+ 3,
263
+ 3
264
+ ]
265
+ ],
266
+ "unet_max_num_features": 320,
267
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
268
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
269
+ "resampling_fn_data_kwargs": {
270
+ "is_seg": false,
271
+ "order": 3,
272
+ "order_z": 0,
273
+ "force_separate_z": null
274
+ },
275
+ "resampling_fn_seg_kwargs": {
276
+ "is_seg": true,
277
+ "order": 1,
278
+ "order_z": 0,
279
+ "force_separate_z": null
280
+ },
281
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
282
+ "resampling_fn_probabilities_kwargs": {
283
+ "is_seg": false,
284
+ "order": 1,
285
+ "order_z": 0,
286
+ "force_separate_z": null
287
+ },
288
+ "batch_dice": false,
289
+ "next_stage": "3d_cascade_fullres"
290
+ },
291
+ "3d_fullres": {
292
+ "data_identifier": "nnUNetPlans_3d_fullres",
293
+ "preprocessor_name": "DefaultPreprocessor",
294
+ "batch_size": 2,
295
+ "patch_size": [
296
+ 128,
297
+ 128,
298
+ 128
299
+ ],
300
+ "median_image_size_in_voxels": [
301
+ 225.0,
302
+ 227.0,
303
+ 239.0
304
+ ],
305
+ "spacing": [
306
+ 1.5,
307
+ 1.5,
308
+ 1.5
309
+ ],
310
+ "normalization_schemes": [
311
+ "CTNormalization"
312
+ ],
313
+ "use_mask_for_norm": [
314
+ false
315
+ ],
316
+ "UNet_class_name": "PlainConvUNet",
317
+ "UNet_base_num_features": 32,
318
+ "n_conv_per_stage_encoder": [
319
+ 2,
320
+ 2,
321
+ 2,
322
+ 2,
323
+ 2,
324
+ 2
325
+ ],
326
+ "n_conv_per_stage_decoder": [
327
+ 2,
328
+ 2,
329
+ 2,
330
+ 2,
331
+ 2
332
+ ],
333
+ "num_pool_per_axis": [
334
+ 5,
335
+ 5,
336
+ 5
337
+ ],
338
+ "pool_op_kernel_sizes": [
339
+ [
340
+ 1,
341
+ 1,
342
+ 1
343
+ ],
344
+ [
345
+ 2,
346
+ 2,
347
+ 2
348
+ ],
349
+ [
350
+ 2,
351
+ 2,
352
+ 2
353
+ ],
354
+ [
355
+ 2,
356
+ 2,
357
+ 2
358
+ ],
359
+ [
360
+ 2,
361
+ 2,
362
+ 2
363
+ ],
364
+ [
365
+ 2,
366
+ 2,
367
+ 2
368
+ ]
369
+ ],
370
+ "conv_kernel_sizes": [
371
+ [
372
+ 3,
373
+ 3,
374
+ 3
375
+ ],
376
+ [
377
+ 3,
378
+ 3,
379
+ 3
380
+ ],
381
+ [
382
+ 3,
383
+ 3,
384
+ 3
385
+ ],
386
+ [
387
+ 3,
388
+ 3,
389
+ 3
390
+ ],
391
+ [
392
+ 3,
393
+ 3,
394
+ 3
395
+ ],
396
+ [
397
+ 3,
398
+ 3,
399
+ 3
400
+ ]
401
+ ],
402
+ "unet_max_num_features": 320,
403
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
404
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
405
+ "resampling_fn_data_kwargs": {
406
+ "is_seg": false,
407
+ "order": 3,
408
+ "order_z": 0,
409
+ "force_separate_z": null
410
+ },
411
+ "resampling_fn_seg_kwargs": {
412
+ "is_seg": true,
413
+ "order": 1,
414
+ "order_z": 0,
415
+ "force_separate_z": null
416
+ },
417
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
418
+ "resampling_fn_probabilities_kwargs": {
419
+ "is_seg": false,
420
+ "order": 1,
421
+ "order_z": 0,
422
+ "force_separate_z": null
423
+ },
424
+ "batch_dice": true
425
+ },
426
+ "3d_cascade_fullres": {
427
+ "inherits_from": "3d_fullres",
428
+ "previous_stage": "3d_lowres"
429
+ }
430
+ },
431
+ "experiment_planner_used": "ExperimentPlanner",
432
+ "label_manager": "LabelManager",
433
+ "foreground_intensity_properties_per_channel": {
434
+ "0": {
435
+ "max": 36911.0,
436
+ "mean": 367.32929817099546,
437
+ "median": 283.0,
438
+ "min": -34461.0,
439
+ "percentile_00_5": -96.0,
440
+ "percentile_99_5": 1514.0,
441
+ "std": 320.8587389393513
442
+ }
443
+ }
444
+ }
293/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
293/dataset.json ADDED
@@ -0,0 +1,34 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "channel_names": {
8
+ "0": "CT"
9
+ },
10
+ "labels": {
11
+ "background": 0,
12
+ "heart": 1,
13
+ "aorta": 2,
14
+ "pulmonary_vein": 3,
15
+ "brachiocephalic_trunk": 4,
16
+ "subclavian_artery_right": 5,
17
+ "subclavian_artery_left": 6,
18
+ "common_carotid_artery_right": 7,
19
+ "common_carotid_artery_left": 8,
20
+ "brachiocephalic_vein_left": 9,
21
+ "brachiocephalic_vein_right": 10,
22
+ "atrial_appendage_left": 11,
23
+ "superior_vena_cava": 12,
24
+ "inferior_vena_cava": 13,
25
+ "portal_vein_and_splenic_vein": 14,
26
+ "iliac_artery_left": 15,
27
+ "iliac_artery_right": 16,
28
+ "iliac_vena_left": 17,
29
+ "iliac_vena_right": 18
30
+ },
31
+ "numTraining": 1559,
32
+ "file_ending": ".nii.gz",
33
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
34
+ }
293/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,198 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 1001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.bias",
85
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.weight",
86
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.bias",
87
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.weight",
88
+ "decoder.encoder.stages.5.0.convs.0.conv.bias",
89
+ "decoder.encoder.stages.5.0.convs.0.conv.weight",
90
+ "decoder.encoder.stages.5.0.convs.0.norm.bias",
91
+ "decoder.encoder.stages.5.0.convs.0.norm.weight",
92
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.bias",
93
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.weight",
94
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.bias",
95
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.weight",
96
+ "decoder.encoder.stages.5.0.convs.1.conv.bias",
97
+ "decoder.encoder.stages.5.0.convs.1.conv.weight",
98
+ "decoder.encoder.stages.5.0.convs.1.norm.bias",
99
+ "decoder.encoder.stages.5.0.convs.1.norm.weight",
100
+ "decoder.stages.0.convs.0.all_modules.0.bias",
101
+ "decoder.stages.0.convs.0.all_modules.0.weight",
102
+ "decoder.stages.0.convs.0.all_modules.1.bias",
103
+ "decoder.stages.0.convs.0.all_modules.1.weight",
104
+ "decoder.stages.0.convs.1.all_modules.0.bias",
105
+ "decoder.stages.0.convs.1.all_modules.0.weight",
106
+ "decoder.stages.0.convs.1.all_modules.1.bias",
107
+ "decoder.stages.0.convs.1.all_modules.1.weight",
108
+ "decoder.stages.1.convs.0.all_modules.0.bias",
109
+ "decoder.stages.1.convs.0.all_modules.0.weight",
110
+ "decoder.stages.1.convs.0.all_modules.1.bias",
111
+ "decoder.stages.1.convs.0.all_modules.1.weight",
112
+ "decoder.stages.1.convs.1.all_modules.0.bias",
113
+ "decoder.stages.1.convs.1.all_modules.0.weight",
114
+ "decoder.stages.1.convs.1.all_modules.1.bias",
115
+ "decoder.stages.1.convs.1.all_modules.1.weight",
116
+ "decoder.stages.2.convs.0.all_modules.0.bias",
117
+ "decoder.stages.2.convs.0.all_modules.0.weight",
118
+ "decoder.stages.2.convs.0.all_modules.1.bias",
119
+ "decoder.stages.2.convs.0.all_modules.1.weight",
120
+ "decoder.stages.2.convs.1.all_modules.0.bias",
121
+ "decoder.stages.2.convs.1.all_modules.0.weight",
122
+ "decoder.stages.2.convs.1.all_modules.1.bias",
123
+ "decoder.stages.2.convs.1.all_modules.1.weight",
124
+ "decoder.stages.3.convs.0.all_modules.0.bias",
125
+ "decoder.stages.3.convs.0.all_modules.0.weight",
126
+ "decoder.stages.3.convs.0.all_modules.1.bias",
127
+ "decoder.stages.3.convs.0.all_modules.1.weight",
128
+ "decoder.stages.3.convs.1.all_modules.0.bias",
129
+ "decoder.stages.3.convs.1.all_modules.0.weight",
130
+ "decoder.stages.3.convs.1.all_modules.1.bias",
131
+ "decoder.stages.3.convs.1.all_modules.1.weight",
132
+ "decoder.stages.4.convs.0.all_modules.0.bias",
133
+ "decoder.stages.4.convs.0.all_modules.0.weight",
134
+ "decoder.stages.4.convs.0.all_modules.1.bias",
135
+ "decoder.stages.4.convs.0.all_modules.1.weight",
136
+ "decoder.stages.4.convs.1.all_modules.0.bias",
137
+ "decoder.stages.4.convs.1.all_modules.0.weight",
138
+ "decoder.stages.4.convs.1.all_modules.1.bias",
139
+ "decoder.stages.4.convs.1.all_modules.1.weight",
140
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
156
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
157
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
158
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
159
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
160
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
161
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
162
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
163
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
164
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
165
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
166
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
167
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
168
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
169
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
170
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
171
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
172
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
173
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
174
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
175
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
176
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
177
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
178
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
179
+ "encoder.stages.4.0.convs.1.all_modules.1.weight",
180
+ "encoder.stages.5.0.convs.0.all_modules.0.bias",
181
+ "encoder.stages.5.0.convs.0.all_modules.0.weight",
182
+ "encoder.stages.5.0.convs.0.all_modules.1.bias",
183
+ "encoder.stages.5.0.convs.0.all_modules.1.weight",
184
+ "encoder.stages.5.0.convs.1.all_modules.0.bias",
185
+ "encoder.stages.5.0.convs.1.all_modules.0.weight",
186
+ "encoder.stages.5.0.convs.1.all_modules.1.bias",
187
+ "encoder.stages.5.0.convs.1.all_modules.1.weight"
188
+ ],
189
+ "identity": {
190
+ "configuration": "3d_fullres",
191
+ "fold": 0,
192
+ "trainer_name": "nnUNetTrainerNoMirroring"
193
+ },
194
+ "inference_allowed_mirroring_axes": [],
195
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
196
+ "source_nnunet_version": "v2.8.1",
197
+ "spatial_dims": 3
198
+ }
293/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:05853c9aa732d87da0aa4ff6e4726253c381c720ea6d7fa74352dd3edcd08c61
3
+ size 124846831
293/plans.json ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset293_TotalSegmentator_part3_cardiac_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 1.5,
6
+ 1.5,
7
+ 1.5
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 227,
11
+ 227,
12
+ 240
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 47,
30
+ "patch_size": [
31
+ 256,
32
+ 256
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 227.0,
36
+ 239.0
37
+ ],
38
+ "spacing": [
39
+ 1.5,
40
+ 1.5
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2,
56
+ 2,
57
+ 2
58
+ ],
59
+ "n_conv_per_stage_decoder": [
60
+ 2,
61
+ 2,
62
+ 2,
63
+ 2,
64
+ 2,
65
+ 2
66
+ ],
67
+ "num_pool_per_axis": [
68
+ 6,
69
+ 6
70
+ ],
71
+ "pool_op_kernel_sizes": [
72
+ [
73
+ 1,
74
+ 1
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ],
88
+ [
89
+ 2,
90
+ 2
91
+ ],
92
+ [
93
+ 2,
94
+ 2
95
+ ],
96
+ [
97
+ 2,
98
+ 2
99
+ ]
100
+ ],
101
+ "conv_kernel_sizes": [
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ],
110
+ [
111
+ 3,
112
+ 3
113
+ ],
114
+ [
115
+ 3,
116
+ 3
117
+ ],
118
+ [
119
+ 3,
120
+ 3
121
+ ],
122
+ [
123
+ 3,
124
+ 3
125
+ ],
126
+ [
127
+ 3,
128
+ 3
129
+ ]
130
+ ],
131
+ "unet_max_num_features": 512,
132
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
133
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
134
+ "resampling_fn_data_kwargs": {
135
+ "is_seg": false,
136
+ "order": 3,
137
+ "order_z": 0,
138
+ "force_separate_z": null
139
+ },
140
+ "resampling_fn_seg_kwargs": {
141
+ "is_seg": true,
142
+ "order": 1,
143
+ "order_z": 0,
144
+ "force_separate_z": null
145
+ },
146
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
147
+ "resampling_fn_probabilities_kwargs": {
148
+ "is_seg": false,
149
