Update model card, app.json (patch size + VRAM plan) and inference configs
Browse files- README.md +57 -3
- total-3mm/app.json +527 -143
- total/Prediction.yml +1 -1
- total/app.json +531 -143
- total_mr-3mm/app.json +260 -77
- total_mr/app.json +261 -77
README.md
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license: apache-2.0
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---
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license: apache-2.0
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library_name: konfai
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pipeline_tag: image-segmentation
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tags:
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- medical-imaging
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- segmentation
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- totalsegmentator
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- ct
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- mri
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- konfai
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---
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# TotalSegmentator-KonfAI
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KonfAI-accelerated adaptation of [**TotalSegmentator**](https://github.com/wasserth/TotalSegmentator) —
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whole-body multi-organ **CT / MRI segmentation**, built with [**KonfAI**](https://github.com/vboussot/KonfAI).
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## 🧩 Models
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| Task | Modality | Labels | Ensemble | Notes |
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|:--|:--|:--:|:--:|:--|
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| `total` | CT | 117 | 5 | full accuracy |
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| `total-3mm` | CT | 117 | 1 | fast (3 mm) |
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| `total_mr` | MRI | 50 | 2 | |
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| `total_mr-3mm` | MRI | 50 | 1 | fast (3 mm) |
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3D residual UNet · patch `[96, 128, 160]` · resampled to 1.5 mm.
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## 🚀 Usage
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```bash
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pip install totalsegmentator-konfai
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totalsegmentator-konfai segment total -i input_ct.nii.gz -o output/
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```
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- **Generic runner:** `konfai-apps infer VBoussot/TotalSegmentator-KonfAI:total -i input_ct.nii.gz -o output/`
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- **Interactive:** [**SlicerKonfAI**](https://github.com/vboussot/SlicerKonfAI) — the ⚙ *Advanced* dialog overrides patch size and batch size.
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## ⚡ Performance & VRAM
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Benchmarked on an **NVIDIA RTX PRO 5000 (24 GB)**, half precision (autocast), full 5-model ensemble. The batch size is **auto-selected from your free GPU VRAM**.
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| Free VRAM | Batch (auto) | Peak VRAM |
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|:--|:--|:--|
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| 8 GB | 4 | ~8 GB |
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| 16 GB | 8 | ~15 GB |
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| 24 GB | 12 | ~23 GB |
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Single-model peak: batch 4 → 5.6 GB · 8 → 10.6 GB · 12 → 15.6 GB (the 5-model ensemble adds ~15 %).
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≈ **110 s / case** for the full ensemble (scales with case size). Override with `--patch-size` / `--batch-size`.
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## 🔗 Links
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- 🧠 **Original TotalSegmentator:** [github.com/wasserth/TotalSegmentator](https://github.com/wasserth/TotalSegmentator)
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- 🧠 **KonfAI:** [github.com/vboussot/KonfAI](https://github.com/vboussot/KonfAI)
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- 📦 **PyPI:** [totalsegmentator-konfai](https://pypi.org/project/totalsegmentator-konfai/)
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total-3mm/app.json
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{
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"display_name": "Segmentation: TotalSegmentator 3mm",
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"short_description": "<b>Description:</b><br>Lightweight KonfAI adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator</a> trained at <b>3 mm resolution</b>, reducing GPU/RAM requirements while segmenting <b>118 anatomical structures</b> in whole-body CT.<br><br><b>How to cite:</b><br><cite>J. Wasserthal et al., <i>TotalSegmentator: Robust Segmentation of 104 Anatomical Structures in CT Images</i>, Radiology: AI, 2023.</cite>",
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"description": "<b>Description:</b><br>KonfAI-optimized version of the original nnU-Net-based TotalSegmentator 3 mm model.<br><br><b>Capabilities:</b><br>
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"tta": 0,
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"mc_dropout": 0,
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"models": [
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"inputs": {
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},
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"outputs": {
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},
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"inputs_evaluations": {
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"terminology": {
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}
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-
}
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{
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"display_name": "Segmentation: TotalSegmentator 3mm",
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"short_description": "<b>Description:</b><br>Lightweight KonfAI adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator</a> trained at <b>3 mm resolution</b>, reducing GPU/RAM requirements while segmenting <b>118 anatomical structures</b> in whole-body CT.<br><br><b>How to cite:</b><br><cite>J. Wasserthal et al., <i>TotalSegmentator: Robust Segmentation of 104 Anatomical Structures in CT Images</i>, Radiology: AI, 2023.</cite>",
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"description": "<b>Description:</b><br>KonfAI-optimized version of the original nnU-Net-based TotalSegmentator 3 mm model.<br><br><b>Capabilities:</b><br>\u2022 Whole-body CT segmentation of <b>118 structures</b> (organs, bones, muscles, vessels)<br>\u2022 Reduced computational footprint for lower memory and faster throughput<br>\u2022 <b>3 mm isotropic</b> inference for easier deployment on large datasets<br><br><b>Training data:</b><br>Trained on <b>1204 clinically-derived CT scans</b> with strong diversity in contrast phases, scanner types and pathologies, with expert-reviewed manual annotations<br><br><b>How to cite:</b><br><cite>J. Wasserthal et al., <i>TotalSegmentator: Robust Segmentation of 104 Anatomical Structures in CT Images</i>, Radiology: AI, 2023.</cite>",
