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Update model card, app.json (patch size + VRAM plan) and inference configs

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Files changed (5) hide show
  1. CBCT/app.json +60 -25
  2. Finetune/app.json +60 -25
  3. MR/app.json +69 -32
  4. MR_CBCT/app.json +69 -32
  5. README.md +58 -3
CBCT/app.json CHANGED
@@ -4,37 +4,72 @@
4
  "description": "<b>Description:</b><br>Supervised whole-body CBCT-to-sCT model trained using SynthRAD 2023 and SynthRAD 2025 Task 2 datasets, distributed as five validation-fold checkpoints (<code>CV_0.pt</code> to <code>CV_4.pt</code>). Training pairs are aligned with IMPACTReg. The available Task 2 data include 291 patients from SynthRAD 2023 and 638 patients from SynthRAD 2025, for 929 patients in total.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>Whole-body paired CT-CBCT volumes come from SynthRAD 2023 Task 2 (<code>brain</code>, <code>pelvis</code>) and SynthRAD 2025 Task 2 (<code>AB</code>, <code>HN</code>, <code>TH</code>). Additional OOD evaluation cohorts are available for <code>AB_ood</code>, <code>HN_ood</code>, and <code>TH_ood</code>. Pairs are aligned with IMPACTReg, and the associated transform files are available at <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2023-impact-registration\">synthrad2023-impact-registration</a> and <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2025-impact-registration\">synthrad2025-impact-registration</a>. The files <code>CrossValidation_0.txt</code> to <code>CrossValidation_4.txt</code> correspond to validation folds for the distributed checkpoints, and <code>Validation.txt</code> contains 150 release-validation patients.<br><br><b>Release performance (CV overall, n=150):</b><br>Dice 0.758, MAE 53.55 HU, SSIM 0.939, PSNR 32.09 dB, SAM 13.70, Reg 1.04, Uncertainty 784.24.<br><br><b>Inference note:</b><br>The prediction pipeline supports test-time augmentation and writes an averaged <code>InferenceStack</code> output that can also be used for uncertainty estimation.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
  "tta": 2,
6
  "mc_dropout": false,
7
- "models": ["CV_0.pt", "CV_1.pt", "CV_2.pt", "CV_3.pt", "CV_4.pt"],
 
 
 
 
 
 
8
  "inputs": {
9
- "CBCT": {
10
- "display_name": "CBCT",
11
- "volume_type": "VOLUME",
12
- "required": true
13
- }
14
  },
15
-
16
  "outputs": {
17
- "sCT": {
18
- "display_name": "sCT",
19
- "volume_type": "VOLUME",
20
- "required": true
21
- }
22
- },
23
-
24
- "inputs_evaluations": {
25
- "Image": {
26
- "Evaluation.yml": {
27
- "sCT": {
28
  "display_name": "sCT",
29
  "volume_type": "VOLUME",
30
  "required": true
31
- },
32
- "CT": {
33
- "display_name": "CT",
34
- "volume_type": "VOLUME",
35
- "required": true
36
- }
37
  }
38
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
39
  }
40
  }
 