+ "order": 1,
150
+ "order_z": 0,
151
+ "force_separate_z": null
152
+ },
153
+ "batch_dice": true
154
+ },
155
+ "3d_lowres": {
156
+ "data_identifier": "nnUNetPlans_3d_lowres",
157
+ "preprocessor_name": "DefaultPreprocessor",
158
+ "batch_size": 2,
159
+ "patch_size": [
160
+ 128,
161
+ 128,
162
+ 128
163
+ ],
164
+ "median_image_size_in_voxels": [
165
+ 196,
166
+ 196,
167
+ 206
168
+ ],
169
+ "spacing": [
170
+ 1.7389111114500002,
171
+ 1.7389111114500002,
172
+ 1.7389111114500002
173
+ ],
174
+ "normalization_schemes": [
175
+ "CTNormalization"
176
+ ],
177
+ "use_mask_for_norm": [
178
+ false
179
+ ],
180
+ "UNet_class_name": "PlainConvUNet",
181
+ "UNet_base_num_features": 32,
182
+ "n_conv_per_stage_encoder": [
183
+ 2,
184
+ 2,
185
+ 2,
186
+ 2,
187
+ 2,
188
+ 2
189
+ ],
190
+ "n_conv_per_stage_decoder": [
191
+ 2,
192
+ 2,
193
+ 2,
194
+ 2,
195
+ 2
196
+ ],
197
+ "num_pool_per_axis": [
198
+ 5,
199
+ 5,
200
+ 5
201
+ ],
202
+ "pool_op_kernel_sizes": [
203
+ [
204
+ 1,
205
+ 1,
206
+ 1
207
+ ],
208
+ [
209
+ 2,
210
+ 2,
211
+ 2
212
+ ],
213
+ [
214
+ 2,
215
+ 2,
216
+ 2
217
+ ],
218
+ [
219
+ 2,
220
+ 2,
221
+ 2
222
+ ],
223
+ [
224
+ 2,
225
+ 2,
226
+ 2
227
+ ],
228
+ [
229
+ 2,
230
+ 2,
231
+ 2
232
+ ]
233
+ ],
234
+ "conv_kernel_sizes": [
235
+ [
236
+ 3,
237
+ 3,
238
+ 3
239
+ ],
240
+ [
241
+ 3,
242
+ 3,
243
+ 3
244
+ ],
245
+ [
246
+ 3,
247
+ 3,
248
+ 3
249
+ ],
250
+ [
251
+ 3,
252
+ 3,
253
+ 3
254
+ ],
255
+ [
256
+ 3,
257
+ 3,
258
+ 3
259
+ ],
260
+ [
261
+ 3,
262
+ 3,
263
+ 3
264
+ ]
265
+ ],
266
+ "unet_max_num_features": 320,
267
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
268
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
269
+ "resampling_fn_data_kwargs": {
270
+ "is_seg": false,
271
+ "order": 3,
272
+ "order_z": 0,
273
+ "force_separate_z": null
274
+ },
275
+ "resampling_fn_seg_kwargs": {
276
+ "is_seg": true,
277
+ "order": 1,
278
+ "order_z": 0,
279
+ "force_separate_z": null
280
+ },
281
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
282
+ "resampling_fn_probabilities_kwargs": {
283
+ "is_seg": false,
284
+ "order": 1,
285
+ "order_z": 0,
286
+ "force_separate_z": null
287
+ },
288
+ "batch_dice": false,
289
+ "next_stage": "3d_cascade_fullres"
290
+ },
291
+ "3d_fullres": {
292
+ "data_identifier": "nnUNetPlans_3d_fullres",
293
+ "preprocessor_name": "DefaultPreprocessor",
294
+ "batch_size": 2,
295
+ "patch_size": [
296
+ 128,
297
+ 128,
298
+ 128
299
+ ],
300
+ "median_image_size_in_voxels": [
301
+ 227.0,
302
+ 227.0,
303
+ 239.0
304
+ ],
305
+ "spacing": [
306
+ 1.5,
307
+ 1.5,
308
+ 1.5
309
+ ],
310
+ "normalization_schemes": [
311
+ "CTNormalization"
312
+ ],
313
+ "use_mask_for_norm": [
314
+ false
315
+ ],
316
+ "UNet_class_name": "PlainConvUNet",
317
+ "UNet_base_num_features": 32,
318
+ "n_conv_per_stage_encoder": [
319
+ 2,
320
+ 2,
321
+ 2,
322
+ 2,
323
+ 2,
324
+ 2
325
+ ],
326
+ "n_conv_per_stage_decoder": [
327
+ 2,
328
+ 2,
329
+ 2,
330
+ 2,
331
+ 2
332
+ ],
333
+ "num_pool_per_axis": [
334
+ 5,
335
+ 5,
336
+ 5
337
+ ],
338
+ "pool_op_kernel_sizes": [
339
+ [
340
+ 1,
341
+ 1,
342
+ 1
343
+ ],
344
+ [
345
+ 2,
346
+ 2,
347
+ 2
348
+ ],
349
+ [
350
+ 2,
351
+ 2,
352
+ 2
353
+ ],
354
+ [
355
+ 2,
356
+ 2,
357
+ 2
358
+ ],
359
+ [
360
+ 2,
361
+ 2,
362
+ 2
363
+ ],
364
+ [
365
+ 2,
366
+ 2,
367
+ 2
368
+ ]
369
+ ],
370
+ "conv_kernel_sizes": [
371
+ [
372
+ 3,
373
+ 3,
374
+ 3
375
+ ],
376
+ [
377
+ 3,
378
+ 3,
379
+ 3
380
+ ],
381
+ [
382
+ 3,
383
+ 3,
384
+ 3
385
+ ],
386
+ [
387
+ 3,
388
+ 3,
389
+ 3
390
+ ],
391
+ [
392
+ 3,
393
+ 3,
394
+ 3
395
+ ],
396
+ [
397
+ 3,
398
+ 3,
399
+ 3
400
+ ]
401
+ ],
402
+ "unet_max_num_features": 320,
403
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
404
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
405
+ "resampling_fn_data_kwargs": {
406
+ "is_seg": false,
407
+ "order": 3,
408
+ "order_z": 0,
409
+ "force_separate_z": null
410
+ },
411
+ "resampling_fn_seg_kwargs": {
412
+ "is_seg": true,
413
+ "order": 1,
414
+ "order_z": 0,
415
+ "force_separate_z": null
416
+ },
417
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
418
+ "resampling_fn_probabilities_kwargs": {
419
+ "is_seg": false,
420
+ "order": 1,
421
+ "order_z": 0,
422
+ "force_separate_z": null
423
+ },
424
+ "batch_dice": true
425
+ },
426
+ "3d_cascade_fullres": {
427
+ "inherits_from": "3d_fullres",
428
+ "previous_stage": "3d_lowres"
429
+ }
430
+ },
431
+ "experiment_planner_used": "ExperimentPlanner",
432
+ "label_manager": "LabelManager",
433
+ "foreground_intensity_properties_per_channel": {
434
+ "0": {
435
+ "max": 6666.0,
436
+ "mean": 142.1977119916391,
437
+ "median": 108.0,
438
+ "min": -1551.0,
439
+ "percentile_00_5": -101.0,
440
+ "percentile_99_5": 813.0,
441
+ "std": 154.74032651622053
442
+ }
443
+ }
444
+ }
294/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
294/dataset.json ADDED
@@ -0,0 +1,39 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "channel_names": {
8
+ "0": "CT"
9
+ },
10
+ "labels": {
11
+ "background": 0,
12
+ "humerus_left": 1,
13
+ "humerus_right": 2,
14
+ "scapula_left": 3,
15
+ "scapula_right": 4,
16
+ "clavicula_left": 5,
17
+ "clavicula_right": 6,
18
+ "femur_left": 7,
19
+ "femur_right": 8,
20
+ "hip_left": 9,
21
+ "hip_right": 10,
22
+ "spinal_cord": 11,
23
+ "gluteus_maximus_left": 12,
24
+ "gluteus_maximus_right": 13,
25
+ "gluteus_medius_left": 14,
26
+ "gluteus_medius_right": 15,
27
+ "gluteus_minimus_left": 16,
28
+ "gluteus_minimus_right": 17,
29
+ "autochthon_left": 18,
30
+ "autochthon_right": 19,
31
+ "iliopsoas_left": 20,
32
+ "iliopsoas_right": 21,
33
+ "brain": 22,
34
+ "skull": 23
35
+ },
36
+ "numTraining": 1559,
37
+ "file_ending": ".nii.gz",
38
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
39
+ }
294/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,198 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 1001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.bias",
85
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.weight",
86
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.bias",
87
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.weight",
88
+ "decoder.encoder.stages.5.0.convs.0.conv.bias",
89
+ "decoder.encoder.stages.5.0.convs.0.conv.weight",
90
+ "decoder.encoder.stages.5.0.convs.0.norm.bias",
91
+ "decoder.encoder.stages.5.0.convs.0.norm.weight",
92
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.bias",
93
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.weight",
94
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.bias",
95
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.weight",
96
+ "decoder.encoder.stages.5.0.convs.1.conv.bias",
97
+ "decoder.encoder.stages.5.0.convs.1.conv.weight",
98
+ "decoder.encoder.stages.5.0.convs.1.norm.bias",
99
+ "decoder.encoder.stages.5.0.convs.1.norm.weight",
100
+ "decoder.stages.0.convs.0.all_modules.0.bias",
101
+ "decoder.stages.0.convs.0.all_modules.0.weight",
102
+ "decoder.stages.0.convs.0.all_modules.1.bias",
103
+ "decoder.stages.0.convs.0.all_modules.1.weight",
104
+ "decoder.stages.0.convs.1.all_modules.0.bias",
105
+ "decoder.stages.0.convs.1.all_modules.0.weight",
106
+ "decoder.stages.0.convs.1.all_modules.1.bias",
107
+ "decoder.stages.0.convs.1.all_modules.1.weight",
108
+ "decoder.stages.1.convs.0.all_modules.0.bias",
109
+ "decoder.stages.1.convs.0.all_modules.0.weight",
110
+ "decoder.stages.1.convs.0.all_modules.1.bias",
111
+ "decoder.stages.1.convs.0.all_modules.1.weight",
112
+ "decoder.stages.1.convs.1.all_modules.0.bias",
113
+ "decoder.stages.1.convs.1.all_modules.0.weight",
114
+ "decoder.stages.1.convs.1.all_modules.1.bias",
115
+ "decoder.stages.1.convs.1.all_modules.1.weight",
116
+ "decoder.stages.2.convs.0.all_modules.0.bias",
117
+ "decoder.stages.2.convs.0.all_modules.0.weight",
118
+ "decoder.stages.2.convs.0.all_modules.1.bias",
119
+ "decoder.stages.2.convs.0.all_modules.1.weight",
120
+ "decoder.stages.2.convs.1.all_modules.0.bias",
121
+ "decoder.stages.2.convs.1.all_modules.0.weight",
122
+ "decoder.stages.2.convs.1.all_modules.1.bias",
123
+ "decoder.stages.2.convs.1.all_modules.1.weight",
124
+ "decoder.stages.3.convs.0.all_modules.0.bias",
125
+ "decoder.stages.3.convs.0.all_modules.0.weight",
126
+ "decoder.stages.3.convs.0.all_modules.1.bias",
127
+ "decoder.stages.3.convs.0.all_modules.1.weight",
128
+ "decoder.stages.3.convs.1.all_modules.0.bias",
129
+ "decoder.stages.3.convs.1.all_modules.0.weight",
130
+ "decoder.stages.3.convs.1.all_modules.1.bias",
131
+ "decoder.stages.3.convs.1.all_modules.1.weight",
132
+ "decoder.stages.4.convs.0.all_modules.0.bias",
133
+ "decoder.stages.4.convs.0.all_modules.0.weight",
134
+ "decoder.stages.4.convs.0.all_modules.1.bias",
135
+ "decoder.stages.4.convs.0.all_modules.1.weight",
136
+ "decoder.stages.4.convs.1.all_modules.0.bias",
137
+ "decoder.stages.4.convs.1.all_modules.0.weight",
138
+ "decoder.stages.4.convs.1.all_modules.1.bias",
139
+ "decoder.stages.4.convs.1.all_modules.1.weight",
140
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
156
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
157
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
158
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
159
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
160
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
161
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
162
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
163
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
164
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
165
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
166
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
167
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
168
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
169
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
170
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
171
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
172
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
173
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
174
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
175
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
176
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
177
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
178
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
179
+ "encoder.stages.4.0.convs.1.all_modules.1.weight",
180
+ "encoder.stages.5.0.convs.0.all_modules.0.bias",
181
+ "encoder.stages.5.0.convs.0.all_modules.0.weight",
182
+ "encoder.stages.5.0.convs.0.all_modules.1.bias",
183
+ "encoder.stages.5.0.convs.0.all_modules.1.weight",
184
+ "encoder.stages.5.0.convs.1.all_modules.0.bias",
185
+ "encoder.stages.5.0.convs.1.all_modules.0.weight",
186
+ "encoder.stages.5.0.convs.1.all_modules.1.bias",
187
+ "encoder.stages.5.0.convs.1.all_modules.1.weight"
188
+ ],
189
+ "identity": {
190
+ "configuration": "3d_fullres",
191
+ "fold": 0,
192
+ "trainer_name": "nnUNetTrainerNoMirroring"
193
+ },
194
+ "inference_allowed_mirroring_axes": [],
195
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
196
+ "source_nnunet_version": "v2.8.1",
197
+ "spatial_dims": 3
198
+ }
294/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:19ad998ac5b4c7927287e745c3283fab9d2885cf6da57ae7956b4d8d4e2e7488
3
+ size 124862931
294/plans.json ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset294_TotalSegmentator_part4_muscles_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 1.5,
6
+ 1.5,
