Update README.md
Browse files
README.md
CHANGED
|
@@ -9,24 +9,48 @@ The model was trained on a large-scale multi-center CT dataset with expert-annot
|
|
| 9 |
```bash
|
| 10 |
"labels": {
|
| 11 |
"background": 0,
|
| 12 |
-
"
|
| 13 |
-
"
|
| 14 |
-
"
|
| 15 |
-
"
|
| 16 |
-
"
|
| 17 |
-
"
|
| 18 |
-
"
|
| 19 |
-
"
|
| 20 |
-
"
|
| 21 |
-
"
|
| 22 |
-
"
|
| 23 |
-
"
|
| 24 |
-
"
|
| 25 |
-
"
|
| 26 |
-
"
|
| 27 |
-
"
|
| 28 |
-
"
|
| 29 |
-
"
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 30 |
}
|
| 31 |
```
|
| 32 |
|
|
@@ -56,7 +80,7 @@ nnUNet_eval/
|
|
| 56 |
|
| 57 |
```bash
|
| 58 |
nnUNet_results/
|
| 59 |
-
└──
|
| 60 |
```
|
| 61 |
|
| 62 |
#### 2.3 Run inference
|
|
@@ -68,7 +92,7 @@ export nnUNet_predictions="./nnUNet_predictions"
|
|
| 68 |
export nnUNet_eval="./nnUNet_eval"
|
| 69 |
|
| 70 |
GPU_ID=0
|
| 71 |
-
DATASET=
|
| 72 |
|
| 73 |
TRAINER=nnUNetTrainer
|
| 74 |
|
|
|
|
| 9 |
```bash
|
| 10 |
"labels": {
|
| 11 |
"background": 0,
|
| 12 |
+
"aorta": 1,
|
| 13 |
+
"gall_bladder": 2,
|
| 14 |
+
"kidney_left": 3,
|
| 15 |
+
"kidney_right": 4,
|
| 16 |
+
"liver": 5,
|
| 17 |
+
"pancreas_body": 6,
|
| 18 |
+
"pancreas_head": 7,
|
| 19 |
+
"pancreas_tail": 8,
|
| 20 |
+
"postcava": 9,
|
| 21 |
+
"spleen": 10,
|
| 22 |
+
"stomach": 11,
|
| 23 |
+
"adrenal_gland_left": 12,
|
| 24 |
+
"adrenal_gland_right": 13,
|
| 25 |
+
"bladder": 14,
|
| 26 |
+
"celiac_trunk": 15,
|
| 27 |
+
"colon": 16,
|
| 28 |
+
"duodenum": 17,
|
| 29 |
+
"esophagus": 18,
|
| 30 |
+
"prostate": 19,
|
| 31 |
+
"rectum": 20,
|
| 32 |
+
"lung_left": 21,
|
| 33 |
+
"lung_right": 22,
|
| 34 |
+
"vertebrae_L5": 23,
|
| 35 |
+
"vertebrae_L4": 24,
|
| 36 |
+
"vertebrae_L3": 25,
|
| 37 |
+
"vertebrae_L2": 26,
|
| 38 |
+
"vertebrae_L1": 27,
|
| 39 |
+
"vertebrae_T12": 28,
|
| 40 |
+
"vertebrae_T11": 29,
|
| 41 |
+
"vertebrae_T10": 30,
|
| 42 |
+
"vertebrae_T9": 31,
|
| 43 |
+
"vertebrae_T8": 32,
|
| 44 |
+
"trachea": 33,
|
| 45 |
+
"heart": 34,
|
| 46 |
+
"hip_left": 35,
|
| 47 |
+
"hip_right": 36,
|
| 48 |
+
"sacrum": 37,
|
| 49 |
+
"uterus": 38,
|
| 50 |
+
"liver_lesion": 39,
|
| 51 |
+
"pancreatic_lesion": 40,
|
| 52 |
+
"kidney_lesion": 41,
|
| 53 |
+
"colon_lesion": 42
|
| 54 |
}
|
| 55 |
```
|
| 56 |
|
|
|
|
| 80 |
|
| 81 |
```bash
|
| 82 |
nnUNet_results/
|
| 83 |
+
└── Dataset1356/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/
|
| 84 |
```
|
| 85 |
|
| 86 |
#### 2.3 Run inference
|
|
|
|
| 92 |
export nnUNet_eval="./nnUNet_eval"
|
| 93 |
|
| 94 |
GPU_ID=0
|
| 95 |
+
DATASET=1356
|
| 96 |
|
| 97 |
TRAINER=nnUNetTrainer
|
| 98 |
|