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"tta": 0,
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"mc_dropout": 0,
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"models": [
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"M297.pt"
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],
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"inputs": {
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"Volume": {
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"display_name": "Input Volume",
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"volume_type": "VOLUME",
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"required": true
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}
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},
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"outputs": {
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| 18 |
+
"Segmentation": {
|
| 19 |
+
"display_name": "Segmentation",
|
| 20 |
+
"volume_type": "SEGMENTATION",
|
| 21 |
+
"required": true
|
| 22 |
+
}
|
| 23 |
},
|
| 24 |
"inputs_evaluations": {
|
| 25 |
+
"Image": {
|
| 26 |
+
"Evaluation.yml": {
|
| 27 |
+
"Segmentation": {
|
| 28 |
+
"display_name": "Output Segmentation",
|
| 29 |
+
"volume_type": "VOLUME",
|
| 30 |
+
"required": true
|
| 31 |
+
},
|
| 32 |
+
"GT_Segmentation": {
|
| 33 |
+
"display_name": "GT Segmentation",
|
| 34 |
+
"volume_type": "VOLUME",
|
| 35 |
+
"required": true
|
| 36 |
+
}
|
| 37 |
+
}
|
| 38 |
}
|
|
|
|
| 39 |
},
|
| 40 |
"terminology": {
|
| 41 |
+
"1": {
|
| 42 |
+
"name": "spleen",
|
| 43 |
+
"color": "#4B79EA"
|
| 44 |
+
},
|
| 45 |
+
"2": {
|
| 46 |
+
"name": "kidney_right",
|
| 47 |
+
"color": "#A8EA4B"
|
| 48 |
+
},
|
| 49 |
+
"3": {
|
| 50 |
+
"name": "kidney_left",
|
| 51 |
+
"color": "#EA4BD7"
|
| 52 |
+
},
|
| 53 |
+
"4": {
|
| 54 |
+
"name": "gallbladder",
|
| 55 |
+
"color": "#4BEAC0"
|
| 56 |
+
},
|
| 57 |
+
"5": {
|
| 58 |
+
"name": "liver",
|
| 59 |
+
"color": "#EA924B"
|
| 60 |
+
},
|
| 61 |
+
"6": {
|
| 62 |
+
"name": "stomach",
|
| 63 |
+
"color": "#634BEA"
|
| 64 |
+
},
|
| 65 |
+
"7": {
|
| 66 |
+
"name": "pancreas",
|
| 67 |
+
"color": "#4BEA53"
|
| 68 |
+
},
|
| 69 |
+
"8": {
|
| 70 |
+
"name": "adrenal_gland_right",
|
| 71 |
+
"color": "#EA4B82"
|
| 72 |
+
},
|
| 73 |
+
"9": {
|
| 74 |
+
"name": "adrenal_gland_left",
|
| 75 |
+
"color": "#B0EA4B"
|
| 76 |
+
},
|
| 77 |
+
"10": {
|
| 78 |
+
"name": "lung_upper_lobe_left",
|
| 79 |
+
"color": "#EA4BE0"
|
| 80 |
+
},
|
| 81 |
+
"11": {
|
| 82 |
+
"name": "lung_lower_lobe_left",
|
| 83 |
+
"color": "#4BEAB9"
|
| 84 |
+
},
|
| 85 |
+
"12": {
|
| 86 |
+
"name": "lung_upper_lobe_right",
|
| 87 |
+
"color": "#EA8B4B"
|
| 88 |
+
},
|
| 89 |
+
"13": {
|
| 90 |
+
"name": "lung_middle_lobe_right",
|
| 91 |
+
"color": "#5C4BEA"
|
| 92 |
+
},
|
| 93 |
+
"14": {
|
| 94 |
+
"name": "lung_lower_lobe_right",
|
| 95 |
+
"color": "#4BEA5A"
|
| 96 |
+
},
|
| 97 |
+
"15": {
|
| 98 |
+
"name": "esophagus",
|
| 99 |
+
"color": "#EA4B89"
|
| 100 |
+
},
|
| 101 |
+
"16": {
|
| 102 |
+
"name": "trachea",
|
| 103 |
+
"color": "#B7EA4B"
|
| 104 |
+
},
|
| 105 |
+
"17": {
|
| 106 |
+
"name": "thyroid_gland",
|
| 107 |
+
"color": "#EA4BE8"
|
| 108 |
+
},
|
| 109 |
+
"18": {
|
| 110 |
+
"name": "small_bowel",
|
| 111 |
+
"color": "#4BEAB2"
|
| 112 |
+
},
|
| 113 |
+
"19": {
|
| 114 |
+
"name": "duodenum",
|
| 115 |
+
"color": "#EA844B"
|
| 116 |
+
},
|
| 117 |
+
"20": {
|
| 118 |
+
"name": "colon",
|
| 119 |
+
"color": "#554BEA"
|
| 120 |
+
},
|
| 121 |
+
"21": {
|
| 122 |
+
"name": "urinary_bladder",
|
| 123 |
+
"color": "#4BEA61"
|
| 124 |
+
},
|
| 125 |
+
"22": {
|
| 126 |
+
"name": "prostate",
|
| 127 |
+
"color": "#EA4B90"
|
| 128 |
+
},
|
| 129 |
+
"23": {
|
| 130 |
+
"name": "kidney_cyst_left",
|
| 131 |
+
"color": "#BEEA4B"
|
| 132 |
+
},
|
| 133 |
+
"24": {
|
| 134 |
+
"name": "kidney_cyst_right",
|
| 135 |
+
"color": "#E94BEA"
|
| 136 |
+
},
|
| 137 |
+
"25": {
|
| 138 |
+
"name": "sacrum",
|
| 139 |
+
"color": "#4BEAAB"
|
| 140 |
+
},
|
| 141 |
+
"26": {
|
| 142 |
+
"name": "vertebrae_S1",
|
| 143 |
+
"color": "#EA7D4B"
|
| 144 |
+
},
|
| 145 |
+
"27": {
|
| 146 |
+
"name": "vertebrae_L5",
|
| 147 |
+
"color": "#4E4BEA"
|
| 148 |
+
},
|
| 149 |
+
"28": {
|
| 150 |
+
"name": "vertebrae_L4",
|
| 151 |
+
"color": "#4BEA68"
|
| 152 |
+
},
|
| 153 |
+
"29": {
|
| 154 |
+
"name": "vertebrae_L3",
|
| 155 |
+
"color": "#EA4B97"
|
| 156 |
+
},
|
| 157 |
+
"30": {
|
| 158 |
+
"name": "vertebrae_L2",
|
| 159 |
+
"color": "#C5EA4B"
|
| 160 |
+
},
|
| 161 |
+
"31": {
|
| 162 |
+
"name": "vertebrae_L1",
|
| 163 |
+
"color": "#E24BEA"
|
| 164 |
+
},
|
| 165 |
+
"32": {
|
| 166 |
+
"name": "vertebrae_T12",
|
| 167 |
+
"color": "#4BEAA4"
|
| 168 |
+
},
|
| 169 |
+
"33": {
|
| 170 |
+
"name": "vertebrae_T11",
|
| 171 |
+
"color": "#EA764B"
|
| 172 |
+
},
|
| 173 |
+
"34": {
|
| 174 |
+
"name": "vertebrae_T10",
|
| 175 |
+
"color": "#4B55EA"
|
| 176 |
+
},
|
| 177 |
+
"35": {
|
| 178 |
+
"name": "vertebrae_T9",
|
| 179 |
+
"color": "#4BEA6F"
|
| 180 |
+
},
|
| 181 |
+
"36": {
|
| 182 |
+
"name": "vertebrae_T8",
|
| 183 |
+
"color": "#EA4B9F"
|
| 184 |
+
},
|
| 185 |
+
"37": {
|
| 186 |
+
"name": "vertebrae_T7",
|
| 187 |
+
"color": "#CCEA4B"
|
| 188 |
+
},
|
| 189 |
+
"38": {
|
| 190 |
+
"name": "vertebrae_T6",
|
| 191 |
+
"color": "#DB4BEA"
|
| 192 |
+
},
|
| 193 |
+
"39": {
|
| 194 |
+
"name": "vertebrae_T5",
|
| 195 |
+
"color": "#4BEA9D"
|
| 196 |
+
},
|
| 197 |
+
"40": {
|
| 198 |
+
"name": "vertebrae_T4",
|
| 199 |
+
"color": "#EA6F4B"
|
| 200 |
+
},
|
| 201 |
+
"41": {
|
| 202 |
+
"name": "vertebrae_T3",
|
| 203 |
+
"color": "#4B5CEA"
|
| 204 |
+
},
|
| 205 |
+
"42": {
|
| 206 |
+
"name": "vertebrae_T2",
|
| 207 |
+
"color": "#4BEA76"
|
| 208 |
+
},
|
| 209 |
+
"43": {
|
| 210 |
+
"name": "vertebrae_T1",
|
| 211 |
+
"color": "#EA4BA6"
|
| 212 |
+
},
|
| 213 |
+
"44": {
|
| 214 |
+
"name": "vertebrae_C7",
|
| 215 |
+
"color": "#D3EA4B"
|
| 216 |
+
},
|
| 217 |
+
"45": {
|
| 218 |
+
"name": "vertebrae_C6",
|
| 219 |
+
"color": "#D44BEA"
|
| 220 |
+
},
|
| 221 |
+
"46": {
|
| 222 |
+
"name": "vertebrae_C5",
|
| 223 |
+
"color": "#4BEA96"
|
| 224 |
+
},
|
| 225 |
+
"47": {
|
| 226 |
+
"name": "vertebrae_C4",
|
| 227 |
+
"color": "#EA684B"
|
| 228 |
+
},
|
| 229 |
+
"48": {
|
| 230 |
+
"name": "vertebrae_C3",
|
| 231 |
+
"color": "#4B63EA"
|
| 232 |
+
},
|
| 233 |
+
"49": {
|
| 234 |
+
"name": "vertebrae_C2",
|
| 235 |
+
"color": "#4BEA7D"
|
| 236 |
+
},
|
| 237 |
+
"50": {
|
| 238 |
+
"name": "vertebrae_C1",
|
| 239 |
+
"color": "#EA4BAD"
|
| 240 |
+
},
|
| 241 |
+
"51": {
|
| 242 |
+
"name": "heart",
|
| 243 |
+
"color": "#DAEA4B"
|
| 244 |
+
},
|
| 245 |
+
"52": {
|
| 246 |
+
"name": "aorta",
|
| 247 |
+
"color": "#CD4BEA"
|
| 248 |
+
},
|
| 249 |
+
"53": {
|
| 250 |
+
"name": "pulmonary_vein",
|
| 251 |
+
"color": "#4BEA8F"
|
| 252 |
+
},
|
| 253 |
+
"54": {
|
| 254 |
+
"name": "brachiocephalic_trunk",
|
| 255 |
+
"color": "#EA614B"
|
| 256 |
+
},
|
| 257 |
+
"55": {
|
| 258 |
+
"name": "subclavian_artery_right",
|
| 259 |
+
"color": "#4B6AEA"
|
| 260 |
+
},
|
| 261 |
+
"56": {
|
| 262 |
+
"name": "subclavian_artery_left",
|
| 263 |
+
"color": "#4BEA84"
|
| 264 |
+
},
|
| 265 |
+
"57": {
|
| 266 |
+
"name": "common_carotid_artery_right",
|
| 267 |
+
"color": "#EA4BB4"
|
| 268 |
+
},
|
| 269 |
+
"58": {
|
| 270 |
+
"name": "common_carotid_artery_left",
|
| 271 |
+
"color": "#E1EA4B"
|
| 272 |
+
},
|
| 273 |
+
"59": {
|
| 274 |
+
"name": "brachiocephalic_vein_left",
|
| 275 |
+
"color": "#C64BEA"
|
| 276 |
+
},
|
| 277 |
+
"60": {
|
| 278 |
+
"name": "brachiocephalic_vein_right",
|
| 279 |
+
"color": "#4BEA88"
|
| 280 |
+
},
|
| 281 |
+
"61": {
|