4
  "description": "<b>Description:</b><br>Supervised whole-body CBCT-to-sCT model trained using SynthRAD 2023 and SynthRAD 2025 Task 2 datasets, distributed as five validation-fold checkpoints (<code>CV_0.pt</code> to <code>CV_4.pt</code>). Training pairs are aligned with IMPACTReg. The available Task 2 data include 291 patients from SynthRAD 2023 and 638 patients from SynthRAD 2025, for 929 patients in total.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>Whole-body paired CT-CBCT volumes come from SynthRAD 2023 Task 2 (<code>brain</code>, <code>pelvis</code>) and SynthRAD 2025 Task 2 (<code>AB</code>, <code>HN</code>, <code>TH</code>). Additional OOD evaluation cohorts are available for <code>AB_ood</code>, <code>HN_ood</code>, and <code>TH_ood</code>. Pairs are aligned with IMPACTReg, and the associated transform files are available at <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2023-impact-registration\">synthrad2023-impact-registration</a> and <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2025-impact-registration\">synthrad2025-impact-registration</a>. The files <code>CrossValidation_0.txt</code> to <code>CrossValidation_4.txt</code> correspond to validation folds for the distributed checkpoints, and <code>Validation.txt</code> contains 150 release-validation patients.<br><br><b>Release performance (CV overall, n=150):</b><br>Dice 0.758, MAE 53.55 HU, SSIM 0.939, PSNR 32.09 dB, SAM 13.70, Reg 1.04, Uncertainty 784.24.<br><br><b>Inference note:</b><br>The prediction pipeline supports test-time augmentation and writes an averaged <code>InferenceStack</code> output that can also be used for uncertainty estimation.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
  "tta": 2,
6
  "mc_dropout": false,
7
+ "models": [
8
+ "CV_0.pt",
9
+ "CV_1.pt",
10
+ "CV_2.pt",
11
+ "CV_3.pt",
12
+ "CV_4.pt"
13
+ ],
14
  "inputs": {
15
+ "CBCT": {
16
+ "display_name": "CBCT",
17
+ "volume_type": "VOLUME",
18
+ "required": true
19
+ }
20
  },
 
21
  "outputs": {
22
+ "sCT": {
 
 
 
 
 
 
 
 
 
 
23
  "display_name": "sCT",
24
  "volume_type": "VOLUME",
25
  "required": true
 
 
 
 
 
 
26
  }
27
+ },
28
+ "inputs_evaluations": {
29
+ "Image": {
30
+ "Evaluation.yml": {
31
+ "sCT": {
32
+ "display_name": "sCT",
33
+ "volume_type": "VOLUME",
34
+ "required": true
35
+ },
36
+ "CT": {
37
+ "display_name": "CT",
38
+ "volume_type": "VOLUME",
39
+ "required": true
40
+ }
41
+ }
42
+ }
43
+ },
44
+ "patch_size": [
45
+ 1,
46
+ 512,
47
+ 512
48
+ ],
49
+ "vram_plan": {
50
+ "8": {
51
+ "patch_size": [
52
+ 1,
53
+ 512,
54
+ 512
55
+ ],
56
+ "batch_size": 16
57
+ },
58
+ "16": {
59
+ "patch_size": [
60
+ 1,
61
+ 512,
62
+ 512
63
+ ],
64
+ "batch_size": 28
65
+ },
66
+ "24": {
67
+ "patch_size": [
68
+ 1,
69
+ 512,
70
+ 512
71
+ ],
72
+ "batch_size": 48
73
+ }
74
  }
75
  }
Finetune/app.json CHANGED
@@ -4,37 +4,72 @@
4
  "description": "<b>Description:</b><br>Supervised whole-body CBCT-to-sCT model trained using SynthRAD 2023 and SynthRAD 2025 Task 2 datasets, distributed as five validation-fold checkpoints (<code>CV_0.pt</code> to <code>CV_4.pt</code>). Training pairs are aligned with IMPACTReg. The available Task 2 data include 291 patients from SynthRAD 2023 and 638 patients from SynthRAD 2025, for 929 patients in total.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>Whole-body paired CT-CBCT volumes come from SynthRAD 2023 Task 2 (<code>brain</code>, <code>pelvis</code>) and SynthRAD 2025 Task 2 (<code>AB</code>, <code>HN</code>, <code>TH</code>). Additional OOD evaluation cohorts are available for <code>AB_ood</code>, <code>HN_ood</code>, and <code>TH_ood</code>. Pairs are aligned with IMPACTReg, and the associated transform files are available at <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2023-impact-registration\">synthrad2023-impact-registration</a> and <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2025-impact-registration\">synthrad2025-impact-registration</a>. The files <code>CrossValidation_0.txt</code> to <code>CrossValidation_4.txt</code> correspond to validation folds for the distributed checkpoints, and <code>Validation.txt</code> contains 150 release-validation patients.<br><br><b>Release performance (CV overall, n=150):</b><br>Dice 0.758, MAE 53.55 HU, SSIM 0.939, PSNR 32.09 dB, SAM 13.70, Reg 1.04, Uncertainty 784.24.<br><br><b>Inference note:</b><br>The prediction pipeline supports test-time augmentation and writes an averaged <code>InferenceStack</code> output that can also be used for uncertainty estimation.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
  "tta": 2,
6
  "mc_dropout": false,
7
- "models": ["CV_0.pt", "CV_1.pt", "CV_2.pt", "CV_3.pt", "CV_4.pt"],
 