7
+ 1.5
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 227,
11
+ 227,
12
+ 240
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 46,
30
+ "patch_size": [
31
+ 256,
32
+ 256
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 227.0,
36
+ 239.0
37
+ ],
38
+ "spacing": [
39
+ 1.5,
40
+ 1.5
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2,
56
+ 2,
57
+ 2
58
+ ],
59
+ "n_conv_per_stage_decoder": [
60
+ 2,
61
+ 2,
62
+ 2,
63
+ 2,
64
+ 2,
65
+ 2
66
+ ],
67
+ "num_pool_per_axis": [
68
+ 6,
69
+ 6
70
+ ],
71
+ "pool_op_kernel_sizes": [
72
+ [
73
+ 1,
74
+ 1
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ],
88
+ [
89
+ 2,
90
+ 2
91
+ ],
92
+ [
93
+ 2,
94
+ 2
95
+ ],
96
+ [
97
+ 2,
98
+ 2
99
+ ]
100
+ ],
101
+ "conv_kernel_sizes": [
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ],
110
+ [
111
+ 3,
112
+ 3
113
+ ],
114
+ [
115
+ 3,
116
+ 3
117
+ ],
118
+ [
119
+ 3,
120
+ 3
121
+ ],
122
+ [
123
+ 3,
124
+ 3
125
+ ],
126
+ [
127
+ 3,
128
+ 3
129
+ ]
130
+ ],
131
+ "unet_max_num_features": 512,
132
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
133
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
134
+ "resampling_fn_data_kwargs": {
135
+ "is_seg": false,
136
+ "order": 3,
137
+ "order_z": 0,
138
+ "force_separate_z": null
139
+ },
140
+ "resampling_fn_seg_kwargs": {
141
+ "is_seg": true,
142
+ "order": 1,
143
+ "order_z": 0,
144
+ "force_separate_z": null
145
+ },
146
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
147
+ "resampling_fn_probabilities_kwargs": {
148
+ "is_seg": false,
149
+ "order": 1,
150
+ "order_z": 0,
151
+ "force_separate_z": null
152
+ },
153
+ "batch_dice": true
154
+ },
155
+ "3d_lowres": {
156
+ "data_identifier": "nnUNetPlans_3d_lowres",
157
+ "preprocessor_name": "DefaultPreprocessor",
158
+ "batch_size": 2,
159
+ "patch_size": [
160
+ 128,
161
+ 128,
162
+ 128
163
+ ],
164
+ "median_image_size_in_voxels": [
165
+ 196,
166
+ 196,
167
+ 206
168
+ ],
169
+ "spacing": [
170
+ 1.7389111114500002,
171
+ 1.7389111114500002,
172
+ 1.7389111114500002
173
+ ],
174
+ "normalization_schemes": [
175
+ "CTNormalization"
176
+ ],
177
+ "use_mask_for_norm": [
178
+ false
179
+ ],
180
+ "UNet_class_name": "PlainConvUNet",
181
+ "UNet_base_num_features": 32,
182
+ "n_conv_per_stage_encoder": [
183
+ 2,
184
+ 2,
185
+ 2,
186
+ 2,
187
+ 2,
188
+ 2
189
+ ],
190
+ "n_conv_per_stage_decoder": [
191
+ 2,
192
+ 2,
193
+ 2,
194
+ 2,
195
+ 2
196
+ ],
197
+ "num_pool_per_axis": [
198
+ 5,
199
+ 5,
200
+ 5
201
+ ],
202
+ "pool_op_kernel_sizes": [
203
+ [
204
+ 1,
205
+ 1,
206
+ 1
207
+ ],
208
+ [
209
+ 2,
210
+ 2,
211
+ 2
212
+ ],
213
+ [
214
+ 2,
215
+ 2,
216
+ 2
217
+ ],
218
+ [
219
+ 2,
220
+ 2,
221
+ 2
222
+ ],
223
+ [
224
+ 2,
225
+ 2,
226
+ 2
227
+ ],
228
+ [
229
+ 2,
230
+ 2,
231
+ 2
232
+ ]
233
+ ],
234
+ "conv_kernel_sizes": [
235
+ [
236
+ 3,
237
+ 3,
238
+ 3
239
+ ],
240
+ [
241
+ 3,
242
+ 3,
243
+ 3
244
+ ],
245
+ [
246
+ 3,
247
+ 3,
248
+ 3
249
+ ],
250
+ [
251
+ 3,
252
+ 3,
253
+ 3
254
+ ],
255
+ [
256
+ 3,
257
+ 3,
258
+ 3
259
+ ],
260
+ [
261
+ 3,
262
+ 3,
263
+ 3
264
+ ]
265
+ ],
266
+ "unet_max_num_features": 320,
267
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
268
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
269
+ "resampling_fn_data_kwargs": {
270
+ "is_seg": false,
271
+ "order": 3,
272
+ "order_z": 0,
273
+ "force_separate_z": null
274
+ },
275
+ "resampling_fn_seg_kwargs": {
276
+ "is_seg": true,
277
+ "order": 1,
278
+ "order_z": 0,
279
+ "force_separate_z": null
280
+ },
281
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
282
+ "resampling_fn_probabilities_kwargs": {
283
+ "is_seg": false,
284
+ "order": 1,
285
+ "order_z": 0,
286
+ "force_separate_z": null
287
+ },
288
+ "batch_dice": false,
289
+ "next_stage": "3d_cascade_fullres"
290
+ },
291
+ "3d_fullres": {
292
+ "data_identifier": "nnUNetPlans_3d_fullres",
293
+ "preprocessor_name": "DefaultPreprocessor",
294
+ "batch_size": 2,
295
+ "patch_size": [
296
+ 128,
297
+ 128,
298
+ 128
299
+ ],
300
+ "median_image_size_in_voxels": [
301
+ 227.0,
302
+ 227.0,
303
+ 239.0
304
+ ],
305
+ "spacing": [
306
+ 1.5,
307
+ 1.5,
308
+ 1.5
309
+ ],
310
+ "normalization_schemes": [
311
+ "CTNormalization"
312
+ ],
313
+ "use_mask_for_norm": [
314
+ false
315
+ ],
316
+ "UNet_class_name": "PlainConvUNet",
317
+ "UNet_base_num_features": 32,
318
+ "n_conv_per_stage_encoder": [
319
+ 2,
320
+ 2,
321
+ 2,
322
+ 2,
323
+ 2,
324
+ 2
325
+ ],
326
+ "n_conv_per_stage_decoder": [
327
+ 2,
328
+ 2,
329
+ 2,
330
+ 2,
331
+ 2
332
+ ],
333
+ "num_pool_per_axis": [
334
+ 5,
335
+ 5,
336
+ 5
337
+ ],
338
+ "pool_op_kernel_sizes": [
339
+ [
340
+ 1,
341
+ 1,
342
+ 1
343
+ ],
344
+ [
345
+ 2,
346
+ 2,
347
+ 2
348
+ ],
349
+ [
350
+ 2,
351
+ 2,
352
+ 2
353
+ ],
354
+ [
355
+ 2,
356
+ 2,
357
+ 2
358
+ ],
359
+ [
360
+ 2,
361
+ 2,
362
+ 2
363
+ ],
364
+ [
365
+ 2,
366
+ 2,
367
+ 2
368
+ ]
369
+ ],
370
+ "conv_kernel_sizes": [
371
+ [
372
+ 3,
373
+ 3,
374
+ 3
375
+ ],
376
+ [
377
+ 3,
378
+ 3,
379
+ 3
380
+ ],
381
+ [
382
+ 3,
383
+ 3,
384
+ 3
385
+ ],
386
+ [
387
+ 3,
388
+ 3,
389
+ 3
390
+ ],
391
+ [
392
+ 3,
393
+ 3,
394
+ 3
395
+ ],
396
+ [
397
+ 3,
398
+ 3,
399
+ 3
400
+ ]
401
+ ],
402
+ "unet_max_num_features": 320,
403
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
404
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
405
+ "resampling_fn_data_kwargs": {
406
+ "is_seg": false,
407
+ "order": 3,
408
+ "order_z": 0,
409
+ "force_separate_z": null
410
+ },
411
+ "resampling_fn_seg_kwargs": {
412
+ "is_seg": true,
413
+ "order": 1,
414
+ "order_z": 0,
415
+ "force_separate_z": null
416
+ },
417
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
418
+ "resampling_fn_probabilities_kwargs": {
419
+ "is_seg": false,
420
+ "order": 1,
421
+ "order_z": 0,
422
+ "force_separate_z": null
423
+ },
424
+ "batch_dice": true
425
+ },
426
+ "3d_cascade_fullres": {
427
+ "inherits_from": "3d_fullres",
428
+ "previous_stage": "3d_lowres"
429
+ }
430
+ },
431
+ "experiment_planner_used": "ExperimentPlanner",
432
+ "label_manager": "LabelManager",
433
+ "foreground_intensity_properties_per_channel": {
434
+ "0": {
435
+ "max": 44594.0,
436
+ "mean": 174.82106003593222,
437
+ "median": 52.0,
438
+ "min": -49831.0,
439
+ "percentile_00_5": -197.0,
440
+ "percentile_99_5": 1729.0,
441
+ "std": 362.496044938386
442
+ }
443
+ }
444
+ }
295/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
295/dataset.json ADDED
@@ -0,0 +1,42 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "channel_names": {
8
+ "0": "CT"
9
+ },
10
+ "labels": {
11
+ "background": 0,
12
+ "rib_left_1": 1,
13
+ "rib_left_2": 2,
14
+ "rib_left_3": 3,
15
+ "rib_left_4": 4,
16
+ "rib_left_5": 5,
17
+ "rib_left_6": 6,
18
+ "rib_left_7": 7,
19
+ "rib_left_8": 8,
20
+ "rib_left_9": 9,
21
+ "rib_left_10": 10,
22
+ "rib_left_11": 11,
23
+ "rib_left_12": 12,
24
+ "rib_right_1": 13,
25
+ "rib_right_2": 14,
26
+ "rib_right_3": 15,
27
+ "rib_right_4": 16,
28
+ "rib_right_5": 17,
29
+ "rib_right_6": 18,
30
+ "rib_right_7": 19,
31
+ "rib_right_8": 20,
32
+ "rib_right_9": 21,
33
+ "rib_right_10": 22,
34
+ "rib_right_11": 23,
35
+ "rib_right_12": 24,
36
+ "sternum": 25,
37
+ "costal_cartilages": 26
38
+ },
39
+ "numTraining": 1559,
40
+ "file_ending": ".nii.gz",
41
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
42
+ }
295/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,198 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 1001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.bias",
85
+ "decoder.encoder.stages.5.0.convs.0.all_modules.0.weight",
86
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.bias",
87
+ "decoder.encoder.stages.5.0.convs.0.all_modules.1.weight",
88
+ "decoder.encoder.stages.5.0.convs.0.conv.bias",
89
+ "decoder.encoder.stages.5.0.convs.0.conv.weight",
90
+ "decoder.encoder.stages.5.0.convs.0.norm.bias",
91
+ "decoder.encoder.stages.5.0.convs.0.norm.weight",
92
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.bias",
93
+ "decoder.encoder.stages.5.0.convs.1.all_modules.0.weight",
94
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.bias",
95
+ "decoder.encoder.stages.5.0.convs.1.all_modules.1.weight",
96
+ "decoder.encoder.stages.5.0.convs.1.conv.bias",
97
+ "decoder.encoder.stages.5.0.convs.1.conv.weight",
98
+ "decoder.encoder.stages.5.0.convs.1.norm.bias",
99
+ "decoder.encoder.stages.5.0.convs.1.norm.weight",
100
+ "decoder.stages.0.convs.0.all_modules.0.bias",
101
+ "decoder.stages.0.convs.0.all_modules.0.weight",
102
+ "decoder.stages.0.convs.0.all_modules.1.bias",
103
+ "decoder.stages.0.convs.0.all_modules.1.weight",
104
+ "decoder.stages.0.convs.1.all_modules.0.bias",
105
+ "decoder.stages.0.convs.1.all_modules.0.weight",
106
+ "decoder.stages.0.convs.1.all_modules.1.bias",
107
+ "decoder.stages.0.convs.1.all_modules.1.weight",
108
+ "decoder.stages.1.convs.0.all_modules.0.bias",
109
+ "decoder.stages.1.convs.0.all_modules.0.weight",
110
+ "decoder.stages.1.convs.0.all_modules.1.bias",
111
+ "decoder.stages.1.convs.0.all_modules.1.weight",
112
+ "decoder.stages.1.convs.1.all_modules.0.bias",
113
+ "decoder.stages.1.convs.1.all_modules.0.weight",
114
+ "decoder.stages.1.convs.1.all_modules.1.bias",
115
+ "decoder.stages.1.convs.1.all_modules.1.weight",
116
+ "decoder.stages.2.convs.0.all_modules.0.bias",
117
+ "decoder.stages.2.convs.0.all_modules.0.weight",
118
+ "decoder.stages.2.convs.0.all_modules.1.bias",
119
+ "decoder.stages.2.convs.0.all_modules.1.weight",
120
+ "decoder.stages.2.convs.1.all_modules.0.bias",
121
+ "decoder.stages.2.convs.1.all_modules.0.weight",
122
+ "decoder.stages.2.convs.1.all_modules.1.bias",
123
+ "decoder.stages.2.convs.1.all_modules.1.weight",
124
+ "decoder.stages.3.convs.0.all_modules.0.bias",
125
+ "decoder.stages.3.convs.0.all_modules.0.weight",
126
+ "decoder.stages.3.convs.0.all_modules.1.bias",
127
+ "decoder.stages.3.convs.0.all_modules.1.weight",
128
+ "decoder.stages.3.convs.1.all_modules.0.bias",
129
+ "decoder.stages.3.convs.1.all_modules.0.weight",
130
+ "decoder.stages.3.convs.1.all_modules.1.bias",
131
+ "decoder.stages.3.convs.1.all_modules.1.weight",
132
+ "decoder.stages.4.convs.0.all_modules.0.bias",
133
+ "decoder.stages.4.convs.0.all_modules.0.weight",
134
+ "decoder.stages.4.convs.0.all_modules.1.bias",
135
+ "decoder.stages.4.convs.0.all_modules.1.weight",
136
+ "decoder.stages.4.convs.1.all_modules.0.bias",
137
+ "decoder.stages.4.convs.1.all_modules.0.weight",
138
+ "decoder.stages.4.convs.1.all_modules.1.bias",
139
+ "decoder.stages.4.convs.1.all_modules.1.weight",
140
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
156
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
157
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
158
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
159
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
160
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
161
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
162
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
163
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
164
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
165
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
166
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
167
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
168
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
169
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
170
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
171
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
172