| 282 |
+
"name": "atrial_appendage_left",
|
| 283 |
+
"color": "#EA5B4B"
|
| 284 |
+
},
|
| 285 |
+
"62": {
|
| 286 |
+
"name": "superior_vena_cava",
|
| 287 |
+
"color": "#4B71EA"
|
| 288 |
+
},
|
| 289 |
+
"63": {
|
| 290 |
+
"name": "inferior_vena_cava",
|
| 291 |
+
"color": "#4BEA8B"
|
| 292 |
+
},
|
| 293 |
+
"64": {
|
| 294 |
+
"name": "portal_vein_and_splenic_vein",
|
| 295 |
+
"color": "#EA4BBA"
|
| 296 |
+
},
|
| 297 |
+
"65": {
|
| 298 |
+
"name": "iliac_artery_left",
|
| 299 |
+
"color": "#E8EA4B"
|
| 300 |
+
},
|
| 301 |
+
"66": {
|
| 302 |
+
"name": "iliac_artery_right",
|
| 303 |
+
"color": "#BF4BEA"
|
| 304 |
+
},
|
| 305 |
+
"67": {
|
| 306 |
+
"name": "iliac_vena_left",
|
| 307 |
+
"color": "#4BEA82"
|
| 308 |
+
},
|
| 309 |
+
"68": {
|
| 310 |
+
"name": "iliac_vena_right",
|
| 311 |
+
"color": "#EA544B"
|
| 312 |
+
},
|
| 313 |
+
"69": {
|
| 314 |
+
"name": "humerus_left",
|
| 315 |
+
"color": "#4B78EA"
|
| 316 |
+
},
|
| 317 |
+
"70": {
|
| 318 |
+
"name": "humerus_right",
|
| 319 |
+
"color": "#4BEA92"
|
| 320 |
+
},
|
| 321 |
+
"71": {
|
| 322 |
+
"name": "scapula_left",
|
| 323 |
+
"color": "#EA4BC1"
|
| 324 |
+
},
|
| 325 |
+
"72": {
|
| 326 |
+
"name": "scapula_right",
|
| 327 |
+
"color": "#EAEA4B"
|
| 328 |
+
},
|
| 329 |
+
"73": {
|
| 330 |
+
"name": "clavicula_left",
|
| 331 |
+
"color": "#B84BEA"
|
| 332 |
+
},
|
| 333 |
+
"74": {
|
| 334 |
+
"name": "clavicula_right",
|
| 335 |
+
"color": "#4BEA79"
|
| 336 |
+
},
|
| 337 |
+
"75": {
|
| 338 |
+
"name": "femur_left",
|
| 339 |
+
"color": "#EA4D4B"
|
| 340 |
+
},
|
| 341 |
+
"76": {
|
| 342 |
+
"name": "femur_right",
|
| 343 |
+
"color": "#4B7FEA"
|
| 344 |
+
},
|
| 345 |
+
"77": {
|
| 346 |
+
"name": "hip_left",
|
| 347 |
+
"color": "#4BEA99"
|
| 348 |
+
},
|
| 349 |
+
"78": {
|
| 350 |
+
"name": "hip_right",
|
| 351 |
+
"color": "#EA4BC8"
|
| 352 |
+
},
|
| 353 |
+
"79": {
|
| 354 |
+
"name": "spinal_cord",
|
| 355 |
+
"color": "#EAEC4B"
|
| 356 |
+
},
|
| 357 |
+
"80": {
|
| 358 |
+
"name": "gluteus_maximus_left",
|
| 359 |
+
"color": "#B14BEA"
|
| 360 |
+
},
|
| 361 |
+
"81": {
|
| 362 |
+
"name": "gluteus_maximus_right",
|
| 363 |
+
"color": "#4BEA72"
|
| 364 |
+
},
|
| 365 |
+
"82": {
|
| 366 |
+
"name": "gluteus_medius_left",
|
| 367 |
+
"color": "#EA4B54"
|
| 368 |
+
},
|
| 369 |
+
"83": {
|
| 370 |
+
"name": "gluteus_medius_right",
|
| 371 |
+
"color": "#4B86EA"
|
| 372 |
+
},
|
| 373 |
+
"84": {
|
| 374 |
+
"name": "gluteus_minimus_left",
|
| 375 |
+
"color": "#4BEAA0"
|
| 376 |
+
},
|
| 377 |
+
"85": {
|
| 378 |
+
"name": "gluteus_minimus_right",
|
| 379 |
+
"color": "#EA4BCF"
|
| 380 |
+
},
|
| 381 |
+
"86": {
|
| 382 |
+
"name": "autochthon_left",
|
| 383 |
+
"color": "#EAF34B"
|
| 384 |
+
},
|
| 385 |
+
"87": {
|
| 386 |
+
"name": "autochthon_right",
|
| 387 |
+
"color": "#AA4BEA"
|
| 388 |
+
},
|
| 389 |
+
"88": {
|
| 390 |
+
"name": "iliopsoas_left",
|
| 391 |
+
"color": "#4BEA6B"
|
| 392 |
+
},
|
| 393 |
+
"89": {
|
| 394 |
+
"name": "iliopsoas_right",
|
| 395 |
+
"color": "#EA4B5B"
|
| 396 |
+
},
|
| 397 |
+
"90": {
|
| 398 |
+
"name": "brain",
|
| 399 |
+
"color": "#4B8DEA"
|
| 400 |
+
},
|
| 401 |
+
"91": {
|
| 402 |
+
"name": "skull",
|
| 403 |
+
"color": "#4BEAA7"
|
| 404 |
+
},
|
| 405 |
+
"92": {
|
| 406 |
+
"name": "rib_left_1",
|
| 407 |
+
"color": "#EA4BD6"
|
| 408 |
+
},
|
| 409 |
+
"93": {
|
| 410 |
+
"name": "rib_left_2",
|
| 411 |
+
"color": "#EAFC4B"
|
| 412 |
+
},
|
| 413 |
+
"94": {
|
| 414 |
+
"name": "rib_left_3",
|
| 415 |
+
"color": "#A34BEA"
|
| 416 |
+
},
|
| 417 |
+
"95": {
|
| 418 |
+
"name": "rib_left_4",
|
| 419 |
+
"color": "#4BEA64"
|
| 420 |
+
},
|
| 421 |
+
"96": {
|
| 422 |
+
"name": "rib_left_5",
|
| 423 |
+
"color": "#EA4B62"
|
| 424 |
+
},
|
| 425 |
+
"97": {
|
| 426 |
+
"name": "rib_left_6",
|
| 427 |
+
"color": "#4B94EA"
|
| 428 |
+
},
|
| 429 |
+
"98": {
|
| 430 |
+
"name": "rib_left_7",
|
| 431 |
+
"color": "#4BEAAE"
|
| 432 |
+
},
|
| 433 |
+
"99": {
|
| 434 |
+
"name": "rib_left_8",
|
| 435 |
+
"color": "#EA4BDD"
|
| 436 |
+
},
|
| 437 |
+
"100": {
|
| 438 |
+
"name": "rib_left_9",
|
| 439 |
+
"color": "#F0EA4B"
|
| 440 |
+
},
|
| 441 |
+
"101": {
|
| 442 |
+
"name": "rib_left_10",
|
| 443 |
+
"color": "#9C4BEA"
|
| 444 |
+
},
|
| 445 |
+
"102": {
|
| 446 |
+
"name": "rib_left_11",
|
| 447 |
+
"color": "#4BEA5D"
|
| 448 |
+
},
|
| 449 |
+
"103": {
|
| 450 |
+
"name": "rib_left_12",
|
| 451 |
+
"color": "#EA4B69"
|
| 452 |
+
},
|
| 453 |
+
"104": {
|
| 454 |
+
"name": "rib_right_1",
|
| 455 |
+
"color": "#4B9BEA"
|
| 456 |
+
},
|
| 457 |
+
"105": {
|
| 458 |
+
"name": "rib_right_2",
|
| 459 |
+
"color": "#4BEAB5"
|
| 460 |
+
},
|
| 461 |
+
"106": {
|
| 462 |
+
"name": "rib_right_3",
|
| 463 |
+
"color": "#EA4BE4"
|
| 464 |
+
},
|
| 465 |
+
"107": {
|
| 466 |
+
"name": "rib_right_4",
|
| 467 |
+
"color": "#E9EA4B"
|
| 468 |
+
},
|
| 469 |
+
"108": {
|
| 470 |
+
"name": "rib_right_5",
|
| 471 |
+
"color": "#954BEA"
|
| 472 |
+
},
|
| 473 |
+
"109": {
|
| 474 |
+
"name": "rib_right_6",
|
| 475 |
+
"color": "#4BEA56"
|
| 476 |
+
},
|
| 477 |
+
"110": {
|
| 478 |
+
"name": "rib_right_7",
|
| 479 |
+
"color": "#EA4B70"
|
| 480 |
+
},
|
| 481 |
+
"111": {
|
| 482 |
+
"name": "rib_right_8",
|
| 483 |
+
"color": "#4BA2EA"
|
| 484 |
+
},
|
| 485 |
+
"112": {
|
| 486 |
+
"name": "rib_right_9",
|
| 487 |
+
"color": "#4BEABC"
|
| 488 |
+
},
|
| 489 |
+
"113": {
|
| 490 |
+
"name": "rib_right_10",
|
| 491 |
+
"color": "#EA4BEB"
|
| 492 |
+
},
|
| 493 |
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"114": {
|
| 494 |
+
"name": "rib_right_11",
|
| 495 |
+
"color": "#E2EA4B"
|
| 496 |
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},
|
| 497 |
+
"115": {
|
| 498 |
+
"name": "rib_right_12",
|
| 499 |
+
"color": "#8E4BEA"
|
| 500 |
+
},
|
| 501 |
+
"116": {
|
| 502 |
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"name": "sternum",
|
| 503 |
+
"color": "#4BEA4F"
|
| 504 |
+
},
|
| 505 |
+
"117": {
|
| 506 |
+
"name": "costal_cartilages",
|
| 507 |
+
"color": "#61EA4B"
|
| 508 |
+
}
|
| 509 |
+
},
|
| 510 |
+
"patch_size": [
|
| 511 |
+
96,
|
| 512 |
+
128,
|
| 513 |
+
160
|
| 514 |
+
],
|
| 515 |
+
"vram_plan": {
|
| 516 |
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"8": {
|
| 517 |
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"patch_size": [
|
| 518 |
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96,
|
| 519 |
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128,
|
| 520 |
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160
|
| 521 |
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],
|
| 522 |
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"batch_size": 4
|
| 523 |
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},
|
| 524 |
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"16": {
|
| 525 |
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"patch_size": [
|
| 526 |
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96,
|
| 527 |
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128,
|
| 528 |
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160
|
| 529 |
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],
|
| 530 |
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"batch_size": 8
|
| 531 |
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},
|
| 532 |
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"24": {
|
| 533 |
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"patch_size": [
|
| 534 |
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96,
|
| 535 |
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128,
|
| 536 |
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160
|
| 537 |
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],