 
 
 
 
 
8
  "inputs": {
9
- "CBCT": {
10
- "display_name": "CBCT",
11
- "volume_type": "VOLUME",
12
- "required": true
13
- }
14
  },
15
-
16
  "outputs": {
17
- "sCT": {
18
- "display_name": "sCT",
19
- "volume_type": "VOLUME",
20
- "required": true
21
- }
22
- },
23
-
24
- "inputs_evaluations": {
25
- "Image": {
26
- "Evaluation.yml": {
27
- "sCT": {
28
  "display_name": "sCT",
29
  "volume_type": "VOLUME",
30
  "required": true
31
- },
32
- "CT": {
33
- "display_name": "CT",
34
- "volume_type": "VOLUME",
35
- "required": true
36
- }
37
  }
38
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
39
  }
40
  }
 
4
  "description": "<b>Description:</b><br>Supervised whole-body CBCT-to-sCT model trained using SynthRAD 2023 and SynthRAD 2025 Task 2 datasets, distributed as five validation-fold checkpoints (<code>CV_0.pt</code> to <code>CV_4.pt</code>). Training pairs are aligned with IMPACTReg. The available Task 2 data include 291 patients from SynthRAD 2023 and 638 patients from SynthRAD 2025, for 929 patients in total.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>Whole-body paired CT-CBCT volumes come from SynthRAD 2023 Task 2 (<code>brain</code>, <code>pelvis</code>) and SynthRAD 2025 Task 2 (<code>AB</code>, <code>HN</code>, <code>TH</code>). Additional OOD evaluation cohorts are available for <code>AB_ood</code>, <code>HN_ood</code>, and <code>TH_ood</code>. Pairs are aligned with IMPACTReg, and the associated transform files are available at <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2023-impact-registration\">synthrad2023-impact-registration</a> and <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2025-impact-registration\">synthrad2025-impact-registration</a>. The files <code>CrossValidation_0.txt</code> to <code>CrossValidation_4.txt</code> correspond to validation folds for the distributed checkpoints, and <code>Validation.txt</code> contains 150 release-validation patients.<br><br><b>Release performance (CV overall, n=150):</b><br>Dice 0.758, MAE 53.55 HU, SSIM 0.939, PSNR 32.09 dB, SAM 13.70, Reg 1.04, Uncertainty 784.24.<br><br><b>Inference note:</b><br>The prediction pipeline supports test-time augmentation and writes an averaged <code>InferenceStack</code> output that can also be used for uncertainty estimation.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
  "tta": 2,
6
  "mc_dropout": false,
7
+ "models": [
8
+ "CV_0.pt",
9
+ "CV_1.pt",
10
+ "CV_2.pt",
11
+ "CV_3.pt",
12
+ "CV_4.pt"
13
+ ],
14
  "inputs": {
15
+ "CBCT": {
16
+ "display_name": "CBCT",
17
+ "volume_type": "VOLUME",
18
+ "required": true
19
+ }
20
  },
 
21
  "outputs": {
22
+ "sCT": {
 
 
 
 
 
 
 
 
 
 
23
  "display_name": "sCT",
24
  "volume_type": "VOLUME",
25
  "required": true
 
 
 
 
 