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
173
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
174
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
175
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
176
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
177
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
178
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
179
+ "encoder.stages.4.0.convs.1.all_modules.1.weight",
180
+ "encoder.stages.5.0.convs.0.all_modules.0.bias",
181
+ "encoder.stages.5.0.convs.0.all_modules.0.weight",
182
+ "encoder.stages.5.0.convs.0.all_modules.1.bias",
183
+ "encoder.stages.5.0.convs.0.all_modules.1.weight",
184
+ "encoder.stages.5.0.convs.1.all_modules.0.bias",
185
+ "encoder.stages.5.0.convs.1.all_modules.0.weight",
186
+ "encoder.stages.5.0.convs.1.all_modules.1.bias",
187
+ "encoder.stages.5.0.convs.1.all_modules.1.weight"
188
+ ],
189
+ "identity": {
190
+ "configuration": "3d_fullres",
191
+ "fold": 0,
192
+ "trainer_name": "nnUNetTrainerNoMirroring"
193
+ },
194
+ "inference_allowed_mirroring_axes": [],
195
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
196
+ "source_nnunet_version": "v2.8.1",
197
+ "spatial_dims": 3
198
+ }
295/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:21e3b82a32f2ad8f8902714fcb2b60a6e21d5219b0fb4daa979fe256d9072985
3
+ size 124872593
295/plans.json ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset295_TotalSegmentator_part5_ribs_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 1.5,
6
+ 1.5,
7
+ 1.5
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 227,
11
+ 227,
12
+ 240
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 46,
30
+ "patch_size": [
31
+ 256,
32
+ 256
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 227.0,
36
+ 239.0
37
+ ],
38
+ "spacing": [
39
+ 1.5,
40
+ 1.5
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2,
56
+ 2,
57
+ 2
58
+ ],
59
+ "n_conv_per_stage_decoder": [
60
+ 2,
61
+ 2,
62
+ 2,
63
+ 2,
64
+ 2,
65
+ 2
66
+ ],
67
+ "num_pool_per_axis": [
68
+ 6,
69
+ 6
70
+ ],
71
+ "pool_op_kernel_sizes": [
72
+ [
73
+ 1,
74
+ 1
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ],
88
+ [
89
+ 2,
90
+ 2
91
+ ],
92
+ [
93
+ 2,
94
+ 2
95
+ ],
96
+ [
97
+ 2,
98
+ 2
99
+ ]
100
+ ],
101
+ "conv_kernel_sizes": [
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ],
110
+ [
111
+ 3,
112
+ 3
113
+ ],
114
+ [
115
+ 3,
116
+ 3
117
+ ],
118
+ [
119
+ 3,
120
+ 3
121
+ ],
122
+ [
123
+ 3,
124
+ 3
125
+ ],
126
+ [
127
+ 3,
128
+ 3
129
+ ]
130
+ ],
131
+ "unet_max_num_features": 512,
132
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
133
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
134
+ "resampling_fn_data_kwargs": {
135
+ "is_seg": false,
136
+ "order": 3,
137
+ "order_z": 0,
138
+ "force_separate_z": null
139
+ },
140
+ "resampling_fn_seg_kwargs": {
141
+ "is_seg": true,
142
+ "order": 1,
143
+ "order_z": 0,
144
+ "force_separate_z": null
145
+ },
146
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
147
+ "resampling_fn_probabilities_kwargs": {
148
+ "is_seg": false,
149
+ "order": 1,
150
+ "order_z": 0,
151
+ "force_separate_z": null
152
+ },
153
+ "batch_dice": true
154
+ },
155
+ "3d_lowres": {
156
+ "data_identifier": "nnUNetPlans_3d_lowres",
157
+ "preprocessor_name": "DefaultPreprocessor",
158
+ "batch_size": 2,
159
+ "patch_size": [
160
+ 128,
161
+ 128,
162
+ 128
163
+ ],
164
+ "median_image_size_in_voxels": [
165
+ 196,
166
+ 196,
167
+ 206
168
+ ],
169
+ "spacing": [
170
+ 1.7389111114500002,
171
+ 1.7389111114500002,
172
+ 1.7389111114500002
173
+ ],
174
+ "normalization_schemes": [
175
+ "CTNormalization"
176
+ ],
177
+ "use_mask_for_norm": [
178
+ false
179
+ ],
180
+ "UNet_class_name": "PlainConvUNet",
181
+ "UNet_base_num_features": 32,
182
+ "n_conv_per_stage_encoder": [
183
+ 2,
184
+ 2,
185
+ 2,
186
+ 2,
187
+ 2,
188
+ 2
189
+ ],
190
+ "n_conv_per_stage_decoder": [
191
+ 2,
192
+ 2,
193
+ 2,
194
+ 2,
195
+ 2
196
+ ],
197
+ "num_pool_per_axis": [
198
+ 5,
199
+ 5,
200
+ 5
201
+ ],
202
+ "pool_op_kernel_sizes": [
203
+ [
204
+ 1,
205
+ 1,
206
+ 1
207
+ ],
208
+ [
209
+ 2,
210
+ 2,
211
+ 2
212
+ ],
213
+ [
214
+ 2,
215
+ 2,
216
+ 2
217
+ ],
218
+ [
219
+ 2,
220
+ 2,
221
+ 2
222
+ ],
223
+ [
224
+ 2,
225
+ 2,
226
+ 2
227
+ ],
228
+ [
229
+ 2,
230
+ 2,
231
+ 2
232
+ ]
233
+ ],
234
+ "conv_kernel_sizes": [
235
+ [
236
+ 3,
237
+ 3,
238
+ 3
239
+ ],
240
+ [
241
+ 3,
242
+ 3,
243
+ 3
244
+ ],
245
+ [
246
+ 3,
247
+ 3,
248
+ 3
249
+ ],
250
+ [
251
+ 3,
252
+ 3,
253
+ 3
254
+ ],
255
+ [
256
+ 3,
257
+ 3,
258
+ 3
259
+ ],
260
+ [
261
+ 3,
262
+ 3,
263
+ 3
264
+ ]
265
+ ],
266
+ "unet_max_num_features": 320,
267
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
268
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
269
+ "resampling_fn_data_kwargs": {
270
+ "is_seg": false,
271
+ "order": 3,
272
+ "order_z": 0,
273
+ "force_separate_z": null
274
+ },
275
+ "resampling_fn_seg_kwargs": {
276
+ "is_seg": true,
277
+ "order": 1,
278
+ "order_z": 0,
279
+ "force_separate_z": null
280
+ },
281
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
282
+ "resampling_fn_probabilities_kwargs": {
283
+ "is_seg": false,
284
+ "order": 1,
285
+ "order_z": 0,
286
+ "force_separate_z": null
287
+ },
288
+ "batch_dice": false,
289
+ "next_stage": "3d_cascade_fullres"
290
+ },
291
+ "3d_fullres": {
292
+ "data_identifier": "nnUNetPlans_3d_fullres",
293
+ "preprocessor_name": "DefaultPreprocessor",
294
+ "batch_size": 2,
295
+ "patch_size": [
296
+ 128,
297
+ 128,
298
+ 128
299
+ ],
300
+ "median_image_size_in_voxels": [
301
+ 227.0,
302
+ 227.0,
303
+ 239.0
304
+ ],
305
+ "spacing": [
306
+ 1.5,
307
+ 1.5,
308
+ 1.5
309
+ ],
310
+ "normalization_schemes": [
311
+ "CTNormalization"
312
+ ],
313
+ "use_mask_for_norm": [
314
+ false
315
+ ],
316
+ "UNet_class_name": "PlainConvUNet",
317
+ "UNet_base_num_features": 32,
318
+ "n_conv_per_stage_encoder": [
319
+ 2,
320
+ 2,
321
+ 2,
322
+ 2,
323
+ 2,
324
+ 2
325
+ ],
326
+ "n_conv_per_stage_decoder": [
327
+ 2,
328
+ 2,
329
+ 2,
330
+ 2,
331
+ 2
332
+ ],
333
+ "num_pool_per_axis": [
334
+ 5,
335
+ 5,
336
+ 5
337
+ ],
338
+ "pool_op_kernel_sizes": [
339
+ [
340
+ 1,
341
+ 1,
342
+ 1
343
+ ],
344
+ [
345
+ 2,
346
+ 2,
347
+ 2
348
+ ],
349
+ [
350
+ 2,
351
+ 2,
352
+ 2
353
+ ],
354
+ [
355
+ 2,
356
+ 2,
357
+ 2
358
+ ],
359
+ [
360
+ 2,
361
+ 2,
362
+ 2
363
+ ],
364
+ [
365
+ 2,
366
+ 2,
367
+ 2
368
+ ]
369
+ ],
370
+ "conv_kernel_sizes": [
371
+ [
372
+ 3,
373
+ 3,
374
+ 3
375
+ ],
376
+ [
377
+ 3,
378
+ 3,
379
+ 3
380
+ ],
381
+ [
382
+ 3,
383
+ 3,
384
+ 3
385
+ ],
386
+ [
387
+ 3,
388
+ 3,
389
+ 3
390
+ ],
391
+ [
392
+ 3,
393
+ 3,
394
+ 3
395
+ ],
396
+ [
397
+ 3,
398
+ 3,
399
+ 3
400
+ ]
401
+ ],
402
+ "unet_max_num_features": 320,
403
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
404
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
405
+ "resampling_fn_data_kwargs": {
406
+ "is_seg": false,
407
+ "order": 3,
408
+ "order_z": 0,
409
+ "force_separate_z": null
410
+ },
411
+ "resampling_fn_seg_kwargs": {
412
+ "is_seg": true,
413
+ "order": 1,
414
+ "order_z": 0,
415
+ "force_separate_z": null
416
+ },
417
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
418
+ "resampling_fn_probabilities_kwargs": {
419
+ "is_seg": false,
420
+ "order": 1,
421
+ "order_z": 0,
422
+ "force_separate_z": null
423
+ },
424
+ "batch_dice": true
425
+ },
426
+ "3d_cascade_fullres": {
427
+ "inherits_from": "3d_fullres",
428
+ "previous_stage": "3d_lowres"
429
+ }
430
+ },
431
+ "experiment_planner_used": "ExperimentPlanner",
432
+ "label_manager": "LabelManager",
433
+ "foreground_intensity_properties_per_channel": {
434
+ "0": {
435
+ "max": 21501.0,
436
+ "mean": 291.98966240726804,
437
+ "median": 220.0,
438
+ "min": -2437.0,
439
+ "percentile_00_5": -110.0,
440
+ "percentile_99_5": 1302.0,
441
+ "std": 261.53174290110513
442
+ }
443
+ }
444
+ }
297/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
297/dataset.json ADDED
@@ -0,0 +1,133 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "channel_names": {
8
+ "0": "CT"
9
+ },
10
+ "labels": {
11
+ "background": 0,
12
+ "spleen": 1,
13
+ "kidney_right": 2,
14
+ "kidney_left": 3,
15
+ "gallbladder": 4,
16
+ "liver": 5,
17
+ "stomach": 6,
18
+ "pancreas": 7,
19
+ "adrenal_gland_right": 8,
20
+ "adrenal_gland_left": 9,
21
+ "lung_upper_lobe_left": 10,
22
+ "lung_lower_lobe_left": 11,
23
+ "lung_upper_lobe_right": 12,
24
+ "lung_middle_lobe_right": 13,
25
+ "lung_lower_lobe_right": 14,
26
+ "esophagus": 15,
27
+ "trachea": 16,
28
+ "thyroid_gland": 17,
29
+ "small_bowel": 18,
30
+ "duodenum": 19,
31
+ "colon": 20,
32
+ "urinary_bladder": 21,
33
+ "prostate": 22,
34
+ "kidney_cyst_left": 23,
35
+ "kidney_cyst_right": 24,
36
+ "sacrum": 25,
37
+ "vertebrae_S1": 26,
38
+ "vertebrae_L5": 27,
39
+ "vertebrae_L4": 28,
40
+ "vertebrae_L3": 29,
41
+ "vertebrae_L2": 30,
42
+ "vertebrae_L1": 31,
43
+ "vertebrae_T12": 32,
44
+ "vertebrae_T11": 33,
45
+ "vertebrae_T10": 34,
46
+ "vertebrae_T9": 35,
47
+ "vertebrae_T8": 36,
48
+ "vertebrae_T7": 37,
49
+ "vertebrae_T6": 38,
50
+ "vertebrae_T5": 39,
51
+ "vertebrae_T4": 40,
52
+ "vertebrae_T3": 41,
53
+ "vertebrae_T2": 42,
54
+ "vertebrae_T1": 43,
55
+ "vertebrae_C7": 44,
56
+ "vertebrae_C6": 45,
57
+ "vertebrae_C5": 46,
58
+ "vertebrae_C4": 47,
59
+ "vertebrae_C3": 48,
60
+ "vertebrae_C2": 49,
61
+ "vertebrae_C1": 50,
62
+ "heart": 51,
63
+ "aorta": 52,
64
+ "pulmonary_vein": 53,
65
+ "brachiocephalic_trunk": 54,
66
+ "subclavian_artery_right": 55,
67
+ "subclavian_artery_left": 56,
68
+ "common_carotid_artery_right": 57,
69
+ "common_carotid_artery_left": 58,
70
+ "brachiocephalic_vein_left": 59,
71
+ "brachiocephalic_vein_right": 60,
72
+ "atrial_appendage_left": 61,
73
+ "superior_vena_cava": 62,
74
+ "inferior_vena_cava": 63,
75
+ "portal_vein_and_splenic_vein": 64,
76
+ "iliac_artery_left": 65,
77
+ "iliac_artery_right": 66,
78
+ "iliac_vena_left": 67,
79
+ "iliac_vena_right": 68,
80
+ "humerus_left": 69,
81
+ "humerus_right": 70,
82
+ "scapula_left": 71,
83
+ "scapula_right": 72,
84
+ "clavicula_left": 73,
85
+ "clavicula_right": 74,
86
+ "femur_left": 75,
87
+ "femur_right": 76,
88
+ "hip_left": 77,
89
+ "hip_right": 78,
90
+ "spinal_cord": 79,
91
+ "gluteus_maximus_left": 80,
92
+ "gluteus_maximus_right": 81,
93
+ "gluteus_medius_left": 82,
94
+ "gluteus_medius_right": 83,
95
+ "gluteus_minimus_left": 84,
96
+ "gluteus_minimus_right": 85,
97
+ "autochthon_left": 86,
98
+ "autochthon_right": 87,
99
+ "iliopsoas_left": 88,
100
+ "iliopsoas_right": 89,
101
+ "brain": 90,
102
+ "skull": 91,
103
+ "rib_left_1": 92,
104
+ "rib_left_2": 93,
105
+ "rib_left_3": 94,
106
+ "rib_left_4": 95,
107
+ "rib_left_5": 96,
108
+ "rib_left_6": 97,
109
+ "rib_left_7": 98,
110
+ "rib_left_8": 99,
111
+ "rib_left_9": 100,
112
+ "rib_left_10": 101,
113
+ "rib_left_11": 102,
114
+ "rib_left_12": 103,
115
+ "rib_right_1": 104,
116
+ "rib_right_2": 105,
117
+ "rib_right_3": 106,
118
+ "rib_right_4": 107,
119
+ "rib_right_5": 108,
120
+ "rib_right_6": 109,
121
+ "rib_right_7": 110,
122
+ "rib_right_8": 111,
123
+ "rib_right_9": 112,
124
+ "rib_right_10": 113,
125
+ "rib_right_11": 114,
126
+ "rib_right_12": 115,
127
+ "sternum": 116,
128
+ "costal_cartilages": 117
129
+ },
130
+ "numTraining": 1559,
131
+ "file_ending": ".nii.gz",
132
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
133
+ }
297/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,166 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 4001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.stages.0.convs.0.all_modules.0.bias",