|
| 538 |
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"batch_size": 12
|
| 539 |
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}
|
| 540 |
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|
| 541 |
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}
|
total/Prediction.yml
CHANGED
|
@@ -60,7 +60,7 @@ Predictor:
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|
| 60 |
Head:Softmax:
|
| 61 |
OutputDataset:
|
| 62 |
name_class: OutSameAsGroupDataset
|
| 63 |
-
before_reduction_transforms:
|
| 64 |
Softmax:
|
| 65 |
dim: 0
|
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Argmax:
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| 60 |
Head:Softmax:
|
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OutputDataset:
|
| 62 |
name_class: OutSameAsGroupDataset
|
| 63 |
+
before_reduction_transforms:
|
| 64 |
Softmax:
|
| 65 |
dim: 0
|
| 66 |
Argmax:
|
total/app.json
CHANGED
|
@@ -1,157 +1,545 @@
|
|
| 1 |
{
|
| 2 |
"display_name": "Segmentation: Total Segmentator",
|
| 3 |
"short_description": "<b>Description:</b><br>KonfAI-accelerated adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator</a>, delivering fast whole-body CT segmentation of <b>118 anatomical structures</b> (1.5 mm resolution) with reduced inference cost compared to the original nnU-Net implementation.<br><br><b>How to cite:</b><br><cite>J. Wasserthal et al., <i>TotalSegmentator: Robust Segmentation of 104 Anatomical Structures in CT Images</i>, Radiology: AI, 2023.</cite>",
|
| 4 |
-
"description": "<b>Description:</b><br>This model is an optimized adaptation of the original <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator</a> for the <b>KonfAI</b> deep learning framework.<br><br><b>Capabilities:</b><br>
|
| 5 |
"tta": 0,
|
| 6 |
"mc_dropout": 0,
|
| 7 |
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"models": [
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| 156 |
}
|
| 157 |
-
}
|
|
|
|
| 1 |
{
|
| 2 |
"display_name": "Segmentation: Total Segmentator",
|
| 3 |
"short_description": "<b>Description:</b><br>KonfAI-accelerated adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator</a>, delivering fast whole-body CT segmentation of <b>118 anatomical structures</b> (1.5 mm resolution) with reduced inference cost compared to the original nnU-Net implementation.<br><br><b>How to cite:</b><br><cite>J. Wasserthal et al., <i>TotalSegmentator: Robust Segmentation of 104 Anatomical Structures in CT Images</i>, Radiology: AI, 2023.</cite>",
|
| 4 |
+
"description": "<b>Description:</b><br>This model is an optimized adaptation of the original <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator</a> for the <b>KonfAI</b> deep learning framework.<br><br><b>Capabilities:</b><br>\u2022 Segmentation of <b>118 anatomical classes</b> covering organs, bones, muscles, and vessels<br>\u2022 Enhanced runtime and memory efficiency vs. the original nnU-Net implementation<br>\u2022 High-resolution input: <b>1.5 mm isotropic</b><br><br><b>Training data:</b><br>Trained on a diverse dataset of <b>1204 whole-body CT examinations</b> including different scanners, acquisition settings, contrast phases, and major pathologies (27 organs, 59 bones, 10 muscles, 8 vessels), with manual expert-reviewed annotations<br><br><b>How to cite:</b><br><cite>J. Wasserthal et al., <i>TotalSegmentator: Robust Segmentation of 104 Anatomical Structures in CT Images</i>, Radiology: AI, 2023.</cite>",
|
| 5 |
"tta": 0,
|
| 6 |
"mc_dropout": 0,
|
| 7 |
+
"models": [
|
| 8 |
+
"M291.pt",
|
| 9 |
+
"M292.pt",
|
| 10 |
+
"M293.pt",
|
| 11 |
+
"M294.pt",
|
| 12 |
+
"M295.pt"
|
| 13 |
+
],
|
| 14 |
"inputs": {
|
| 15 |
+
"Volume": {
|
| 16 |
+
"display_name": "Input Volume",
|
| 17 |
+
"volume_type": "VOLUME",
|
| 18 |
+
"required": true
|
| 19 |
+
}
|
| 20 |
},
|
| 21 |
"outputs": {
|
| 22 |
+
"Segmentation": {
|
| 23 |
+
"display_name": "Segmentation",
|
| 24 |
+
"volume_type": "SEGMENTATION",
|
| 25 |
+
"required": true
|
| 26 |
+
}
|
| 27 |
},
|
| 28 |
"inputs_evaluations": {
|
| 29 |
+
"Image": {
|
| 30 |
+
"Evaluation.yml": {
|
| 31 |
+
"Segmentation": {
|
| 32 |
+
"display_name": "Output Segmentation",
|
| 33 |
+
"volume_type": "VOLUME",
|
| 34 |
+
"required": true
|
| 35 |
+
},
|
| 36 |
+
"GT_Segmentation": {
|
| 37 |
+
"display_name": "GT Segmentation",
|
| 38 |
+
"volume_type": "VOLUME",
|
| 39 |
+
"required": true
|
| 40 |
+
}
|
| 41 |
+
}
|
| 42 |
}
|
|
|
|
| 43 |
},
|
| 44 |
"terminology": {
|
| 45 |
+
"1": {
|
| 46 |
+
"name": "spleen",
|
| 47 |
+
"color": "#4B79EA"
|
| 48 |
+
},
|
| 49 |
+
"2": {
|
| 50 |
+
"name": "kidney_right",
|
| 51 |
+
"color": "#A8EA4B"
|
| 52 |
+
},
|
| 53 |
+
"3": {
|
| 54 |
+
"name": "kidney_left",
|
| 55 |
+
"color": "#EA4BD7"
|
| 56 |
+
},
|
| 57 |
+
"4": {
|
| 58 |
+
"name": "gallbladder",
|
| 59 |
+
"color": "#4BEAC0"
|
| 60 |
+
},
|
| 61 |
+
"5": {
|
| 62 |
+
"name": "liver",
|
| 63 |
+
"color": "#EA924B"
|
| 64 |
+
},
|
| 65 |
+
"6": {
|
| 66 |
+
"name": "stomach",
|
| 67 |
+
"color": "#634BEA"
|
| 68 |
+
},
|
| 69 |
+
"7": {
|
| 70 |
+
"name": "pancreas",
|
| 71 |
+
"color": "#4BEA53"
|
| 72 |
+
},
|
| 73 |
+
"8": {
|
| 74 |
+
"name": "adrenal_gland_right",
|
| 75 |
+
"color": "#EA4B82"
|
| 76 |
+
},
|
| 77 |
+
"9": {
|
| 78 |
+
"name": "adrenal_gland_left",
|
| 79 |
+
"color": "#B0EA4B"
|
| 80 |
+
},
|
| 81 |
+
"10": {
|
| 82 |
+
"name": "lung_upper_lobe_left",
|
| 83 |
+
"color": "#EA4BE0"
|
| 84 |
+
},
|
| 85 |
+
"11": {
|
| 86 |
+
"name": "lung_lower_lobe_left",
|
| 87 |
+
"color": "#4BEAB9"
|
| 88 |
+
},
|
| 89 |
+
"12": {
|
| 90 |
+
"name": "lung_upper_lobe_right",
|
| 91 |
+
"color": "#EA8B4B"
|
| 92 |
+
},
|
| 93 |
+
"13": {
|
| 94 |
+
"name": "lung_middle_lobe_right",
|
| 95 |
+
"color": "#5C4BEA"
|
| 96 |
+
},
|
| 97 |
+
"14": {
|
| 98 |
+
"name": "lung_lower_lobe_right",
|
| 99 |
+
"color": "#4BEA5A"
|
| 100 |
+
},
|
| 101 |
+
"15": {
|
| 102 |
+
"name": "esophagus",
|
| 103 |
+
"color": "#EA4B89"
|
| 104 |
+
},
|
| 105 |
+
"16": {
|
| 106 |
+
"name": "trachea",
|
| 107 |
+
"color": "#B7EA4B"
|
| 108 |
+
},
|
| 109 |
+
"17": {
|
| 110 |
+
"name": "thyroid_gland",
|
| 111 |
+
"color": "#EA4BE8"
|
| 112 |
+
},
|
| 113 |
+
"18": {
|
| 114 |
+
"name": "small_bowel",
|
| 115 |
+
"color": "#4BEAB2"
|
| 116 |
+
},
|
| 117 |
+
"19": {
|
| 118 |
+
"name": "duodenum",
|
| 119 |
+
"color": "#EA844B"
|
| 120 |
+
},
|
| 121 |
+
"20": {
|
| 122 |
+
"name": "colon",
|
| 123 |
+
"color": "#554BEA"
|
| 124 |
+
},
|
| 125 |
+
"21": {
|
| 126 |
+
"name": "urinary_bladder",
|
| 127 |
+
"color": "#4BEA61"
|
| 128 |
+
},
|
| 129 |
+
"22": {
|
| 130 |
+
"name": "prostate",
|
| 131 |
+
"color": "#EA4B90"
|
| 132 |
+
},
|
| 133 |
+
"23": {
|
| 134 |
+
"name": "kidney_cyst_left",
|
| 135 |
+
"color": "#BEEA4B"
|
| 136 |
+
},
|
| 137 |
+
"24": {
|
| 138 |
+
"name": "kidney_cyst_right",
|
| 139 |
+
"color": "#E94BEA"
|
| 140 |
+
},
|
| 141 |
+
"25": {
|
| 142 |
+
"name": "sacrum",
|
| 143 |
+
"color": "#4BEAAB"
|
| 144 |
+
},
|
| 145 |
+
"26": {
|
| 146 |
+
"name": "vertebrae_S1",
|
| 147 |
+
"color": "#EA7D4B"
|
| 148 |
+
},
|
| 149 |
+
"27": {
|
| 150 |
+
"name": "vertebrae_L5",
|
| 151 |
+
"color": "#4E4BEA"
|
| 152 |
+
},
|
| 153 |
+
"28": {
|
| 154 |
+
"name": "vertebrae_L4",
|
| 155 |
+
"color": "#4BEA68"
|
| 156 |
+
},
|
| 157 |
+
"29": {
|
| 158 |
+
"name": "vertebrae_L3",
|
| 159 |
+
"color": "#EA4B97"
|
| 160 |
+
},
|
| 161 |
+
"30": {
|
| 162 |
+
"name": "vertebrae_L2",
|
| 163 |
+
"color": "#C5EA4B"
|
| 164 |
+
},
|
| 165 |
+
"31": {
|
| 166 |
+
"name": "vertebrae_L1",
|
| 167 |
+
"color": "#E24BEA"
|
| 168 |
+
},
|
| 169 |
+
"32": {
|
| 170 |
+
"name": "vertebrae_T12",
|
| 171 |
+
"color": "#4BEAA4"