 
26
  }
27
+ },
28
+ "inputs_evaluations": {
29
+ "Image": {
30
+ "Evaluation.yml": {
31
+ "sCT": {
32
+ "display_name": "sCT",
33
+ "volume_type": "VOLUME",
34
+ "required": true
35
+ },
36
+ "CT": {
37
+ "display_name": "CT",
38
+ "volume_type": "VOLUME",
39
+ "required": true
40
+ }
41
+ }
42
+ }
43
+ },
44
+ "patch_size": [
45
+ 1,
46
+ 512,
47
+ 512
48
+ ],
49
+ "vram_plan": {
50
+ "8": {
51
+ "patch_size": [
52
+ 1,
53
+ 512,
54
+ 512
55
+ ],
56
+ "batch_size": 16
57
+ },
58
+ "16": {
59
+ "patch_size": [
60
+ 1,
61
+ 512,
62
+ 512
63
+ ],
64
+ "batch_size": 28
65
+ },
66
+ "24": {
67
+ "patch_size": [
68
+ 1,
69
+ 512,
70
+ 512
71
+ ],
72
+ "batch_size": 48
73
+ }
74
  }
75
  }
MR/app.json CHANGED
@@ -1,38 +1,75 @@
1
  {
2
- "display_name": "Synthesis: MR",
3
- "short_description": "Supervised whole-body MR-to-sCT model for SynthRAD Task 1.<br><br><b>Training data:</b><br>805 paired CT-MR cases including OOD cohorts.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
4
- "description": "<b>Description:</b><br>Supervised whole-body MR-to-sCT model trained using SynthRAD 2023 and SynthRAD 2025 Task 1 datasets, distributed as five validation-fold checkpoints (<code>CV_0.pt</code> to <code>CV_4.pt</code>). Training pairs are aligned with IMPACTReg. The available Task 1 data include 317 patients from SynthRAD 2023, 410 patients from SynthRAD 2025, and 78 additional OOD paired CT-MR cases, for 805 training patients in total.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>Whole-body paired CT-MR volumes come from SynthRAD 2023 Task 1 (<code>brain</code>, <code>pelvis</code>), SynthRAD 2025 Task 1 (<code>AB</code>, <code>HN</code>, <code>TH</code>), and additional OOD cohorts including <code>CSIRO</code>, <code>GA</code>, <code>MR_Linac</code>, and <code>MR_Rennes</code>. Pairs are aligned with IMPACTReg, and the associated transform files are available at <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2023-impact-registration\">synthrad2023-impact-registration</a> and <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2025-impact-registration\">synthrad2025-impact-registration</a>. The files <code>CrossValidation_0.txt</code> to <code>CrossValidation_4.txt</code> correspond to validation folds for the distributed checkpoints, and <code>Validation.txt</code> contains 140 release-validation patients.<br><br><b>Release performance (CV overall, n=140):</b><br>Dice 0.698, MAE 67.49 HU, SSIM 0.959, PSNR 29.28 dB, SAM 21.98, Reg 0.622.<br><br><b>Inference note:</b><br>A body mask is estimated automatically at inference time and used to crop valid anatomy support before writing the output volume.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
- "tta": 2,
6
- "mc_dropout": false,
7
- "models": ["CV_0.pt", "CV_1.pt", "CV_2.pt", "CV_3.pt", "CV_4.pt"],
8
- "inputs": {
9
- "MR": {
10
- "display_name": "MR",
11
- "volume_type": "VOLUME",
12
- "required": true
13
- }
14
- },
15
- "outputs": {
16
- "sCT": {
17
- "display_name": "sCT",
18
- "volume_type": "VOLUME",
19
- "required": true
20
- }
21
- },
22
- "inputs_evaluations": {
23
- "Image": {
24
- "Evaluation.yml": {
25
  "sCT": {
26
- "display_name": "sCT",
27
- "volume_type": "VOLUME",
28
- "required": true
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
29
  },
30
- "CT": {
31
- "display_name": "CT",
32
- "volume_type": "VOLUME",
33
- "required": true
 
 
 