85
+ "decoder.stages.0.convs.0.all_modules.0.weight",
86
+ "decoder.stages.0.convs.0.all_modules.1.bias",
87
+ "decoder.stages.0.convs.0.all_modules.1.weight",
88
+ "decoder.stages.0.convs.1.all_modules.0.bias",
89
+ "decoder.stages.0.convs.1.all_modules.0.weight",
90
+ "decoder.stages.0.convs.1.all_modules.1.bias",
91
+ "decoder.stages.0.convs.1.all_modules.1.weight",
92
+ "decoder.stages.1.convs.0.all_modules.0.bias",
93
+ "decoder.stages.1.convs.0.all_modules.0.weight",
94
+ "decoder.stages.1.convs.0.all_modules.1.bias",
95
+ "decoder.stages.1.convs.0.all_modules.1.weight",
96
+ "decoder.stages.1.convs.1.all_modules.0.bias",
97
+ "decoder.stages.1.convs.1.all_modules.0.weight",
98
+ "decoder.stages.1.convs.1.all_modules.1.bias",
99
+ "decoder.stages.1.convs.1.all_modules.1.weight",
100
+ "decoder.stages.2.convs.0.all_modules.0.bias",
101
+ "decoder.stages.2.convs.0.all_modules.0.weight",
102
+ "decoder.stages.2.convs.0.all_modules.1.bias",
103
+ "decoder.stages.2.convs.0.all_modules.1.weight",
104
+ "decoder.stages.2.convs.1.all_modules.0.bias",
105
+ "decoder.stages.2.convs.1.all_modules.0.weight",
106
+ "decoder.stages.2.convs.1.all_modules.1.bias",
107
+ "decoder.stages.2.convs.1.all_modules.1.weight",
108
+ "decoder.stages.3.convs.0.all_modules.0.bias",
109
+ "decoder.stages.3.convs.0.all_modules.0.weight",
110
+ "decoder.stages.3.convs.0.all_modules.1.bias",
111
+ "decoder.stages.3.convs.0.all_modules.1.weight",
112
+ "decoder.stages.3.convs.1.all_modules.0.bias",
113
+ "decoder.stages.3.convs.1.all_modules.0.weight",
114
+ "decoder.stages.3.convs.1.all_modules.1.bias",
115
+ "decoder.stages.3.convs.1.all_modules.1.weight",
116
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
117
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
118
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
119
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
120
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
121
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
122
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
123
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
124
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
125
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
126
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
127
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
128
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
129
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
130
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
131
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
132
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
133
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
134
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
135
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
136
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
137
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
138
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
139
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
140
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.4.0.convs.1.all_modules.1.weight"
156
+ ],
157
+ "identity": {
158
+ "configuration": "3d_fullres",
159
+ "fold": 0,
160
+ "trainer_name": "nnUNetTrainer_4000epochs_NoMirroring"
161
+ },
162
+ "inference_allowed_mirroring_axes": [],
163
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
164
+ "source_nnunet_version": "v2.8.1",
165
+ "spatial_dims": 3
166
+ }
297/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:555219a8d42ecd620c9c4be82eb3944f9bb4587b033fdfb13a7b71075d7bb23d
3
+ size 66422798
297/plans.json ADDED
@@ -0,0 +1,282 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset297_TotalSegmentator_total_3mm_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 3.0,
6
+ 3.0,
7
+ 3.0
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 114,
11
+ 114,
12
+ 120
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 145,
30
+ "patch_size": [
31
+ 128,
32
+ 128
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 114.0,
36
+ 120.0
37
+ ],
38
+ "spacing": [
39
+ 3.0,
40
+ 3.0
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2,
56
+ 2
57
+ ],
58
+ "n_conv_per_stage_decoder": [
59
+ 2,
60
+ 2,
61
+ 2,
62
+ 2,
63
+ 2
64
+ ],
65
+ "num_pool_per_axis": [
66
+ 5,
67
+ 5
68
+ ],
69
+ "pool_op_kernel_sizes": [
70
+ [
71
+ 1,
72
+ 1
73
+ ],
74
+ [
75
+ 2,
76
+ 2
77
+ ],
78
+ [
79
+ 2,
80
+ 2
81
+ ],
82
+ [
83
+ 2,
84
+ 2
85
+ ],
86
+ [
87
+ 2,
88
+ 2
89
+ ],
90
+ [
91
+ 2,
92
+ 2
93
+ ]
94
+ ],
95
+ "conv_kernel_sizes": [
96
+ [
97
+ 3,
98
+ 3
99
+ ],
100
+ [
101
+ 3,
102
+ 3
103
+ ],
104
+ [
105
+ 3,
106
+ 3
107
+ ],
108
+ [
109
+ 3,
110
+ 3
111
+ ],
112
+ [
113
+ 3,
114
+ 3
115
+ ],
116
+ [
117
+ 3,
118
+ 3
119
+ ]
120
+ ],
121
+ "unet_max_num_features": 512,
122
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
123
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
124
+ "resampling_fn_data_kwargs": {
125
+ "is_seg": false,
126
+ "order": 3,
127
+ "order_z": 0,
128
+ "force_separate_z": null
129
+ },
130
+ "resampling_fn_seg_kwargs": {
131
+ "is_seg": true,
132
+ "order": 1,
133
+ "order_z": 0,
134
+ "force_separate_z": null
135
+ },
136
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
137
+ "resampling_fn_probabilities_kwargs": {
138
+ "is_seg": false,
139
+ "order": 1,
140
+ "order_z": 0,
141
+ "force_separate_z": null
142
+ },
143
+ "batch_dice": true
144
+ },
145
+ "3d_fullres": {
146
+ "data_identifier": "nnUNetPlans_3d_fullres",
147
+ "preprocessor_name": "DefaultPreprocessor",
148
+ "batch_size": 2,
149
+ "patch_size": [
150
+ 112,
151
+ 112,
152
+ 128
153
+ ],
154
+ "median_image_size_in_voxels": [
155
+ 114.0,
156
+ 114.0,
157
+ 120.0
158
+ ],
159
+ "spacing": [
160
+ 3.0,
161
+ 3.0,
162
+ 3.0
163
+ ],
164
+ "normalization_schemes": [
165
+ "CTNormalization"
166
+ ],
167
+ "use_mask_for_norm": [
168
+ false
169
+ ],
170
+ "UNet_class_name": "PlainConvUNet",
171
+ "UNet_base_num_features": 32,
172
+ "n_conv_per_stage_encoder": [
173
+ 2,
174
+ 2,
175
+ 2,
176
+ 2,
177
+ 2
178
+ ],
179
+ "n_conv_per_stage_decoder": [
180
+ 2,
181
+ 2,
182
+ 2,
183
+ 2
184
+ ],
185
+ "num_pool_per_axis": [
186
+ 4,
187
+ 4,
188
+ 4
189
+ ],
190
+ "pool_op_kernel_sizes": [
191
+ [
192
+ 1,
193
+ 1,
194
+ 1
195
+ ],
196
+ [
197
+ 2,
198
+ 2,
199
+ 2
200
+ ],
201
+ [
202
+ 2,
203
+ 2,
204
+ 2
205
+ ],
206
+ [
207
+ 2,
208
+ 2,
209
+ 2
210
+ ],
211
+ [
212
+ 2,
213
+ 2,
214
+ 2
215
+ ]
216
+ ],
217
+ "conv_kernel_sizes": [
218
+ [
219
+ 3,
220
+ 3,
221
+ 3
222
+ ],
223
+ [
224
+ 3,
225
+ 3,
226
+ 3
227
+ ],
228
+ [
229
+ 3,
230
+ 3,
231
+ 3
232
+ ],
233
+ [
234
+ 3,
235
+ 3,
236
+ 3
237
+ ],
238
+ [
239
+ 3,
240
+ 3,
241
+ 3
242
+ ]
243
+ ],
244
+ "unet_max_num_features": 320,
245
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
246
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
247
+ "resampling_fn_data_kwargs": {
248
+ "is_seg": false,
249
+ "order": 3,
250
+ "order_z": 0,
251
+ "force_separate_z": null
252
+ },
253
+ "resampling_fn_seg_kwargs": {
254
+ "is_seg": true,
255
+ "order": 1,
256
+ "order_z": 0,
257
+ "force_separate_z": null
258
+ },
259
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
260
+ "resampling_fn_probabilities_kwargs": {
261
+ "is_seg": false,
262
+ "order": 1,
263
+ "order_z": 0,
264
+ "force_separate_z": null
265
+ },
266
+ "batch_dice": false
267
+ }
268
+ },
269
+ "experiment_planner_used": "ExperimentPlanner",
270
+ "label_manager": "LabelManager",
271
+ "foreground_intensity_properties_per_channel": {
272
+ "0": {
273
+ "max": 37283.0,
274
+ "mean": -50.38697721419439,
275
+ "median": 42.0,
276
+ "min": -28071.0,
277
+ "percentile_00_5": -1004.0,
278
+ "percentile_99_5": 1588.0,
279
+ "std": 503.39235619144
280
+ }
281
+ }
282
+ }
298/conversion.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [],
10
+ "source_checkpoint": "checkpoint_final.pth"
11
+ }
12
+ ],
13
+ "schema_version": "nnunet-mlx.conversion.v1",
14
+ "source_profile": "totalsegmentator-v2-ct",
15
+ "spatial_dims": 3
16
+ }
298/dataset.json ADDED
@@ -0,0 +1,133 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "channel_names": {
8
+ "0": "CT"
9
+ },
10
+ "labels": {
11
+ "background": 0,
12
+ "spleen": 1,
13
+ "kidney_right": 2,
14
+ "kidney_left": 3,
15
+ "gallbladder": 4,
16
+ "liver": 5,
17
+ "stomach": 6,
18
+ "pancreas": 7,
19
+ "adrenal_gland_right": 8,
20
+ "adrenal_gland_left": 9,
21
+ "lung_upper_lobe_left": 10,
22
+ "lung_lower_lobe_left": 11,
23
+ "lung_upper_lobe_right": 12,
24
+ "lung_middle_lobe_right": 13,
25
+ "lung_lower_lobe_right": 14,
26
+ "esophagus": 15,
27
+ "trachea": 16,
28
+ "thyroid_gland": 17,
29
+ "small_bowel": 18,
30
+ "duodenum": 19,
31
+ "colon": 20,
32
+ "urinary_bladder": 21,
33
+ "prostate": 22,
34
+ "kidney_cyst_left": 23,
35
+ "kidney_cyst_right": 24,
36
+ "sacrum": 25,
37
+ "vertebrae_S1": 26,
38
+ "vertebrae_L5": 27,
39
+ "vertebrae_L4": 28,
40
+ "vertebrae_L3": 29,
41
+ "vertebrae_L2": 30,
42
+ "vertebrae_L1": 31,
43
+ "vertebrae_T12": 32,
44
+ "vertebrae_T11": 33,
45
+ "vertebrae_T10": 34,
46
+ "vertebrae_T9": 35,
47
+ "vertebrae_T8": 36,
48
+ "vertebrae_T7": 37,
49
+ "vertebrae_T6": 38,
50
+ "vertebrae_T5": 39,
51
+ "vertebrae_T4": 40,
52
+ "vertebrae_T3": 41,
53
+ "vertebrae_T2": 42,
54
+ "vertebrae_T1": 43,
55
+ "vertebrae_C7": 44,
56
+ "vertebrae_C6": 45,
57
+ "vertebrae_C5": 46,
58
+ "vertebrae_C4": 47,
59
+ "vertebrae_C3": 48,
60
+ "vertebrae_C2": 49,
61
+ "vertebrae_C1": 50,
62
+ "heart": 51,
63
+ "aorta": 52,
64
+ "pulmonary_vein": 53,
65
+ "brachiocephalic_trunk": 54,
66
+ "subclavian_artery_right": 55,
67
+ "subclavian_artery_left": 56,
68
+ "common_carotid_artery_right": 57,
69
+ "common_carotid_artery_left": 58,
70
+ "brachiocephalic_vein_left": 59,
71
+ "brachiocephalic_vein_right": 60,
72
+ "atrial_appendage_left": 61,
73
+ "superior_vena_cava": 62,
74
+ "inferior_vena_cava": 63,
75
+ "portal_vein_and_splenic_vein": 64,
76
+ "iliac_artery_left": 65,
77
+ "iliac_artery_right": 66,
78
+ "iliac_vena_left": 67,
79
+ "iliac_vena_right": 68,
80
+ "humerus_left": 69,
81
+ "humerus_right": 70,
82
+ "scapula_left": 71,
83
+ "scapula_right": 72,
84
+ "clavicula_left": 73,
85
+ "clavicula_right": 74,
86
+ "femur_left": 75,
87
+ "femur_right": 76,
88
+ "hip_left": 77,
89
+ "hip_right": 78,
90
+ "spinal_cord": 79,
91
+ "gluteus_maximus_left": 80,
92
+ "gluteus_maximus_right": 81,
93
+ "gluteus_medius_left": 82,
94
+ "gluteus_medius_right": 83,
95
+ "gluteus_minimus_left": 84,
96
+ "gluteus_minimus_right": 85,
97
+ "autochthon_left": 86,
98
+ "autochthon_right": 87,
99
+ "iliopsoas_left": 88,
100
+ "iliopsoas_right": 89,
101
+ "brain": 90,
102
+ "skull": 91,
103
+ "rib_left_1": 92,
104
+ "rib_left_2": 93,
105
+ "rib_left_3": 94,
106
+ "rib_left_4": 95,
107
+ "rib_left_5": 96,
108
+ "rib_left_6": 97,
109
+ "rib_left_7": 98,
110
+ "rib_left_8": 99,
111
+ "rib_left_9": 100,
112
+ "rib_left_10": 101,
113
+ "rib_left_11": 102,
114
+ "rib_left_12": 103,
115
+ "rib_right_1": 104,
116
+ "rib_right_2": 105,
117
+ "rib_right_3": 106,
118
+ "rib_right_4": 107,
119
+ "rib_right_5": 108,
120
+ "rib_right_6": 109,
121
+ "rib_right_7": 110,
122
+ "rib_right_8": 111,
123
+ "rib_right_9": 112,
124
+ "rib_right_10": 113,
125
+ "rib_right_11": 114,
126
+ "rib_right_12": 115,
127
+ "sternum": 116,
128
+ "costal_cartilages": 117
129
+ },
130
+ "numTraining": 1559,
131
+ "file_ending": ".nii.gz",
132
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
133
+ }