|
| 172 |
+
},
|
| 173 |
+
"33": {
|
| 174 |
+
"name": "vertebrae_T11",
|
| 175 |
+
"color": "#EA764B"
|
| 176 |
+
},
|
| 177 |
+
"34": {
|
| 178 |
+
"name": "vertebrae_T10",
|
| 179 |
+
"color": "#4B55EA"
|
| 180 |
+
},
|
| 181 |
+
"35": {
|
| 182 |
+
"name": "vertebrae_T9",
|
| 183 |
+
"color": "#4BEA6F"
|
| 184 |
+
},
|
| 185 |
+
"36": {
|
| 186 |
+
"name": "vertebrae_T8",
|
| 187 |
+
"color": "#EA4B9F"
|
| 188 |
+
},
|
| 189 |
+
"37": {
|
| 190 |
+
"name": "vertebrae_T7",
|
| 191 |
+
"color": "#CCEA4B"
|
| 192 |
+
},
|
| 193 |
+
"38": {
|
| 194 |
+
"name": "vertebrae_T6",
|
| 195 |
+
"color": "#DB4BEA"
|
| 196 |
+
},
|
| 197 |
+
"39": {
|
| 198 |
+
"name": "vertebrae_T5",
|
| 199 |
+
"color": "#4BEA9D"
|
| 200 |
+
},
|
| 201 |
+
"40": {
|
| 202 |
+
"name": "vertebrae_T4",
|
| 203 |
+
"color": "#EA6F4B"
|
| 204 |
+
},
|
| 205 |
+
"41": {
|
| 206 |
+
"name": "vertebrae_T3",
|
| 207 |
+
"color": "#4B5CEA"
|
| 208 |
+
},
|
| 209 |
+
"42": {
|
| 210 |
+
"name": "vertebrae_T2",
|
| 211 |
+
"color": "#4BEA76"
|
| 212 |
+
},
|
| 213 |
+
"43": {
|
| 214 |
+
"name": "vertebrae_T1",
|
| 215 |
+
"color": "#EA4BA6"
|
| 216 |
+
},
|
| 217 |
+
"44": {
|
| 218 |
+
"name": "vertebrae_C7",
|
| 219 |
+
"color": "#D3EA4B"
|
| 220 |
+
},
|
| 221 |
+
"45": {
|
| 222 |
+
"name": "vertebrae_C6",
|
| 223 |
+
"color": "#D44BEA"
|
| 224 |
+
},
|
| 225 |
+
"46": {
|
| 226 |
+
"name": "vertebrae_C5",
|
| 227 |
+
"color": "#4BEA96"
|
| 228 |
+
},
|
| 229 |
+
"47": {
|
| 230 |
+
"name": "vertebrae_C4",
|
| 231 |
+
"color": "#EA684B"
|
| 232 |
+
},
|
| 233 |
+
"48": {
|
| 234 |
+
"name": "vertebrae_C3",
|
| 235 |
+
"color": "#4B63EA"
|
| 236 |
+
},
|
| 237 |
+
"49": {
|
| 238 |
+
"name": "vertebrae_C2",
|
| 239 |
+
"color": "#4BEA7D"
|
| 240 |
+
},
|
| 241 |
+
"50": {
|
| 242 |
+
"name": "vertebrae_C1",
|
| 243 |
+
"color": "#EA4BAD"
|
| 244 |
+
},
|
| 245 |
+
"51": {
|
| 246 |
+
"name": "heart",
|
| 247 |
+
"color": "#DAEA4B"
|
| 248 |
+
},
|
| 249 |
+
"52": {
|
| 250 |
+
"name": "aorta",
|
| 251 |
+
"color": "#CD4BEA"
|
| 252 |
+
},
|
| 253 |
+
"53": {
|
| 254 |
+
"name": "pulmonary_vein",
|
| 255 |
+
"color": "#4BEA8F"
|
| 256 |
+
},
|
| 257 |
+
"54": {
|
| 258 |
+
"name": "brachiocephalic_trunk",
|
| 259 |
+
"color": "#EA614B"
|
| 260 |
+
},
|
| 261 |
+
"55": {
|
| 262 |
+
"name": "subclavian_artery_right",
|
| 263 |
+
"color": "#4B6AEA"
|
| 264 |
+
},
|
| 265 |
+
"56": {
|
| 266 |
+
"name": "subclavian_artery_left",
|
| 267 |
+
"color": "#4BEA84"
|
| 268 |
+
},
|
| 269 |
+
"57": {
|
| 270 |
+
"name": "common_carotid_artery_right",
|
| 271 |
+
"color": "#EA4BB4"
|
| 272 |
+
},
|
| 273 |
+
"58": {
|
| 274 |
+
"name": "common_carotid_artery_left",
|
| 275 |
+
"color": "#E1EA4B"
|
| 276 |
+
},
|
| 277 |
+
"59": {
|
| 278 |
+
"name": "brachiocephalic_vein_left",
|
| 279 |
+
"color": "#C64BEA"
|
| 280 |
+
},
|
| 281 |
+
"60": {
|
| 282 |
+
"name": "brachiocephalic_vein_right",
|
| 283 |
+
"color": "#4BEA88"
|
| 284 |
+
},
|
| 285 |
+
"61": {
|
| 286 |
+
"name": "atrial_appendage_left",
|
| 287 |
+
"color": "#EA5B4B"
|
| 288 |
+
},
|
| 289 |
+
"62": {
|
| 290 |
+
"name": "superior_vena_cava",
|
| 291 |
+
"color": "#4B71EA"
|
| 292 |
+
},
|
| 293 |
+
"63": {
|
| 294 |
+
"name": "inferior_vena_cava",
|
| 295 |
+
"color": "#4BEA8B"
|
| 296 |
+
},
|
| 297 |
+
"64": {
|
| 298 |
+
"name": "portal_vein_and_splenic_vein",
|
| 299 |
+
"color": "#EA4BBA"
|
| 300 |
+
},
|
| 301 |
+
"65": {
|
| 302 |
+
"name": "iliac_artery_left",
|
| 303 |
+
"color": "#E8EA4B"
|
| 304 |
+
},
|
| 305 |
+
"66": {
|
| 306 |
+
"name": "iliac_artery_right",
|
| 307 |
+
"color": "#BF4BEA"
|
| 308 |
+
},
|
| 309 |
+
"67": {
|
| 310 |
+
"name": "iliac_vena_left",
|
| 311 |
+
"color": "#4BEA82"
|
| 312 |
+
},
|
| 313 |
+
"68": {
|
| 314 |
+
"name": "iliac_vena_right",
|
| 315 |
+
"color": "#EA544B"
|
| 316 |
+
},
|
| 317 |
+
"69": {
|
| 318 |
+
"name": "humerus_left",
|
| 319 |
+
"color": "#4B78EA"
|
| 320 |
+
},
|
| 321 |
+
"70": {
|
| 322 |
+
"name": "humerus_right",
|
| 323 |
+
"color": "#4BEA92"
|
| 324 |
+
},
|
| 325 |
+
"71": {
|
| 326 |
+
"name": "scapula_left",
|
| 327 |
+
"color": "#EA4BC1"
|
| 328 |
+
},
|
| 329 |
+
"72": {
|
| 330 |
+
"name": "scapula_right",
|
| 331 |
+
"color": "#EAEA4B"
|
| 332 |
+
},
|
| 333 |
+
"73": {
|
| 334 |
+
"name": "clavicula_left",
|
| 335 |
+
"color": "#B84BEA"
|
| 336 |
+
},
|
| 337 |
+
"74": {
|
| 338 |
+
"name": "clavicula_right",
|
| 339 |
+
"color": "#4BEA79"
|
| 340 |
+
},
|
| 341 |
+
"75": {
|
| 342 |
+
"name": "femur_left",
|
| 343 |
+
"color": "#EA4D4B"
|
| 344 |
+
},
|
| 345 |
+
"76": {
|
| 346 |
+
"name": "femur_right",
|
| 347 |
+
"color": "#4B7FEA"
|
| 348 |
+
},
|
| 349 |
+
"77": {
|
| 350 |
+
"name": "hip_left",
|
| 351 |
+
"color": "#4BEA99"
|
| 352 |
+
},
|
| 353 |
+
"78": {
|
| 354 |
+
"name": "hip_right",
|
| 355 |
+
"color": "#EA4BC8"
|
| 356 |
+
},
|
| 357 |
+
"79": {
|
| 358 |
+
"name": "spinal_cord",
|
| 359 |
+
"color": "#EAEC4B"
|
| 360 |
+
},
|
| 361 |
+
"80": {
|
| 362 |
+
"name": "gluteus_maximus_left",
|
| 363 |
+
"color": "#B14BEA"
|
| 364 |
+
},
|
| 365 |
+
"81": {
|
| 366 |
+
"name": "gluteus_maximus_right",
|
| 367 |
+
"color": "#4BEA72"
|
| 368 |
+
},
|
| 369 |
+
"82": {
|
| 370 |
+
"name": "gluteus_medius_left",
|
| 371 |
+
"color": "#EA4B54"
|
| 372 |
+
},
|
| 373 |
+
"83": {
|
| 374 |
+
"name": "gluteus_medius_right",
|
| 375 |
+
"color": "#4B86EA"
|
| 376 |
+
},
|
| 377 |
+
"84": {
|
| 378 |
+
"name": "gluteus_minimus_left",
|
| 379 |
+
"color": "#4BEAA0"
|
| 380 |
+
},
|
| 381 |
+
"85": {
|
| 382 |
+
"name": "gluteus_minimus_right",
|
| 383 |
+
"color": "#EA4BCF"
|
| 384 |
+
},
|
| 385 |
+
"86": {
|
| 386 |
+
"name": "autochthon_left",
|
| 387 |
+
"color": "#EAF34B"
|
| 388 |
+
},
|
| 389 |
+
"87": {
|
| 390 |
+
"name": "autochthon_right",
|
| 391 |
+
"color": "#AA4BEA"
|
| 392 |
+
},
|
| 393 |
+
"88": {
|
| 394 |
+
"name": "iliopsoas_left",
|
| 395 |
+
"color": "#4BEA6B"
|
| 396 |
+
},
|
| 397 |
+
"89": {
|
| 398 |
+
"name": "iliopsoas_right",
|
| 399 |
+
"color": "#EA4B5B"
|
| 400 |
+
},
|
| 401 |
+
"90": {
|
| 402 |
+
"name": "brain",
|
| 403 |
+
"color": "#4B8DEA"
|
| 404 |
+
},
|
| 405 |
+
"91": {
|
| 406 |
+
"name": "skull",
|
| 407 |
+
"color": "#4BEAA7"
|
| 408 |
+
},
|
| 409 |
+
"92": {
|
| 410 |
+
"name": "rib_left_1",
|
| 411 |
+
"color": "#EA4BD6"
|
| 412 |
+
},
|
| 413 |
+
"93": {
|
| 414 |
+
"name": "rib_left_2",
|
| 415 |
+
"color": "#EAFC4B"
|
| 416 |
+
},
|
| 417 |
+
"94": {
|
| 418 |
+
"name": "rib_left_3",
|
| 419 |
+
"color": "#A34BEA"
|
| 420 |
+
},
|
| 421 |
+
"95": {
|
| 422 |
+
"name": "rib_left_4",
|
| 423 |
+
"color": "#4BEA64"
|
| 424 |
+
},
|
| 425 |
+
"96": {
|
| 426 |
+
"name": "rib_left_5",
|
| 427 |
+
"color": "#EA4B62"
|
| 428 |
+
},
|
| 429 |
+
"97": {
|
| 430 |
+
"name": "rib_left_6",
|
| 431 |
+
"color": "#4B94EA"
|
| 432 |
+
},
|
| 433 |
+
"98": {
|
| 434 |
+
"name": "rib_left_7",
|
| 435 |
+
"color": "#4BEAAE"
|
| 436 |
+
},
|
| 437 |
+
"99": {
|
| 438 |
+
"name": "rib_left_8",
|
| 439 |
+
"color": "#EA4BDD"
|
| 440 |
+
},
|
| 441 |
+
"100": {
|
| 442 |
+
"name": "rib_left_9",
|
| 443 |
+
"color": "#F0EA4B"
|
| 444 |
+
},
|
| 445 |
+
"101": {
|
| 446 |
+
"name": "rib_left_10",
|
| 447 |
+
"color": "#9C4BEA"
|
| 448 |
+
},
|
| 449 |
+
"102": {
|
| 450 |
+
"name": "rib_left_11",
|
| 451 |
+
"color": "#4BEA5D"
|
| 452 |
+
},
|
| 453 |
+
"103": {
|
| 454 |
+
"name": "rib_left_12",
|
| 455 |
+
"color": "#EA4B69"
|
| 456 |
+
},
|
| 457 |
+
"104": {
|
| 458 |
+
"name": "rib_right_1",
|
| 459 |
+
"color": "#4B9BEA"
|
| 460 |
+
},
|
| 461 |
+
"105": {
|
| 462 |
+
"name": "rib_right_2",
|
| 463 |
+
"color": "#4BEAB5"
|
| 464 |
+
},
|
| 465 |
+
"106": {
|
| 466 |
+
"name": "rib_right_3",
|
| 467 |