34
  }
35
- }
36
  }
37
- }
38
  }
 
1
  {
2
+ "display_name": "Synthesis: MR",
3
+ "short_description": "Supervised whole-body MR-to-sCT model for SynthRAD Task 1.<br><br><b>Training data:</b><br>805 paired CT-MR cases including OOD cohorts.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
4
+ "description": "<b>Description:</b><br>Supervised whole-body MR-to-sCT model trained using SynthRAD 2023 and SynthRAD 2025 Task 1 datasets, distributed as five validation-fold checkpoints (<code>CV_0.pt</code> to <code>CV_4.pt</code>). Training pairs are aligned with IMPACTReg. The available Task 1 data include 317 patients from SynthRAD 2023, 410 patients from SynthRAD 2025, and 78 additional OOD paired CT-MR cases, for 805 training patients in total.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>Whole-body paired CT-MR volumes come from SynthRAD 2023 Task 1 (<code>brain</code>, <code>pelvis</code>), SynthRAD 2025 Task 1 (<code>AB</code>, <code>HN</code>, <code>TH</code>), and additional OOD cohorts including <code>CSIRO</code>, <code>GA</code>, <code>MR_Linac</code>, and <code>MR_Rennes</code>. Pairs are aligned with IMPACTReg, and the associated transform files are available at <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2023-impact-registration\">synthrad2023-impact-registration</a> and <a href=\"https://huggingface.co/datasets/VBoussot/synthrad2025-impact-registration\">synthrad2025-impact-registration</a>. The files <code>CrossValidation_0.txt</code> to <code>CrossValidation_4.txt</code> correspond to validation folds for the distributed checkpoints, and <code>Validation.txt</code> contains 140 release-validation patients.<br><br><b>Release performance (CV overall, n=140):</b><br>Dice 0.698, MAE 67.49 HU, SSIM 0.959, PSNR 29.28 dB, SAM 21.98, Reg 0.622.<br><br><b>Inference note:</b><br>A body mask is estimated automatically at inference time and used to crop valid anatomy support before writing the output volume.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
+ "tta": 2,
6
+ "mc_dropout": false,
7
+ "models": [
8
+ "CV_0.pt",
9
+ "CV_1.pt",
10
+ "CV_2.pt",
11
+ "CV_3.pt",
12
+ "CV_4.pt"
13
+ ],
14
+ "inputs": {
15
+ "MR": {
16
+ "display_name": "MR",
17
+ "volume_type": "VOLUME",
18
+ "required": true
19
+ }
20
+ },
21
+ "outputs": {
 
 
 
22
  "sCT": {
23
+ "display_name": "sCT",
24
+ "volume_type": "VOLUME",
25
+ "required": true
26
+ }
27
+ },
28
+ "inputs_evaluations": {
29
+ "Image": {
30
+ "Evaluation.yml": {
31
+ "sCT": {
32
+ "display_name": "sCT",
33
+ "volume_type": "VOLUME",
34
+ "required": true
35
+ },
36
+ "CT": {
37
+ "display_name": "CT",
38
+ "volume_type": "VOLUME",
39
+ "required": true
40
+ }
41
+ }
42
+ }
43
+ },
44
+ "patch_size": [
45
+ 1,
46
+ 512,
47
+ 512
48
+ ],
49
+ "vram_plan": {
50
+ "8": {
51
+ "patch_size": [
52
+ 1,
53
+ 512,
54
+ 512
55
+ ],
56
+ "batch_size": 16
57
+ },
58
+ "16": {
59
+ "patch_size": [
60
+ 1,
61
+ 512,
62
+ 512
63
+ ],
64
+ "batch_size": 28
65
  },
66
+ "24": {
67
+ "patch_size": [
68
+ 1,
69
+ 512,
70
+ 512
71
+ ],
72
+ "batch_size": 48
73
  }
 