298/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,166 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 4001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.stages.0.convs.0.all_modules.0.bias",
85
+ "decoder.stages.0.convs.0.all_modules.0.weight",
86
+ "decoder.stages.0.convs.0.all_modules.1.bias",
87
+ "decoder.stages.0.convs.0.all_modules.1.weight",
88
+ "decoder.stages.0.convs.1.all_modules.0.bias",
89
+ "decoder.stages.0.convs.1.all_modules.0.weight",
90
+ "decoder.stages.0.convs.1.all_modules.1.bias",
91
+ "decoder.stages.0.convs.1.all_modules.1.weight",
92
+ "decoder.stages.1.convs.0.all_modules.0.bias",
93
+ "decoder.stages.1.convs.0.all_modules.0.weight",
94
+ "decoder.stages.1.convs.0.all_modules.1.bias",
95
+ "decoder.stages.1.convs.0.all_modules.1.weight",
96
+ "decoder.stages.1.convs.1.all_modules.0.bias",
97
+ "decoder.stages.1.convs.1.all_modules.0.weight",
98
+ "decoder.stages.1.convs.1.all_modules.1.bias",
99
+ "decoder.stages.1.convs.1.all_modules.1.weight",
100
+ "decoder.stages.2.convs.0.all_modules.0.bias",
101
+ "decoder.stages.2.convs.0.all_modules.0.weight",
102
+ "decoder.stages.2.convs.0.all_modules.1.bias",
103
+ "decoder.stages.2.convs.0.all_modules.1.weight",
104
+ "decoder.stages.2.convs.1.all_modules.0.bias",
105
+ "decoder.stages.2.convs.1.all_modules.0.weight",
106
+ "decoder.stages.2.convs.1.all_modules.1.bias",
107
+ "decoder.stages.2.convs.1.all_modules.1.weight",
108
+ "decoder.stages.3.convs.0.all_modules.0.bias",
109
+ "decoder.stages.3.convs.0.all_modules.0.weight",
110
+ "decoder.stages.3.convs.0.all_modules.1.bias",
111
+ "decoder.stages.3.convs.0.all_modules.1.weight",
112
+ "decoder.stages.3.convs.1.all_modules.0.bias",
113
+ "decoder.stages.3.convs.1.all_modules.0.weight",
114
+ "decoder.stages.3.convs.1.all_modules.1.bias",
115
+ "decoder.stages.3.convs.1.all_modules.1.weight",
116
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
117
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
118
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
119
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
120
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
121
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
122
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
123
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
124
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
125
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
126
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
127
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
128
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
129
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
130
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
131
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
132
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
133
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
134
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
135
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
136
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
137
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
138
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
139
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
140
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.4.0.convs.1.all_modules.1.weight"
156
+ ],
157
+ "identity": {
158
+ "configuration": "3d_fullres",
159
+ "fold": 0,
160
+ "trainer_name": "nnUNetTrainer_4000epochs_NoMirroring"
161
+ },
162
+ "inference_allowed_mirroring_axes": [],
163
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
164
+ "source_nnunet_version": "v2.8.1",
165
+ "spatial_dims": 3
166
+ }
298/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:907ce214069f41ed1f8b26898ce0baab3a078ed7e51cb2ea32fe0127be1fc095
3
+ size 66422798
298/plans.json ADDED
@@ -0,0 +1,272 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset298_TotalSegmentator_total_6mm_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 6.0,
6
+ 6.0,
7
+ 6.0
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 57,
11
+ 57,
12
+ 60
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 590,
30
+ "patch_size": [
31
+ 64,
32
+ 64
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 57.0,
36
+ 60.0
37
+ ],
38
+ "spacing": [
39
+ 6.0,
40
+ 6.0
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2
56
+ ],
57
+ "n_conv_per_stage_decoder": [
58
+ 2,
59
+ 2,
60
+ 2,
61
+ 2
62
+ ],
63
+ "num_pool_per_axis": [
64
+ 4,
65
+ 4
66
+ ],
67
+ "pool_op_kernel_sizes": [
68
+ [
69
+ 1,
70
+ 1
71
+ ],
72
+ [
73
+ 2,
74
+ 2
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ]
88
+ ],
89
+ "conv_kernel_sizes": [
90
+ [
91
+ 3,
92
+ 3
93
+ ],
94
+ [
95
+ 3,
96
+ 3
97
+ ],
98
+ [
99
+ 3,
100
+ 3
101
+ ],
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ]
110
+ ],
111
+ "unet_max_num_features": 512,
112
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
113
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
114
+ "resampling_fn_data_kwargs": {
115
+ "is_seg": false,
116
+ "order": 3,
117
+ "order_z": 0,
118
+ "force_separate_z": null
119
+ },
120
+ "resampling_fn_seg_kwargs": {
121
+ "is_seg": true,
122
+ "order": 1,
123
+ "order_z": 0,
124
+ "force_separate_z": null
125
+ },
126
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
127
+ "resampling_fn_probabilities_kwargs": {
128
+ "is_seg": false,
129
+ "order": 1,
130
+ "order_z": 0,
131
+ "force_separate_z": null
132
+ },
133
+ "batch_dice": true
134
+ },
135
+ "3d_fullres": {
136
+ "data_identifier": "nnUNetPlans_3d_fullres",
137
+ "preprocessor_name": "DefaultPreprocessor",
138
+ "batch_size": 13,
139
+ "patch_size": [
140
+ 64,
141
+ 64,
142
+ 64
143
+ ],
144
+ "median_image_size_in_voxels": [
145
+ 57.0,
146
+ 57.0,
147
+ 60.0
148
+ ],
149
+ "spacing": [
150
+ 6.0,
151
+ 6.0,
152
+ 6.0
153
+ ],
154
+ "normalization_schemes": [
155
+ "CTNormalization"
156
+ ],
157
+ "use_mask_for_norm": [
158
+ false
159
+ ],
160
+ "UNet_class_name": "PlainConvUNet",
161
+ "UNet_base_num_features": 32,
162
+ "n_conv_per_stage_encoder": [
163
+ 2,
164
+ 2,
165
+ 2,
166
+ 2,
167
+ 2
168
+ ],
169
+ "n_conv_per_stage_decoder": [
170
+ 2,
171
+ 2,
172
+ 2,
173
+ 2
174
+ ],
175
+ "num_pool_per_axis": [
176
+ 4,
177
+ 4,
178
+ 4
179
+ ],
180
+ "pool_op_kernel_sizes": [
181
+ [
182
+ 1,
183
+ 1,
184
+ 1
185
+ ],
186
+ [
187
+ 2,
188
+ 2,
189
+ 2
190
+ ],
191
+ [
192
+ 2,
193
+ 2,
194
+ 2
195
+ ],
196
+ [
197
+ 2,
198
+ 2,
199
+ 2
200
+ ],
201
+ [
202
+ 2,
203
+ 2,
204
+ 2
205
+ ]
206
+ ],
207
+ "conv_kernel_sizes": [
208
+ [
209
+ 3,
210
+ 3,
211
+ 3
212
+ ],
213
+ [
214
+ 3,
215
+ 3,
216
+ 3
217
+ ],
218
+ [
219
+ 3,
220
+ 3,
221
+ 3
222
+ ],
223
+ [
224
+ 3,
225
+ 3,
226
+ 3
227
+ ],
228
+ [
229
+ 3,
230
+ 3,
231
+ 3
232
+ ]
233
+ ],
234
+ "unet_max_num_features": 320,
235
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
236
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
237
+ "resampling_fn_data_kwargs": {
238
+ "is_seg": false,
239
+ "order": 3,
240
+ "order_z": 0,
241
+ "force_separate_z": null
242
+ },
243
+ "resampling_fn_seg_kwargs": {
244
+ "is_seg": true,
245
+ "order": 1,
246
+ "order_z": 0,
247
+ "force_separate_z": null
248
+ },
249
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
250
+ "resampling_fn_probabilities_kwargs": {
251
+ "is_seg": false,
252
+ "order": 1,
253
+ "order_z": 0,
254
+ "force_separate_z": null
255
+ },
256
+ "batch_dice": false
257
+ }
258
+ },
259
+ "experiment_planner_used": "ExperimentPlanner",
260
+ "label_manager": "LabelManager",
261
+ "foreground_intensity_properties_per_channel": {
262
+ "0": {
263
+ "max": 31044.0,
264
+ "mean": -50.4849524394411,
265
+ "median": 41.0,
266
+ "min": -28473.0,
267
+ "percentile_00_5": -1002.0,
268
+ "percentile_99_5": 1584.0,
269
+ "std": 505.81990262489825
270
+ }
271
+ }
272
+ }
300/conversion.json ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architecture": "dynamic_network_architectures.architectures.unet.PlainConvUNet",
3
+ "configuration": "3d_fullres",
4
+ "engine_version": "0.5.2",
5
+ "folds": [
6
+ {
7
+ "checkpoint": "checkpoint_final",
8
+ "fold": 0,
9
+ "mirroring_axes": [
10
+ 0,
11
+ 1,
12
+ 2
13
+ ],
14
+ "source_checkpoint": "checkpoint_final.pth"
15
+ }
16
+ ],
17
+ "schema_version": "nnunet-mlx.conversion.v1",
18
+ "source_profile": "totalsegmentator-v2-ct",
19
+ "spatial_dims": 3
20
+ }
300/dataset.json ADDED
@@ -0,0 +1,18 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "name": "Segmentation of X",
3
+ "description": "Segmentation",
4
+ "reference": "Jakob",
5
+ "licence": "-",
6
+ "release": "0.0",
7
+ "labels": {
8
+ "background": 0,
9
+ "body_trunc": 1,
10
+ "body_extremities": 2
11
+ },
12
+ "numTraining": 1559,
13
+ "channel_names": {
14
+ "0": "CT"
15
+ },
16
+ "file_ending": ".nii.gz",
17
+ "overwrite_image_reader_writer": "NibabelIOWithReorient"
18
+ }
300/fold_0/checkpoint_final/state.json ADDED
@@ -0,0 +1,170 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "current_epoch": 1001,
3
+ "dropped_source_keys": [
4
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.bias",
5
+ "decoder.encoder.stages.0.0.convs.0.all_modules.0.weight",
6
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.bias",
7
+ "decoder.encoder.stages.0.0.convs.0.all_modules.1.weight",
8
+ "decoder.encoder.stages.0.0.convs.0.conv.bias",
9
+ "decoder.encoder.stages.0.0.convs.0.conv.weight",
10
+ "decoder.encoder.stages.0.0.convs.0.norm.bias",
11
+ "decoder.encoder.stages.0.0.convs.0.norm.weight",
12
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.bias",
13
+ "decoder.encoder.stages.0.0.convs.1.all_modules.0.weight",
14
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.bias",
15
+ "decoder.encoder.stages.0.0.convs.1.all_modules.1.weight",
16
+ "decoder.encoder.stages.0.0.convs.1.conv.bias",
17
+ "decoder.encoder.stages.0.0.convs.1.conv.weight",
18
+ "decoder.encoder.stages.0.0.convs.1.norm.bias",
19
+ "decoder.encoder.stages.0.0.convs.1.norm.weight",
20
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.bias",
21
+ "decoder.encoder.stages.1.0.convs.0.all_modules.0.weight",
22
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.bias",
23
+ "decoder.encoder.stages.1.0.convs.0.all_modules.1.weight",
24
+ "decoder.encoder.stages.1.0.convs.0.conv.bias",
25
+ "decoder.encoder.stages.1.0.convs.0.conv.weight",
26
+ "decoder.encoder.stages.1.0.convs.0.norm.bias",
27
+ "decoder.encoder.stages.1.0.convs.0.norm.weight",
28
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.bias",
29
+ "decoder.encoder.stages.1.0.convs.1.all_modules.0.weight",
30
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.bias",
31
+ "decoder.encoder.stages.1.0.convs.1.all_modules.1.weight",
32
+ "decoder.encoder.stages.1.0.convs.1.conv.bias",
33
+ "decoder.encoder.stages.1.0.convs.1.conv.weight",
34
+ "decoder.encoder.stages.1.0.convs.1.norm.bias",
35
+ "decoder.encoder.stages.1.0.convs.1.norm.weight",
36
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.bias",
37
+ "decoder.encoder.stages.2.0.convs.0.all_modules.0.weight",
38
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.bias",
39
+ "decoder.encoder.stages.2.0.convs.0.all_modules.1.weight",
40
+ "decoder.encoder.stages.2.0.convs.0.conv.bias",
41
+ "decoder.encoder.stages.2.0.convs.0.conv.weight",
42
+ "decoder.encoder.stages.2.0.convs.0.norm.bias",
43
+ "decoder.encoder.stages.2.0.convs.0.norm.weight",
44
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.bias",
45
+ "decoder.encoder.stages.2.0.convs.1.all_modules.0.weight",
46