+
"color": "#EA4BE4"
|
| 468 |
+
},
|
| 469 |
+
"107": {
|
| 470 |
+
"name": "rib_right_4",
|
| 471 |
+
"color": "#E9EA4B"
|
| 472 |
+
},
|
| 473 |
+
"108": {
|
| 474 |
+
"name": "rib_right_5",
|
| 475 |
+
"color": "#954BEA"
|
| 476 |
+
},
|
| 477 |
+
"109": {
|
| 478 |
+
"name": "rib_right_6",
|
| 479 |
+
"color": "#4BEA56"
|
| 480 |
+
},
|
| 481 |
+
"110": {
|
| 482 |
+
"name": "rib_right_7",
|
| 483 |
+
"color": "#EA4B70"
|
| 484 |
+
},
|
| 485 |
+
"111": {
|
| 486 |
+
"name": "rib_right_8",
|
| 487 |
+
"color": "#4BA2EA"
|
| 488 |
+
},
|
| 489 |
+
"112": {
|
| 490 |
+
"name": "rib_right_9",
|
| 491 |
+
"color": "#4BEABC"
|
| 492 |
+
},
|
| 493 |
+
"113": {
|
| 494 |
+
"name": "rib_right_10",
|
| 495 |
+
"color": "#EA4BEB"
|
| 496 |
+
},
|
| 497 |
+
"114": {
|
| 498 |
+
"name": "rib_right_11",
|
| 499 |
+
"color": "#E2EA4B"
|
| 500 |
+
},
|
| 501 |
+
"115": {
|
| 502 |
+
"name": "rib_right_12",
|
| 503 |
+
"color": "#8E4BEA"
|
| 504 |
+
},
|
| 505 |
+
"116": {
|
| 506 |
+
"name": "sternum",
|
| 507 |
+
"color": "#4BEA4F"
|
| 508 |
+
},
|
| 509 |
+
"117": {
|
| 510 |
+
"name": "costal_cartilages",
|
| 511 |
+
"color": "#61EA4B"
|
| 512 |
+
}
|
| 513 |
+
},
|
| 514 |
+
"patch_size": [
|
| 515 |
+
96,
|
| 516 |
+
128,
|
| 517 |
+
160
|
| 518 |
+
],
|
| 519 |
+
"vram_plan": {
|
| 520 |
+
"8": {
|
| 521 |
+
"patch_size": [
|
| 522 |
+
96,
|
| 523 |
+
128,
|
| 524 |
+
160
|
| 525 |
+
],
|
| 526 |
+
"batch_size": 4
|
| 527 |
+
},
|
| 528 |
+
"16": {
|
| 529 |
+
"patch_size": [
|
| 530 |
+
96,
|
| 531 |
+
128,
|
| 532 |
+
160
|
| 533 |
+
],
|
| 534 |
+
"batch_size": 8
|
| 535 |
+
},
|
| 536 |
+
"24": {
|
| 537 |
+
"patch_size": [
|
| 538 |
+
96,
|
| 539 |
+
128,
|
| 540 |
+
160
|
| 541 |
+
],
|
| 542 |
+
"batch_size": 12
|
| 543 |
+
}
|
| 544 |
}
|
| 545 |
+
}
|
total_mr-3mm/app.json
CHANGED
|
@@ -1,90 +1,273 @@
|
|
| 1 |
{
|
| 2 |
"display_name": "Segmentation: TotalSegmentator MRI 3mm",
|
| 3 |
-
"short_description": "<b>Description:</b><br>Lightweight KonfAI adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator MRI</a>, enabling fast multimodal segmentation of <b>50 key anatomical structures</b> from <b>MRI and CT</b> scans at <b>3 mm</b> resolution, greatly reducing memory usage and inference time compared to the original nnU-Net workflow.<br><br><b>How to cite:</b><br><cite>T. Akinci D
|
| 4 |
-
"description": "<b>Description:</b><br>This model integrates the reduced-resolution MRI-3mm configuration of TotalSegmentator into the <b>KonfAI</b> accelerated inference pipeline for efficient MRI/CT deployment.<br><br><b>Capabilities:</b><br>
|
| 5 |
"tta": 0,
|
| 6 |
"mc_dropout": 0,
|
| 7 |
-
"models": [
|
|
|
|
|
|
|
| 8 |
"inputs": {
|
| 9 |
-
|
| 10 |
-
|
| 11 |
-
|
| 12 |
-
|
| 13 |
-
|
| 14 |
},
|
| 15 |
"outputs": {
|
| 16 |
-
|
| 17 |
-
|
| 18 |
-
|
| 19 |
-
|
| 20 |
-
|
| 21 |
},
|
| 22 |
"inputs_evaluations": {
|
| 23 |
-
|
| 24 |
-
|
| 25 |
-
|
| 26 |
-
|
| 27 |
-
|
| 28 |
-
|
| 29 |
-
|
| 30 |
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|
| 31 |
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|
| 32 |
-
|
| 33 |
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|
| 34 |
-
|
|
|
|
| 35 |
}
|
| 36 |
-
}
|
| 37 |
},
|
| 38 |
"terminology": {
|
| 39 |
-
|
| 40 |
-
|
| 41 |
-
|
| 42 |
-
|
| 43 |
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|
| 44 |
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|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 89 |
}
|
| 90 |
-
}
|
|
|
|
| 1 |
{
|
| 2 |
"display_name": "Segmentation: TotalSegmentator MRI 3mm",
|
| 3 |
+
"short_description": "<b>Description:</b><br>Lightweight KonfAI adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator MRI</a>, enabling fast multimodal segmentation of <b>50 key anatomical structures</b> from <b>MRI and CT</b> scans at <b>3 mm</b> resolution, greatly reducing memory usage and inference time compared to the original nnU-Net workflow.<br><br><b>How to cite:</b><br><cite>T. Akinci D\u2019Antonoli et al., <i>TotalSegmentator MRI: Robust Sequence-Independent Segmentation of Multiple Anatomic Structures in MRI</i>, Radiology, 2025.</cite>",
|
| 4 |
+
"description": "<b>Description:</b><br>This model integrates the reduced-resolution MRI-3mm configuration of TotalSegmentator into the <b>KonfAI</b> accelerated inference pipeline for efficient MRI/CT deployment.<br><br><b>Capabilities:</b><br>\u2022 Segmentation of <b>50 essential anatomical structures</b> (major organs, key bones, large vessels)<br>\u2022 <b>3 mm</b> isotropic input for high-throughput processing and lower GPU requirements<br>\u2022 Robust to acquisition variability including scanner type, contrast, and sequence parameters<br><br><b>Training data:</b><br>Trained on a diverse cohort of <b>1143 clinical scans</b> including <b>616 MRI</b> (multi-site, multi-scanner, multi-sequence) and <b>527 CT</b>, with expert-validated reference masks<br><br>><b>How to cite:</b><br><cite>T. Akinci D\u2019Antonoli et al., <i>TotalSegmentator MRI: Robust Sequence-Independent Segmentation of Multiple Anatomic Structures in MRI</i>, Radiology, 2025.</cite>",
|
| 5 |
"tta": 0,
|
| 6 |
"mc_dropout": 0,
|
| 7 |
+
"models": [
|
| 8 |
+
"M852.pt"
|
| 9 |
+
],
|
| 10 |
"inputs": {
|
| 11 |
+
"Volume": {
|
| 12 |
+
"display_name": "Input Volume",
|
| 13 |
+
"volume_type": "VOLUME",
|
| 14 |
+
"required": true
|
| 15 |
+
}
|
| 16 |
},
|
| 17 |
"outputs": {
|
| 18 |
+
"Segmentation": {
|
| 19 |
+
"display_name": "Segmentation",
|
| 20 |
+
"volume_type": "SEGMENTATION",
|
| 21 |
+
"required": true
|
| 22 |
+
}
|
| 23 |
},
|
| 24 |
"inputs_evaluations": {
|
| 25 |
+
"Image": {
|
| 26 |
+
"Evaluation.yml": {
|
| 27 |
+
"Segmentation": {
|
| 28 |
+
"display_name": "Output Segmentation",
|
| 29 |
+
"volume_type": "VOLUME",
|
| 30 |
+
"required": true
|
| 31 |
+
},
|
| 32 |
+
"GT_Segmentation": {
|
| 33 |
+
"display_name": "GT Segmentation",
|
| 34 |
+
"volume_type": "VOLUME",
|
| 35 |
+
"required": true
|
| 36 |
+
}
|
| 37 |
+
}
|
| 38 |
}
|
|
|
|
| 39 |
},
|
| 40 |
"terminology": {
|
| 41 |
+
"1": {
|
| 42 |
+
"name": "spleen",
|
| 43 |
+
"color": "#4B79EA"
|
| 44 |
+
},
|
| 45 |
+
"2": {
|
| 46 |
+
"name": "kidney_right",
|
| 47 |
+
"color": "#A8EA4B"
|
| 48 |
+
},
|
| 49 |
+
"3": {
|
| 50 |
+
"name": "kidney_left",
|
| 51 |
+
"color": "#EA4BD7"
|
| 52 |
+
},
|
| 53 |
+
"4": {
|
| 54 |
+
"name": "gallbladder",
|
| 55 |
+
"color": "#4BEAC0"
|
| 56 |
+
},
|
| 57 |
+
"5": {
|
| 58 |
+
"name": "liver",
|
| 59 |
+
"color": "#EA924B"
|
| 60 |
+
},
|
| 61 |
+
"6": {
|
| 62 |
+
"name": "stomach",
|
| 63 |
+
"color": "#634BEA"
|
| 64 |
+
},
|
| 65 |
+
"7": {
|
| 66 |
+
"name": "pancreas",
|
| 67 |
+
"color": "#4BEA53"
|
| 68 |
+
},
|
| 69 |
+
"8": {
|
| 70 |
+
"name": "adrenal_gland_right",
|
| 71 |
+
"color": "#EA4B82"
|
| 72 |
+
},
|
| 73 |
+
"9": {
|
| 74 |
+
"name": "adrenal_gland_left",
|
| 75 |
+
"color": "#B0EA4B"
|
| 76 |
+
},
|
| 77 |
+
"10": {
|
| 78 |
+
"name": "lung_left",
|
| 79 |
+
"color": "#FABEBE"
|
| 80 |
+
},
|
| 81 |
+
"11": {
|
| 82 |
+
"name": "lung_right",
|
| 83 |
+
"color": "#008080"
|
| 84 |
+
},
|
| 85 |
+
"12": {
|
| 86 |
+
"name": "esophagus",
|
| 87 |
+
"color": "#EA4B89"
|
| 88 |
+
},
|
| 89 |
+
"13": {
|
| 90 |
+
"name": "small_bowel",
|
| 91 |
+
"color": "#4BEAB2"
|
| 92 |
+
},
|
| 93 |
+
"14": {
|
| 94 |
+
"name": "duodenum",
|
| 95 |
+
"color": "#EA844B"
|
| 96 |
+
},
|
| 97 |
+
"15": {
|
| 98 |
+
"name": "colon",
|
| 99 |
+
"color": "#554BEA"
|
| 100 |
+
},
|
| 101 |
+
"16": {
|
| 102 |
+
"name": "urinary_bladder",
|
| 103 |
+
"color": "#FB9A99"
|
| 104 |
+
},
|
| 105 |
+
"17": {
|
| 106 |
+
"name": "prostate",
|
| 107 |
+
"color": "#EA4B90"
|
| 108 |
+
},
|
| 109 |
+