74
  }
 
75
  }
MR_CBCT/app.json CHANGED
@@ -1,38 +1,75 @@
1
  {
2
- "display_name": "Synthesis: MR/CBCT",
3
- "short_description": "Supervised whole-body MR/CBCT-to-sCT model.<br><br><b>Training data:</b><br>1734 paired cases from Task 1 + Task 2.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
4
- "description": "<b>Description:</b><br>Supervised whole-body synthesis model distributed as a single checkpoint (<code>CV_0.pt</code>) for MR/CBCT-style inputs. The model follows the same 2.5D synthesis setup used in the ImpactSynth family and produces an sCT volume from a single input volume after automatic body-mask estimation and intensity normalization.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>The model is trained on 1734 IMPACTReg-aligned paired synthesis cases spanning both Task 1 and Task 2 cohorts, combining MR and CBCT supervision in a unified synthesis setup.<br><br><b>Input handling:</b><br>The prediction pipeline accepts a single input volume exposed here as <code>MR or CBCT</code>, estimates a body mask automatically, resamples to the working resolution, applies normalization, and writes an averaged sCT output using test-time augmentation.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
- "tta": 2,
6
- "mc_dropout": false,
7
- "models": ["CV_0.pt", "CV_1.pt", "CV_2.pt", "CV_3.pt", "CV_4.pt"],
8
- "inputs": {
9
- "MR": {
10
- "display_name": "MR or CBCT",
11
- "volume_type": "VOLUME",
12
- "required": true
13
- }
14
- },
15
- "outputs": {
16
- "sCT": {
17
- "display_name": "sCT",
18
- "volume_type": "VOLUME",
19
- "required": true
20
- }
21
- },
22
- "inputs_evaluations": {
23
- "Image": {
24
- "Evaluation.yml": {
25
  "sCT": {
26
- "display_name": "sCT",
27
- "volume_type": "VOLUME",
28
- "required": true
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
29
  },
30
- "CT": {
31
- "display_name": "CT",
32
- "volume_type": "VOLUME",
33
- "required": true
 
 
 
34
  }
35
- }
36
  }
37
- }
38
  }
 
1
  {
2
+ "display_name": "Synthesis: MR/CBCT",
3
+ "short_description": "Supervised whole-body MR/CBCT-to-sCT model.<br><br><b>Training data:</b><br>1734 paired cases from Task 1 + Task 2.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
4
+ "description": "<b>Description:</b><br>Supervised whole-body synthesis model distributed as a single checkpoint (<code>CV_0.pt</code>) for MR/CBCT-style inputs. The model follows the same 2.5D synthesis setup used in the ImpactSynth family and produces an sCT volume from a single input volume after automatic body-mask estimation and intensity normalization.<br><br><b>Architecture and loss:</b><br>2.5D UNet++ with a ResNet34 encoder, trained with KonfAI and optimized using IMPACT-Synth, a perceptual loss leveraging semantic priors from <b>SAM 2.1-s</b>.<br><br><b>Training data:</b><br>The model is trained on 1734 IMPACTReg-aligned paired synthesis cases spanning both Task 1 and Task 2 cohorts, combining MR and CBCT supervision in a unified synthesis setup.<br><br><b>Input handling:</b><br>The prediction pipeline accepts a single input volume exposed here as <code>MR or CBCT</code>, estimates a body mask automatically, resamples to the working resolution, applies normalization, and writes an averaged sCT output using test-time augmentation.<br><br><b>How to cite:</b><br><cite>V. Boussot et al., <i>Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration</i>, arXiv preprint arXiv:2510.21358, <a href=\"https://doi.org/10.48550/arXiv.2510.21358\">https://doi.org/10.48550/arXiv.2510.21358</a>.</cite>",
5
+ "tta": 2,
6
+ "mc_dropout": false,
7
+ "models": [
8
+ "CV_0.pt",
9
+ "CV_1.pt",
10
+ "CV_2.pt",
11
+ "CV_3.pt",
12
+ "CV_4.pt"
13
+ ],
14
+ "inputs": {
15
+ "MR": {
16
+ "display_name": "MR or CBCT",
17
+ "volume_type": "VOLUME",
18
+ "required": true
19
+ }
20
+ },
21
+ "outputs": {
 
 
 