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.bias",
47
+ "decoder.encoder.stages.2.0.convs.1.all_modules.1.weight",
48
+ "decoder.encoder.stages.2.0.convs.1.conv.bias",
49
+ "decoder.encoder.stages.2.0.convs.1.conv.weight",
50
+ "decoder.encoder.stages.2.0.convs.1.norm.bias",
51
+ "decoder.encoder.stages.2.0.convs.1.norm.weight",
52
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.bias",
53
+ "decoder.encoder.stages.3.0.convs.0.all_modules.0.weight",
54
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.bias",
55
+ "decoder.encoder.stages.3.0.convs.0.all_modules.1.weight",
56
+ "decoder.encoder.stages.3.0.convs.0.conv.bias",
57
+ "decoder.encoder.stages.3.0.convs.0.conv.weight",
58
+ "decoder.encoder.stages.3.0.convs.0.norm.bias",
59
+ "decoder.encoder.stages.3.0.convs.0.norm.weight",
60
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.bias",
61
+ "decoder.encoder.stages.3.0.convs.1.all_modules.0.weight",
62
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.bias",
63
+ "decoder.encoder.stages.3.0.convs.1.all_modules.1.weight",
64
+ "decoder.encoder.stages.3.0.convs.1.conv.bias",
65
+ "decoder.encoder.stages.3.0.convs.1.conv.weight",
66
+ "decoder.encoder.stages.3.0.convs.1.norm.bias",
67
+ "decoder.encoder.stages.3.0.convs.1.norm.weight",
68
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.bias",
69
+ "decoder.encoder.stages.4.0.convs.0.all_modules.0.weight",
70
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.bias",
71
+ "decoder.encoder.stages.4.0.convs.0.all_modules.1.weight",
72
+ "decoder.encoder.stages.4.0.convs.0.conv.bias",
73
+ "decoder.encoder.stages.4.0.convs.0.conv.weight",
74
+ "decoder.encoder.stages.4.0.convs.0.norm.bias",
75
+ "decoder.encoder.stages.4.0.convs.0.norm.weight",
76
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.bias",
77
+ "decoder.encoder.stages.4.0.convs.1.all_modules.0.weight",
78
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.bias",
79
+ "decoder.encoder.stages.4.0.convs.1.all_modules.1.weight",
80
+ "decoder.encoder.stages.4.0.convs.1.conv.bias",
81
+ "decoder.encoder.stages.4.0.convs.1.conv.weight",
82
+ "decoder.encoder.stages.4.0.convs.1.norm.bias",
83
+ "decoder.encoder.stages.4.0.convs.1.norm.weight",
84
+ "decoder.stages.0.convs.0.all_modules.0.bias",
85
+ "decoder.stages.0.convs.0.all_modules.0.weight",
86
+ "decoder.stages.0.convs.0.all_modules.1.bias",
87
+ "decoder.stages.0.convs.0.all_modules.1.weight",
88
+ "decoder.stages.0.convs.1.all_modules.0.bias",
89
+ "decoder.stages.0.convs.1.all_modules.0.weight",
90
+ "decoder.stages.0.convs.1.all_modules.1.bias",
91
+ "decoder.stages.0.convs.1.all_modules.1.weight",
92
+ "decoder.stages.1.convs.0.all_modules.0.bias",
93
+ "decoder.stages.1.convs.0.all_modules.0.weight",
94
+ "decoder.stages.1.convs.0.all_modules.1.bias",
95
+ "decoder.stages.1.convs.0.all_modules.1.weight",
96
+ "decoder.stages.1.convs.1.all_modules.0.bias",
97
+ "decoder.stages.1.convs.1.all_modules.0.weight",
98
+ "decoder.stages.1.convs.1.all_modules.1.bias",
99
+ "decoder.stages.1.convs.1.all_modules.1.weight",
100
+ "decoder.stages.2.convs.0.all_modules.0.bias",
101
+ "decoder.stages.2.convs.0.all_modules.0.weight",
102
+ "decoder.stages.2.convs.0.all_modules.1.bias",
103
+ "decoder.stages.2.convs.0.all_modules.1.weight",
104
+ "decoder.stages.2.convs.1.all_modules.0.bias",
105
+ "decoder.stages.2.convs.1.all_modules.0.weight",
106
+ "decoder.stages.2.convs.1.all_modules.1.bias",
107
+ "decoder.stages.2.convs.1.all_modules.1.weight",
108
+ "decoder.stages.3.convs.0.all_modules.0.bias",
109
+ "decoder.stages.3.convs.0.all_modules.0.weight",
110
+ "decoder.stages.3.convs.0.all_modules.1.bias",
111
+ "decoder.stages.3.convs.0.all_modules.1.weight",
112
+ "decoder.stages.3.convs.1.all_modules.0.bias",
113
+ "decoder.stages.3.convs.1.all_modules.0.weight",
114
+ "decoder.stages.3.convs.1.all_modules.1.bias",
115
+ "decoder.stages.3.convs.1.all_modules.1.weight",
116
+ "encoder.stages.0.0.convs.0.all_modules.0.bias",
117
+ "encoder.stages.0.0.convs.0.all_modules.0.weight",
118
+ "encoder.stages.0.0.convs.0.all_modules.1.bias",
119
+ "encoder.stages.0.0.convs.0.all_modules.1.weight",
120
+ "encoder.stages.0.0.convs.1.all_modules.0.bias",
121
+ "encoder.stages.0.0.convs.1.all_modules.0.weight",
122
+ "encoder.stages.0.0.convs.1.all_modules.1.bias",
123
+ "encoder.stages.0.0.convs.1.all_modules.1.weight",
124
+ "encoder.stages.1.0.convs.0.all_modules.0.bias",
125
+ "encoder.stages.1.0.convs.0.all_modules.0.weight",
126
+ "encoder.stages.1.0.convs.0.all_modules.1.bias",
127
+ "encoder.stages.1.0.convs.0.all_modules.1.weight",
128
+ "encoder.stages.1.0.convs.1.all_modules.0.bias",
129
+ "encoder.stages.1.0.convs.1.all_modules.0.weight",
130
+ "encoder.stages.1.0.convs.1.all_modules.1.bias",
131
+ "encoder.stages.1.0.convs.1.all_modules.1.weight",
132
+ "encoder.stages.2.0.convs.0.all_modules.0.bias",
133
+ "encoder.stages.2.0.convs.0.all_modules.0.weight",
134
+ "encoder.stages.2.0.convs.0.all_modules.1.bias",
135
+ "encoder.stages.2.0.convs.0.all_modules.1.weight",
136
+ "encoder.stages.2.0.convs.1.all_modules.0.bias",
137
+ "encoder.stages.2.0.convs.1.all_modules.0.weight",
138
+ "encoder.stages.2.0.convs.1.all_modules.1.bias",
139
+ "encoder.stages.2.0.convs.1.all_modules.1.weight",
140
+ "encoder.stages.3.0.convs.0.all_modules.0.bias",
141
+ "encoder.stages.3.0.convs.0.all_modules.0.weight",
142
+ "encoder.stages.3.0.convs.0.all_modules.1.bias",
143
+ "encoder.stages.3.0.convs.0.all_modules.1.weight",
144
+ "encoder.stages.3.0.convs.1.all_modules.0.bias",
145
+ "encoder.stages.3.0.convs.1.all_modules.0.weight",
146
+ "encoder.stages.3.0.convs.1.all_modules.1.bias",
147
+ "encoder.stages.3.0.convs.1.all_modules.1.weight",
148
+ "encoder.stages.4.0.convs.0.all_modules.0.bias",
149
+ "encoder.stages.4.0.convs.0.all_modules.0.weight",
150
+ "encoder.stages.4.0.convs.0.all_modules.1.bias",
151
+ "encoder.stages.4.0.convs.0.all_modules.1.weight",
152
+ "encoder.stages.4.0.convs.1.all_modules.0.bias",
153
+ "encoder.stages.4.0.convs.1.all_modules.0.weight",
154
+ "encoder.stages.4.0.convs.1.all_modules.1.bias",
155
+ "encoder.stages.4.0.convs.1.all_modules.1.weight"
156
+ ],
157
+ "identity": {
158
+ "configuration": "3d_fullres",
159
+ "fold": 0,
160
+ "trainer_name": "nnUNetTrainer"
161
+ },
162
+ "inference_allowed_mirroring_axes": [
163
+ 0,
164
+ 1,
165
+ 2
166
+ ],
167
+ "schema_version": "nnunet-mlx.inference-checkpoint.v2",
168
+ "source_nnunet_version": "v2.8.1",
169
+ "spatial_dims": 3
170
+ }
300/fold_0/checkpoint_final/weights.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:08ca74c952fbdf493b939cc4c0512d66c34ffe056595d31f6f7fd798b192b61e
3
+ size 66200132
300/plans.json ADDED
@@ -0,0 +1,272 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "dataset_name": "Dataset300_body_6mm_1559subj",
3
+ "plans_name": "nnUNetPlans",
4
+ "original_median_spacing_after_transp": [
5
+ 6.0,
6
+ 6.0,
7
+ 6.0
8
+ ],
9
+ "original_median_shape_after_transp": [
10
+ 57,
11
+ 57,
12
+ 60
13
+ ],
14
+ "image_reader_writer": "NibabelIOWithReorient",
15
+ "transpose_forward": [
16
+ 0,
17
+ 1,
18
+ 2
19
+ ],
20
+ "transpose_backward": [
21
+ 0,
22
+ 1,
23
+ 2
24
+ ],
25
+ "configurations": {
26
+ "2d": {
27
+ "data_identifier": "nnUNetPlans_2d",
28
+ "preprocessor_name": "DefaultPreprocessor",
29
+ "batch_size": 811,
30
+ "patch_size": [
31
+ 64,
32
+ 64
33
+ ],
34
+ "median_image_size_in_voxels": [
35
+ 57.0,
36
+ 60.0
37
+ ],
38
+ "spacing": [
39
+ 6.0,
40
+ 6.0
41
+ ],
42
+ "normalization_schemes": [
43
+ "CTNormalization"
44
+ ],
45
+ "use_mask_for_norm": [
46
+ false
47
+ ],
48
+ "UNet_class_name": "PlainConvUNet",
49
+ "UNet_base_num_features": 32,
50
+ "n_conv_per_stage_encoder": [
51
+ 2,
52
+ 2,
53
+ 2,
54
+ 2,
55
+ 2
56
+ ],
57
+ "n_conv_per_stage_decoder": [
58
+ 2,
59
+ 2,
60
+ 2,
61
+ 2
62
+ ],
63
+ "num_pool_per_axis": [
64
+ 4,
65
+ 4
66
+ ],
67
+ "pool_op_kernel_sizes": [
68
+ [
69
+ 1,
70
+ 1
71
+ ],
72
+ [
73
+ 2,
74
+ 2
75
+ ],
76
+ [
77
+ 2,
78
+ 2
79
+ ],
80
+ [
81
+ 2,
82
+ 2
83
+ ],
84
+ [
85
+ 2,
86
+ 2
87
+ ]
88
+ ],
89
+ "conv_kernel_sizes": [
90
+ [
91
+ 3,
92
+ 3
93
+ ],
94
+ [
95
+ 3,
96
+ 3
97
+ ],
98
+ [
99
+ 3,
100
+ 3
101
+ ],
102
+ [
103
+ 3,
104
+ 3
105
+ ],
106
+ [
107
+ 3,
108
+ 3
109
+ ]
110
+ ],
111
+ "unet_max_num_features": 512,
112
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
113
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
114
+ "resampling_fn_data_kwargs": {
115
+ "is_seg": false,
116
+ "order": 3,
117
+ "order_z": 0,
118
+ "force_separate_z": null
119
+ },
120
+ "resampling_fn_seg_kwargs": {
121
+ "is_seg": true,
122
+ "order": 1,
123
+ "order_z": 0,
124
+ "force_separate_z": null
125
+ },
126
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
127
+ "resampling_fn_probabilities_kwargs": {
128
+ "is_seg": false,
129
+ "order": 1,
130
+ "order_z": 0,
131
+ "force_separate_z": null
132
+ },
133
+ "batch_dice": true
134
+ },
135
+ "3d_fullres": {
136
+ "data_identifier": "nnUNetPlans_3d_fullres",
137
+ "preprocessor_name": "DefaultPreprocessor",
138
+ "batch_size": 20,
139
+ "patch_size": [
140
+ 64,
141
+ 64,
142
+ 64
143
+ ],
144
+ "median_image_size_in_voxels": [
145
+ 57.0,
146
+ 57.0,
147
+ 60.0
148
+ ],
149
+ "spacing": [
150
+ 6.0,
151
+ 6.0,
152
+ 6.0
153
+ ],
154
+ "normalization_schemes": [
155
+ "CTNormalization"
156
+ ],
157
+ "use_mask_for_norm": [
158
+ false
159
+ ],
160
+ "UNet_class_name": "PlainConvUNet",
161
+ "UNet_base_num_features": 32,
162
+ "n_conv_per_stage_encoder": [
163
+ 2,
164
+ 2,
165
+ 2,
166
+ 2,
167
+ 2
168
+ ],
169
+ "n_conv_per_stage_decoder": [
170
+ 2,
171
+ 2,
172
+ 2,
173
+ 2
174
+ ],
175
+ "num_pool_per_axis": [
176
+ 4,
177
+ 4,
178
+ 4
179
+ ],
180
+ "pool_op_kernel_sizes": [
181
+ [
182
+ 1,
183
+ 1,
184
+ 1
185
+ ],
186
+ [
187
+ 2,
188
+ 2,
189
+ 2
190
+ ],
191
+ [
192
+ 2,
193
+ 2,
194
+ 2
195
+ ],
196
+ [
197
+ 2,
198
+ 2,
199
+ 2
200
+ ],
201
+ [
202
+ 2,
203
+ 2,
204
+ 2
205
+ ]
206
+ ],
207
+ "conv_kernel_sizes": [
208
+ [
209
+ 3,
210
+ 3,
211
+ 3
212
+ ],
213
+ [
214
+ 3,
215
+ 3,
216
+ 3
217
+ ],
218
+ [
219
+ 3,
220
+ 3,
221
+ 3
222
+ ],
223
+ [
224
+ 3,
225
+ 3,
226
+ 3
227
+ ],
228
+ [
229
+ 3,
230
+ 3,
231
+ 3
232
+ ]
233
+ ],
234
+ "unet_max_num_features": 320,
235
+ "resampling_fn_data": "resample_data_or_seg_to_shape",
236
+ "resampling_fn_seg": "resample_data_or_seg_to_shape",
237
+ "resampling_fn_data_kwargs": {
238
+ "is_seg": false,
239
+ "order": 3,
240
+ "order_z": 0,
241
+ "force_separate_z": null
242
+ },
243
+ "resampling_fn_seg_kwargs": {
244
+ "is_seg": true,
245
+ "order": 1,
246
+ "order_z": 0,
247
+ "force_separate_z": null
248
+ },
249
+ "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
250
+ "resampling_fn_probabilities_kwargs": {
251
+ "is_seg": false,
252
+ "order": 1,
253
+ "order_z": 0,
254
+ "force_separate_z": null
255
+ },
256
+ "batch_dice": false
257
+ }
258
+ },
259
+ "experiment_planner_used": "ExperimentPlanner",
260
+ "label_manager": "LabelManager",
261
+ "foreground_intensity_properties_per_channel": {
262
+ "0": {
263
+ "max": 31554.0,
264
+ "mean": -43.95634460449219,
265
+ "median": 0.0,
266
+ "min": -42354.0,
267
+ "percentile_00_5": -989.0,
268
+ "percentile_99_5": 1383.0,
269
+ "std": 371.595703125
270
+ }
271
+ }
272
+ }
LICENSE ADDED
@@ -0,0 +1,201 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Apache License
2
+ Version 2.0, January 2004
3
+ http://www.apache.org/licenses/
4
+
5
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
6
+
7
+ 1. Definitions.