"18": {
|
| 110 |
+
"name": "sacrum",
|
| 111 |
+
"color": "#B15928"
|
| 112 |
+
},
|
| 113 |
+
"19": {
|
| 114 |
+
"name": "vertebrae",
|
| 115 |
+
"color": "#6A3D9A"
|
| 116 |
+
},
|
| 117 |
+
"20": {
|
| 118 |
+
"name": "intervertebral_discs",
|
| 119 |
+
"color": "#CAB2D6"
|
| 120 |
+
},
|
| 121 |
+
"21": {
|
| 122 |
+
"name": "spinal_cord",
|
| 123 |
+
"color": "#EAEC4B"
|
| 124 |
+
},
|
| 125 |
+
"22": {
|
| 126 |
+
"name": "heart",
|
| 127 |
+
"color": "#E6BEFF"
|
| 128 |
+
},
|
| 129 |
+
"23": {
|
| 130 |
+
"name": "aorta",
|
| 131 |
+
"color": "#9A6324"
|
| 132 |
+
},
|
| 133 |
+
"24": {
|
| 134 |
+
"name": "inferior_vena_cava",
|
| 135 |
+
"color": "#FFFAC8"
|
| 136 |
+
},
|
| 137 |
+
"25": {
|
| 138 |
+
"name": "portal_vein_and_splenic_vein",
|
| 139 |
+
"color": "#800000"
|
| 140 |
+
},
|
| 141 |
+
"26": {
|
| 142 |
+
"name": "iliac_artery_left",
|
| 143 |
+
"color": "#AaffC3"
|
| 144 |
+
},
|
| 145 |
+
"27": {
|
| 146 |
+
"name": "iliac_artery_right",
|
| 147 |
+
"color": "#808000"
|
| 148 |
+
},
|
| 149 |
+
"28": {
|
| 150 |
+
"name": "iliac_vena_left",
|
| 151 |
+
"color": "#FFD8B1"
|
| 152 |
+
},
|
| 153 |
+
"29": {
|
| 154 |
+
"name": "iliac_vena_right",
|
| 155 |
+
"color": "#000075"
|
| 156 |
+
},
|
| 157 |
+
"30": {
|
| 158 |
+
"name": "humerus_left",
|
| 159 |
+
"color": "#A6CEE3"
|
| 160 |
+
},
|
| 161 |
+
"31": {
|
| 162 |
+
"name": "humerus_right",
|
| 163 |
+
"color": "#B2DF8A"
|
| 164 |
+
},
|
| 165 |
+
"32": {
|
| 166 |
+
"name": "scapula_left",
|
| 167 |
+
"color": "#1F78B4"
|
| 168 |
+
},
|
| 169 |
+
"33": {
|
| 170 |
+
"name": "scapula_right",
|
| 171 |
+
"color": "#33A02C"
|
| 172 |
+
},
|
| 173 |
+
"34": {
|
| 174 |
+
"name": "clavicula_left",
|
| 175 |
+
"color": "#BC80BD"
|
| 176 |
+
},
|
| 177 |
+
"35": {
|
| 178 |
+
"name": "clavicula_right",
|
| 179 |
+
"color": "#FFED6F"
|
| 180 |
+
},
|
| 181 |
+
"36": {
|
| 182 |
+
"name": "femur_left",
|
| 183 |
+
"color": "#CAB2D6"
|
| 184 |
+
},
|
| 185 |
+
"37": {
|
| 186 |
+
"name": "femur_right",
|
| 187 |
+
"color": "#FFFF99"
|
| 188 |
+
},
|
| 189 |
+
"38": {
|
| 190 |
+
"name": "hip_left",
|
| 191 |
+
"color": "#A6CEE3"
|
| 192 |
+
},
|
| 193 |
+
"39": {
|
| 194 |
+
"name": "hip_right",
|
| 195 |
+
"color": "#B2DF8A"
|
| 196 |
+
},
|
| 197 |
+
"40": {
|
| 198 |
+
"name": "gluteus_maximus_left",
|
| 199 |
+
"color": "#66A61E"
|
| 200 |
+
},
|
| 201 |
+
"41": {
|
| 202 |
+
"name": "gluteus_maximus_right",
|
| 203 |
+
"color": "#E6AB02"
|
| 204 |
+
},
|
| 205 |
+
"42": {
|
| 206 |
+
"name": "gluteus_medius_left",
|
| 207 |
+
"color": "#A6761D"
|
| 208 |
+
},
|
| 209 |
+
"43": {
|
| 210 |
+
"name": "gluteus_medius_right",
|
| 211 |
+
"color": "#666666"
|
| 212 |
+
},
|
| 213 |
+
"44": {
|
| 214 |
+
"name": "gluteus_minimus_left",
|
| 215 |
+
"color": "#7FC97F"
|
| 216 |
+
},
|
| 217 |
+
"45": {
|
| 218 |
+
"name": "gluteus_minimus_right",
|
| 219 |
+
"color": "#BEAED4"
|
| 220 |
+
},
|
| 221 |
+
"46": {
|
| 222 |
+
"name": "autochthon_left",
|
| 223 |
+
"color": "#1B9E77"
|
| 224 |
+
},
|
| 225 |
+
"47": {
|
| 226 |
+
"name": "autochthon_right",
|
| 227 |
+
"color": "#D95F02"
|
| 228 |
+
},
|
| 229 |
+
"48": {
|
| 230 |
+
"name": "iliopsoas_left",
|
| 231 |
+
"color": "#7570B3"
|
| 232 |
+
},
|
| 233 |
+
"49": {
|
| 234 |
+
"name": "iliopsoas_right",
|
| 235 |
+
"color": "#E7298A"
|
| 236 |
+
},
|
| 237 |
+
"50": {
|
| 238 |
+
"name": "brain",
|
| 239 |
+
"color": "#8DD3C7"
|
| 240 |
+
}
|
| 241 |
+
},
|
| 242 |
+
"patch_size": [
|
| 243 |
+
96,
|
| 244 |
+
96,
|
| 245 |
+
128
|
| 246 |
+
],
|
| 247 |
+
"vram_plan": {
|
| 248 |
+
"8": {
|
| 249 |
+
"patch_size": [
|
| 250 |
+
96,
|
| 251 |
+
96,
|
| 252 |
+
128
|
| 253 |
+
],
|
| 254 |
+
"batch_size": 4
|
| 255 |
+
},
|
| 256 |
+
"16": {
|
| 257 |
+
"patch_size": [
|
| 258 |
+
96,
|
| 259 |
+
96,
|
| 260 |
+
128
|
| 261 |
+
],
|
| 262 |
+
"batch_size": 8
|
| 263 |
+
},
|
| 264 |
+
"24": {
|
| 265 |
+
"patch_size": [
|
| 266 |
+
96,
|
| 267 |
+
96,
|
| 268 |
+
128
|
| 269 |
+
],
|
| 270 |
+
"batch_size": 12
|
| 271 |
+
}
|
| 272 |
}
|
| 273 |
+
}
|
total_mr/app.json
CHANGED
|
@@ -1,90 +1,274 @@
|
|
| 1 |
{
|
| 2 |
"display_name": "Segmentation: TotalSegmentator MRI",
|
| 3 |
-
"short_description": "<b>Description:</b><br>KonfAI-accelerated adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator MRI</a>, delivering fast multimodal segmentation of <b>80 major anatomical structures</b> from <b>MRI and CT</b> scans, with significantly reduced inference overhead vs. the original nnU-Net workflow.<br><br><b>How to cite:</b><br><cite>T. Akinci D
|
| 4 |
-
"description": "<b>Description:</b><br>This model integrates TotalSegmentator MRI into the <b>KonfAI</b> inference framework to accelerate deployment in MRI/CT multimodal workflows.<br><br><b>Capabilities:</b><br>
|
| 5 |
"tta": 0,
|
| 6 |
"mc_dropout": 0,
|
| 7 |
-
"models": [
|
|
|
|
|
|
|
|
|
|
| 8 |
"inputs": {
|
| 9 |
-
|
| 10 |
-
|
| 11 |
-
|
| 12 |
-
|
| 13 |
-
|
| 14 |
},
|
| 15 |
"outputs": {
|
| 16 |
-
|
| 17 |
-
|
| 18 |
-
|
| 19 |
-
|
| 20 |
-
|
| 21 |
},
|
| 22 |
"inputs_evaluations": {
|
| 23 |
-
|
| 24 |
-
|
| 25 |
-
|
| 26 |
-
|
| 27 |
-
|
| 28 |
-
|
| 29 |
-
|
| 30 |
-
|
| 31 |
-
|
| 32 |
-
|
| 33 |
-
|
| 34 |
-
|
|
|
|
| 35 |
}
|
| 36 |
-
}
|
| 37 |
},
|
| 38 |
"terminology": {
|
| 39 |
-
|
| 40 |
-
|
| 41 |
-
|
| 42 |
-
|
| 43 |
-
|
| 44 |
-
|
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|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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|
| 54 |
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| 55 |
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| 56 |
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| 57 |
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| 59 |
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| 60 |
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|
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
-
|
| 68 |
-
|
| 69 |
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|
| 70 |
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|
| 71 |
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|
| 72 |
-
|
| 73 |
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|
| 74 |
-
|
| 75 |
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|
| 76 |
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|
| 77 |
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|
| 78 |
-
|
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-
|
| 80 |
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|
| 81 |
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|
| 82 |
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|
| 83 |
-
|
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|
| 85 |
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| 86 |
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|
| 87 |
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|
| 88 |
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|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
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|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 89 |
}
|
| 90 |
-
}
|
|
|
|
| 1 |
{
|
| 2 |
"display_name": "Segmentation: TotalSegmentator MRI",
|
| 3 |
+
"short_description": "<b>Description:</b><br>KonfAI-accelerated adaptation of <a href='https://github.com/wasserth/TotalSegmentator'>TotalSegmentator MRI</a>, delivering fast multimodal segmentation of <b>80 major anatomical structures</b> from <b>MRI and CT</b> scans, with significantly reduced inference overhead vs. the original nnU-Net workflow.<br><br><b>How to cite:</b><br><cite>T. Akinci D\u2019Antonoli et al., <i>TotalSegmentator MRI: Robust Sequence-Independent Segmentation of Multiple Anatomic Structures in MRI</i>, Radiology, 2025.</cite>",