22
  "sCT": {
23
+ "display_name": "sCT",
24
+ "volume_type": "VOLUME",
25
+ "required": true
26
+ }
27
+ },
28
+ "inputs_evaluations": {
29
+ "Image": {
30
+ "Evaluation.yml": {
31
+ "sCT": {
32
+ "display_name": "sCT",
33
+ "volume_type": "VOLUME",
34
+ "required": true
35
+ },
36
+ "CT": {
37
+ "display_name": "CT",
38
+ "volume_type": "VOLUME",
39
+ "required": true
40
+ }
41
+ }
42
+ }
43
+ },
44
+ "patch_size": [
45
+ 1,
46
+ 512,
47
+ 512
48
+ ],
49
+ "vram_plan": {
50
+ "8": {
51
+ "patch_size": [
52
+ 1,
53
+ 512,
54
+ 512
55
+ ],
56
+ "batch_size": 16
57
+ },
58
+ "16": {
59
+ "patch_size": [
60
+ 1,
61
+ 512,
62
+ 512
63
+ ],
64
+ "batch_size": 28
65
  },
66
+ "24": {
67
+ "patch_size": [
68
+ 1,
69
+ 512,
70
+ 512
71
+ ],
72
+ "batch_size": 48
73
  }
 
74
  }
 
75
  }
README.md CHANGED
@@ -1,3 +1,58 @@
1
- ---
2
- license: apache-2.0
3
- ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ license: apache-2.0
3
+ library_name: konfai
4
+ pipeline_tag: image-to-image
5
+ tags:
6
+ - medical-imaging
7
+ - synthetic-ct
8
+ - image-synthesis
9
+ - radiotherapy
10
+ - mri
11
+ - cbct
12
+ - konfai
13
+ ---
14
+
15
+ # ImpactSynth β€” Synthetic CT (sCT) from MR / CBCT
16
+
17
+ Whole-body **synthetic CT** generation from **MR** or **CBCT**, built with
18
+ [**KonfAI**](https://github.com/vboussot/KonfAI). Top-ranking models from the
19
+ **[SynthRAD](https://synthrad2023.grand-challenge.org/)** challenge (Tasks 1 & 2).
20
+
21
+ ## 🧩 Models
22
+
23
+ | Model | Input | Output | Description | Ensemble |
24
+ |:--|:--|:--|:--|:--:|
25
+ | `MR` | MR | sCT | MR β†’ sCT (SynthRAD Task 1) | 5 |
26
+ | `CBCT` | CBCT | sCT | CBCT β†’ sCT (SynthRAD Task 2) | 5 |
27
+ | `MR_CBCT` | MR / CBCT | sCT | Joint MR/CBCT β†’ sCT | 5 |
28
+ | `Finetune` | CBCT | sCT | BICMAC fine-tuned CBCT β†’ sCT | 5 |
29
+
30
+ 2.5D UNet++ Β· patch `[1, 512, 512]` Β· 5-model ensemble.
31
+
32
+ ## πŸš€ Usage
33
+
34
+ ```bash
35
+ pip install impact_synth_konfai
36
+ impact-synth-konfai synthesize MR -i input_mr.nii.gz -o output/
37
+ ```
38
+
39
+ - **Generic runner:** `konfai-apps infer VBoussot/ImpactSynth:MR -i input_mr.nii.gz -o output/`
40
+ - **Interactive:** [**SlicerKonfAI**](https://github.com/vboussot/SlicerKonfAI) β€” the βš™ *Advanced* dialog overrides patch size and batch size.
41
+
42
+ ## ⚑ Performance & VRAM
43
+
44
+ Benchmarked on an **NVIDIA RTX PRO 5000 (24 GB)**. The batch size is **auto-selected from your free GPU VRAM**.
45
+
46
+ | Free VRAM | Batch (auto) | Peak VRAM |
47
+ |:--|:--|:--|
48
+ | 8 GB | 16 | ~7.6 GB |
49
+ | 16 GB | 28 | ~15 GB |
50
+ | 24 GB | 48 | ~21.7 GB |
51
+
52
+ β‰ˆ **25 s / case** on the benchmark volume (scales with case size). Override with `--patch-size` / `--batch-size`.
53
+
54
+ ## πŸ”— Links & Citation
55
+
56
+ - 🧠 **KonfAI:** [github.com/vboussot/KonfAI](https://github.com/vboussot/KonfAI)
57
+ - πŸ“¦ **PyPI:** [impact_synth_konfai](https://pypi.org/project/impact_synth_konfai/)
58
+ - πŸ“„ **Paper:** [arXiv:2510.21358](https://arxiv.org/abs/2510.21358)