8
+
9
+ "License" shall mean the terms and conditions for use, reproduction,
10
+ and distribution as defined by Sections 1 through 9 of this document.
11
+
12
+ "Licensor" shall mean the copyright owner or entity authorized by
13
+ the copyright owner that is granting the License.
14
+
15
+ "Legal Entity" shall mean the union of the acting entity and all
16
+ other entities that control, are controlled by, or are under common
17
+ control with that entity. For the purposes of this definition,
18
+ "control" means (i) the power, direct or indirect, to cause the
19
+ direction or management of such entity, whether by contract or
20
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
21
+ outstanding shares, or (iii) beneficial ownership of such entity.
22
+
23
+ "You" (or "Your") shall mean an individual or Legal Entity
24
+ exercising permissions granted by this License.
25
+
26
+ "Source" form shall mean the preferred form for making modifications,
27
+ including but not limited to software source code, documentation
28
+ source, and configuration files.
29
+
30
+ "Object" form shall mean any form resulting from mechanical
31
+ transformation or translation of a Source form, including but
32
+ not limited to compiled object code, generated documentation,
33
+ and conversions to other media types.
34
+
35
+ "Work" shall mean the work of authorship, whether in Source or
36
+ Object form, made available under the License, as indicated by a
37
+ copyright notice that is included in or attached to the work
38
+ (an example is provided in the Appendix below).
39
+
40
+ "Derivative Works" shall mean any work, whether in Source or Object
41
+ form, that is based on (or derived from) the Work and for which the
42
+ editorial revisions, annotations, elaborations, or other modifications
43
+ represent, as a whole, an original work of authorship. For the purposes
44
+ of this License, Derivative Works shall not include works that remain
45
+ separable from, or merely link (or bind by name) to the interfaces of,
46
+ the Work and Derivative Works thereof.
47
+
48
+ "Contribution" shall mean any work of authorship, including
49
+ the original version of the Work and any modifications or additions
50
+ to that Work or Derivative Works thereof, that is intentionally
51
+ submitted to Licensor for inclusion in the Work by the copyright owner
52
+ or by an individual or Legal Entity authorized to submit on behalf of
53
+ the copyright owner. For the purposes of this definition, "submitted"
54
+ means any form of electronic, verbal, or written communication sent
55
+ to the Licensor or its representatives, including but not limited to
56
+ communication on electronic mailing lists, source code control systems,
57
+ and issue tracking systems that are managed by, or on behalf of, the
58
+ Licensor for the purpose of discussing and improving the Work, but
59
+ excluding communication that is conspicuously marked or otherwise
60
+ designated in writing by the copyright owner as "Not a Contribution."
61
+
62
+ "Contributor" shall mean Licensor and any individual or Legal Entity
63
+ on behalf of whom a Contribution has been received by Licensor and
64
+ subsequently incorporated within the Work.
65
+
66
+ 2. Grant of Copyright License. Subject to the terms and conditions of
67
+ this License, each Contributor hereby grants to You a perpetual,
68
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
69
+ copyright license to reproduce, prepare Derivative Works of,
70
+ publicly display, publicly perform, sublicense, and distribute the
71
+ Work and such Derivative Works in Source or Object form.
72
+
73
+ 3. Grant of Patent License. Subject to the terms and conditions of
74
+ this License, each Contributor hereby grants to You a perpetual,
75
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
76
+ (except as stated in this section) patent license to make, have made,
77
+ use, offer to sell, sell, import, and otherwise transfer the Work,
78
+ where such license applies only to those patent claims licensable
79
+ by such Contributor that are necessarily infringed by their
80
+ Contribution(s) alone or by combination of their Contribution(s)
81
+ with the Work to which such Contribution(s) was submitted. If You
82
+ institute patent litigation against any entity (including a
83
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
84
+ or a Contribution incorporated within the Work constitutes direct
85
+ or contributory patent infringement, then any patent licenses
86
+ granted to You under this License for that Work shall terminate
87
+ as of the date such litigation is filed.
88
+
89
+ 4. Redistribution. You may reproduce and distribute copies of the
90
+ Work or Derivative Works thereof in any medium, with or without
91
+ modifications, and in Source or Object form, provided that You
92
+ meet the following conditions:
93
+
94
+ (a) You must give any other recipients of the Work or
95
+ Derivative Works a copy of this License; and
96
+
97
+ (b) You must cause any modified files to carry prominent notices
98
+ stating that You changed the files; and
99
+
100
+ (c) You must retain, in the Source form of any Derivative Works
101
+ that You distribute, all copyright, patent, trademark, and
102
+ attribution notices from the Source form of the Work,
103
+ excluding those notices that do not pertain to any part of
104
+ the Derivative Works; and
105
+
106
+ (d) If the Work includes a "NOTICE" text file as part of its
107
+ distribution, then any Derivative Works that You distribute must
108
+ include a readable copy of the attribution notices contained
109
+ within such NOTICE file, excluding those notices that do not
110
+ pertain to any part of the Derivative Works, in at least one
111
+ of the following places: within a NOTICE text file distributed
112
+ as part of the Derivative Works; within the Source form or
113
+ documentation, if provided along with the Derivative Works; or,
114
+ within a display generated by the Derivative Works, if and
115
+ wherever such third-party notices normally appear. The contents
116
+ of the NOTICE file are for informational purposes only and
117
+ do not modify the License. You may add Your own attribution
118
+ notices within Derivative Works that You distribute, alongside
119
+ or as an addendum to the NOTICE text from the Work, provided
120
+ that such additional attribution notices cannot be construed
121
+ as modifying the License.
122
+
123
+ You may add Your own copyright statement to Your modifications and
124
+ may provide additional or different license terms and conditions
125
+ for use, reproduction, or distribution of Your modifications, or
126
+ for any such Derivative Works as a whole, provided Your use,
127
+ reproduction, and distribution of the Work otherwise complies with
128
+ the conditions stated in this License.
129
+
130
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
131
+ any Contribution intentionally submitted for inclusion in the Work
132
+ by You to the Licensor shall be under the terms and conditions of
133
+ this License, without any additional terms or conditions.
134
+ Notwithstanding the above, nothing herein shall supersede or modify
135
+ the terms of any separate license agreement you may have executed
136
+ with Licensor regarding such Contributions.
137
+
138
+ 6. Trademarks. This License does not grant permission to use the trade
139
+ names, trademarks, service marks, or product names of the Licensor,
140
+ except as required for reasonable and customary use in describing the
141
+ origin of the Work and reproducing the content of the NOTICE file.
142
+
143
+ 7. Disclaimer of Warranty. Unless required by applicable law or
144
+ agreed to in writing, Licensor provides the Work (and each
145
+ Contributor provides its Contributions) on an "AS IS" BASIS,
146
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
147
+ implied, including, without limitation, any warranties or conditions
148
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
149
+ PARTICULAR PURPOSE. You are solely responsible for determining the
150
+ appropriateness of using or redistributing the Work and assume any
151
+ risks associated with Your exercise of permissions under this License.
152
+
153
+ 8. Limitation of Liability. In no event and under no legal theory,
154
+ whether in tort (including negligence), contract, or otherwise,
155
+ unless required by applicable law (such as deliberate and grossly
156
+ negligent acts) or agreed to in writing, shall any Contributor be
157
+ liable to You for damages, including any direct, indirect, special,
158
+ incidental, or consequential damages of any character arising as a
159
+ result of this License or out of the use or inability to use the
160
+ Work (including but not limited to damages for loss of goodwill,
161
+ work stoppage, computer failure or malfunction, or any and all
162
+ other commercial damages or losses), even if such Contributor
163
+ has been advised of the possibility of such damages.
164
+
165
+ 9. Accepting Warranty or Additional Liability. While redistributing
166
+ the Work or Derivative Works thereof, You may choose to offer,
167
+ and charge a fee for, acceptance of support, warranty, indemnity,
168
+ or other liability obligations and/or rights consistent with this
169
+ License. However, in accepting such obligations, You may act only
170
+ on Your own behalf and on Your sole responsibility, not on behalf
171
+ of any other Contributor, and only if You agree to indemnify,
172
+ defend, and hold each Contributor harmless for any liability
173
+ incurred by, or claims asserted against, such Contributor by reason
174
+ of your accepting any such warranty or additional liability.
175
+
176
+ END OF TERMS AND CONDITIONS
177
+
178
+ APPENDIX: How to apply the Apache License to your work.
179
+
180
+ To apply the Apache License to your work, attach the following
181
+ boilerplate notice, with the fields enclosed by brackets "[]"
182
+ replaced with your own identifying information. (Don't include
183
+ the brackets!) The text should be enclosed in the appropriate
184
+ comment syntax for the file format. We also recommend that a
185
+ file or class name and description of purpose be included on the
186
+ same "printed page" as the copyright notice for easier
187
+ identification within third-party archives.
188
+
189
+ Copyright [yyyy] [name of copyright owner]
190
+
191
+ Licensed under the Apache License, Version 2.0 (the "License");
192
+ you may not use this file except in compliance with the License.
193
+ You may obtain a copy of the License at
194
+
195
+ http://www.apache.org/licenses/LICENSE-2.0
196
+
197
+ Unless required by applicable law or agreed to in writing, software
198
+ distributed under the License is distributed on an "AS IS" BASIS,
199
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
200
+ See the License for the specific language governing permissions and
201
+ limitations under the License.
README.md ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ license: apache-2.0
3
+ library_name: mlx
4
+ pipeline_tag: image-segmentation
5
+ tags:
6
+ - apple-silicon
7
+ - medical-imaging
8
+ - segmentation
9
+ - nnunet
10
+ - safetensors
11
+ - research
12
+ ---
13
+
14
+ # TotalSegmentator v2 CT for MLX
15
+
16
+ Native MLX safetensors for TotalSegmentator v2 CT inference on Apple Silicon. The five 1.5 mm standard models are in `291`–`295`, the 3 mm fast model in `297`, the 6 mm coarse model in `298`, and the body crop model in `300`. Each folder includes nnU-Net plans and model metadata.
17
+
18
+ The weights were converted from the [official TotalSegmentator v2.0.0 weight archives](https://github.com/wasserth/TotalSegmentator/releases/tag/v2.0.0-weights) for use with [totalsegmentator-mlx](https://github.com/MedMLX/totalsegmentator-mlx). Conversion changes tensor names and layouts for MLX; the models were not retrained.
19
+
20
+ ```bash
21
+ uv pip install totalsegmentator-mlx huggingface-hub
22
+ hf download MedMLX/totalsegmentator-mlx --local-dir models
23
+ totalsegmentator-mlx predict -i ct.nii.gz -o mask.nii.gz --model-dir models
24
+ ```
25
+
26
+ The `total` and `body` tasks are distributed by the authors under Apache-2.0. See the [upstream repository](https://github.com/wasserth/TotalSegmentator) and the included license for terms and attribution. Please cite TotalSegmentator and nnU-Net as described by the upstream authors. For research and education; outputs require human review.