|
| 4 |
+
"description": "<b>Description:</b><br>This model integrates TotalSegmentator MRI into the <b>KonfAI</b> inference framework to accelerate deployment in MRI/CT multimodal workflows.<br><br><b>Capabilities:</b><br>\u2022 Automatic segmentation of <b>80 major anatomical structures</b> (organs, vessels, skeleton, digestive system)<br>\u2022 Robust to <b>sequence variations</b> across scanners, contrasts, acquisition planes, and sites<br>\u2022 High-resolution input: <b>1.5 mm isotropic</b><br><br><b>Training data:</b><br>Trained on a highly diverse clinical dataset of <b>1143 scans</b> including <b>616 MRI</b> (30 scanners, 4 sites, many contrast types) and <b>527 CT</b> scans, with expert-validated manual segmentations <br><br><b>How to cite:</b><br><cite>T. Akinci D\u2019Antonoli et al., <i>TotalSegmentator MRI: Robust Sequence-Independent Segmentation of Multiple Anatomic Structures in MRI</i>, Radiology, 2025.</cite>",
|
| 5 |
"tta": 0,
|
| 6 |
"mc_dropout": 0,
|
| 7 |
+
"models": [
|
| 8 |
+
"M850.pt",
|
| 9 |
+
"M851.pt"
|
| 10 |
+
],
|
| 11 |
"inputs": {
|
| 12 |
+
"Volume": {
|
| 13 |
+
"display_name": "Input Volume",
|
| 14 |
+
"volume_type": "VOLUME",
|
| 15 |
+
"required": true
|
| 16 |
+
}
|
| 17 |
},
|
| 18 |
"outputs": {
|
| 19 |
+
"Segmentation": {
|
| 20 |
+
"display_name": "Segmentation",
|
| 21 |
+
"volume_type": "SEGMENTATION",
|
| 22 |
+
"required": true
|
| 23 |
+
}
|
| 24 |
},
|
| 25 |
"inputs_evaluations": {
|
| 26 |
+
"Image": {
|
| 27 |
+
"Evaluation.yml": {
|
| 28 |
+
"Segmentation": {
|
| 29 |
+
"display_name": "Output Segmentation",
|
| 30 |
+
"volume_type": "VOLUME",
|
| 31 |
+
"required": true
|
| 32 |
+
},
|
| 33 |
+
"GT_Segmentation": {
|
| 34 |
+
"display_name": "GT Segmentation",
|
| 35 |
+
"volume_type": "VOLUME",
|
| 36 |
+
"required": true
|
| 37 |
+
}
|
| 38 |
+
}
|
| 39 |
}
|
|
|
|
| 40 |
},
|
| 41 |
"terminology": {
|
| 42 |
+
"1": {
|
| 43 |
+
"name": "spleen",
|
| 44 |
+
"color": "#4B79EA"
|
| 45 |
+
},
|
| 46 |
+
"2": {
|
| 47 |
+
"name": "kidney_right",
|
| 48 |
+
"color": "#A8EA4B"
|
| 49 |
+
},
|
| 50 |
+
"3": {
|
| 51 |
+
"name": "kidney_left",
|
| 52 |
+
"color": "#EA4BD7"
|
| 53 |
+
},
|
| 54 |
+
"4": {
|
| 55 |
+
"name": "gallbladder",
|
| 56 |
+
"color": "#4BEAC0"
|
| 57 |
+
},
|
| 58 |
+
"5": {
|
| 59 |
+
"name": "liver",
|
| 60 |
+
"color": "#EA924B"
|
| 61 |
+
},
|
| 62 |
+
"6": {
|
| 63 |
+
"name": "stomach",
|
| 64 |
+
"color": "#634BEA"
|
| 65 |
+
},
|
| 66 |
+
"7": {
|
| 67 |
+
"name": "pancreas",
|
| 68 |
+
"color": "#4BEA53"
|
| 69 |
+
},
|
| 70 |
+
"8": {
|
| 71 |
+
"name": "adrenal_gland_right",
|
| 72 |
+
"color": "#EA4B82"
|
| 73 |
+
},
|
| 74 |
+
"9": {
|
| 75 |
+
"name": "adrenal_gland_left",
|
| 76 |
+
"color": "#B0EA4B"
|
| 77 |
+
},
|
| 78 |
+
"10": {
|
| 79 |
+
"name": "lung_left",
|
| 80 |
+
"color": "#FABEBE"
|
| 81 |
+
},
|
| 82 |
+
"11": {
|
| 83 |
+
"name": "lung_right",
|
| 84 |
+
"color": "#008080"
|
| 85 |
+
},
|
| 86 |
+
"12": {
|
| 87 |
+
"name": "esophagus",
|
| 88 |
+
"color": "#EA4B89"
|
| 89 |
+
},
|
| 90 |
+
"13": {
|
| 91 |
+
"name": "small_bowel",
|
| 92 |
+
"color": "#4BEAB2"
|
| 93 |
+
},
|
| 94 |
+
"14": {
|
| 95 |
+
"name": "duodenum",
|
| 96 |
+
"color": "#EA844B"
|
| 97 |
+
},
|
| 98 |
+
"15": {
|
| 99 |
+
"name": "colon",
|
| 100 |
+
"color": "#554BEA"
|
| 101 |
+
},
|
| 102 |
+
"16": {
|
| 103 |
+
"name": "urinary_bladder",
|
| 104 |
+
"color": "#FB9A99"
|
| 105 |
+
},
|
| 106 |
+
"17": {
|
| 107 |
+
"name": "prostate",
|
| 108 |
+
"color": "#EA4B90"
|
| 109 |
+
},
|
| 110 |
+
"18": {
|
| 111 |
+
"name": "sacrum",
|
| 112 |
+
"color": "#B15928"
|
| 113 |
+
},
|
| 114 |
+
"19": {
|
| 115 |
+
"name": "vertebrae",
|
| 116 |
+
"color": "#6A3D9A"
|
| 117 |
+
},
|
| 118 |
+
"20": {
|
| 119 |
+
"name": "intervertebral_discs",
|
| 120 |
+
"color": "#CAB2D6"
|
| 121 |
+
},
|
| 122 |
+
"21": {
|
| 123 |
+
"name": "spinal_cord",
|
| 124 |
+
"color": "#EAEC4B"
|
| 125 |
+
},
|
| 126 |
+
"22": {
|
| 127 |
+
"name": "heart",
|
| 128 |
+
"color": "#E6BEFF"
|
| 129 |
+
},
|
| 130 |
+
"23": {
|
| 131 |
+
"name": "aorta",
|
| 132 |
+
"color": "#9A6324"
|
| 133 |
+
},
|
| 134 |
+
"24": {
|
| 135 |
+
"name": "inferior_vena_cava",
|
| 136 |
+
"color": "#FFFAC8"
|
| 137 |
+
},
|
| 138 |
+
"25": {
|
| 139 |
+
"name": "portal_vein_and_splenic_vein",
|
| 140 |
+
"color": "#800000"
|
| 141 |
+
},
|
| 142 |
+
"26": {
|
| 143 |
+
"name": "iliac_artery_left",
|
| 144 |
+
"color": "#AaffC3"
|
| 145 |
+
},
|
| 146 |
+
"27": {
|
| 147 |
+
"name": "iliac_artery_right",
|
| 148 |
+
"color": "#808000"
|
| 149 |
+
},
|
| 150 |
+
"28": {
|
| 151 |
+
"name": "iliac_vena_left",
|
| 152 |
+
"color": "#FFD8B1"
|
| 153 |
+
},
|
| 154 |
+
"29": {
|
| 155 |
+
"name": "iliac_vena_right",
|
| 156 |
+
"color": "#000075"
|
| 157 |
+
},
|
| 158 |
+
"30": {
|
| 159 |
+
"name": "humerus_left",
|
| 160 |
+
"color": "#A6CEE3"
|
| 161 |
+
},
|
| 162 |
+
"31": {
|
| 163 |
+
"name": "humerus_right",
|
| 164 |
+
"color": "#B2DF8A"
|
| 165 |
+
},
|
| 166 |
+
"32": {
|
| 167 |
+
"name": "scapula_left",
|
| 168 |
+
"color": "#1F78B4"
|
| 169 |
+
},
|
| 170 |
+
"33": {
|
| 171 |
+
"name": "scapula_right",
|
| 172 |
+
"color": "#33A02C"
|
| 173 |
+
},
|
| 174 |
+
"34": {
|
| 175 |
+
"name": "clavicula_left",
|
| 176 |
+
"color": "#BC80BD"
|
| 177 |
+
},
|
| 178 |
+
"35": {
|
| 179 |
+
"name": "clavicula_right",
|
| 180 |
+
"color": "#FFED6F"
|
| 181 |
+
},
|
| 182 |
+
"36": {
|
| 183 |
+
"name": "femur_left",
|
| 184 |
+
"color": "#CAB2D6"
|
| 185 |
+
},
|
| 186 |
+
"37": {
|
| 187 |
+
"name": "femur_right",
|
| 188 |
+
"color": "#FFFF99"
|
| 189 |
+
},
|
| 190 |
+
"38": {
|
| 191 |
+
"name": "hip_left",
|
| 192 |
+
"color": "#A6CEE3"
|
| 193 |
+
},
|
| 194 |
+
"39": {
|
| 195 |
+
"name": "hip_right",
|
| 196 |
+
"color": "#B2DF8A"
|
| 197 |
+
},
|
| 198 |
+
"40": {
|
| 199 |
+
"name": "gluteus_maximus_left",
|
| 200 |
+
"color": "#66A61E"
|
| 201 |
+
},
|
| 202 |
+
"41": {
|
| 203 |
+
"name": "gluteus_maximus_right",
|
| 204 |
+
"color": "#E6AB02"
|
| 205 |
+
},
|
| 206 |
+
"42": {
|
| 207 |
+
"name": "gluteus_medius_left",
|
| 208 |
+
"color": "#A6761D"
|
| 209 |
+
},
|
| 210 |
+
"43": {
|
| 211 |
+
"name": "gluteus_medius_right",
|
| 212 |
+
"color": "#666666"
|
| 213 |
+
},
|
| 214 |
+
"44": {
|
| 215 |
+
"name": "gluteus_minimus_left",
|
| 216 |
+
"color": "#7FC97F"
|
| 217 |
+
},
|
| 218 |
+
"45": {
|
| 219 |
+
"name": "gluteus_minimus_right",
|
| 220 |
+
"color": "#BEAED4"
|
| 221 |
+
},
|
| 222 |
+
"46": {
|
| 223 |
+
"name": "autochthon_left",
|
| 224 |
+
"color": "#1B9E77"
|
| 225 |
+
},
|
| 226 |
+
"47": {
|
| 227 |
+
"name": "autochthon_right",
|
| 228 |
+
"color": "#D95F02"
|
| 229 |
+
},
|
| 230 |
+
"48": {
|
| 231 |
+
"name": "iliopsoas_left",
|
| 232 |
+
"color": "#7570B3"
|
| 233 |
+
},
|
| 234 |
+
"49": {
|
| 235 |
+
"name": "iliopsoas_right",
|
| 236 |
+
"color": "#E7298A"
|
| 237 |
+
},
|
| 238 |
+
"50": {
|
| 239 |
+
"name": "brain",
|
| 240 |
+
"color": "#8DD3C7"
|
| 241 |
+
}
|
| 242 |
+
},
|
| 243 |
+
"patch_size": [
|
| 244 |
+
96,
|
| 245 |
+
128,
|
| 246 |
+
160
|
| 247 |
+
],
|
| 248 |
+
"vram_plan": {
|
| 249 |
+
"8": {
|
| 250 |
+
"patch_size": [
|
| 251 |
+
96,
|
| 252 |
+
128,
|
| 253 |
+
160
|
| 254 |
+
],
|
| 255 |
+
"batch_size": 4
|
| 256 |
+
},
|
| 257 |
+
"16": {
|
| 258 |
+
"patch_size": [
|
| 259 |
+
96,
|
| 260 |
+
128,
|
| 261 |
+
160
|
| 262 |
+
],
|
| 263 |
+
"batch_size": 8
|
| 264 |
+
},
|
| 265 |
+
"24": {
|
| 266 |
+
"patch_size": [
|
| 267 |
+
96,
|
| 268 |
+
128,
|
| 269 |
+
160
|
| 270 |
+
],
|
| 271 |
+
"batch_size": 12
|
| 272 |
+
}
|
| 273 |
}
|
| 274 |
+
}
|