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ImpactReg

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1 Parent(s): 6ffd54f

Each preset names its demo sample, a case of the fidopt corpus

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Files changed (12) hide show
  1. ConvexAdam_Coarse/app.json +10 -1
  2. ConvexAdam_Composite/app.json +10 -1
  3. ConvexAdam_IMPACT_CBCT/app.json +10 -1
  4. ConvexAdam_IMPACT_MRCT/app.json +14 -1
  5. Elastix_IMPACT_Jacobian/app.json +10 -1
  6. Elastix_IMPACT_Static/app.json +10 -1
  7. FireANTs_Anatomix/app.json +10 -1
  8. FireANTs_IMPACT/app.json +10 -1
  9. FireANTs_IMPACT_MRCT/app.json +14 -1
  10. FireANTs_SyN/app.json +10 -1
  11. Generic_Rigid/app.json +10 -1
  12. Generic_Rigid_BSpline/app.json +10 -1
ConvexAdam_Coarse/app.json CHANGED
@@ -97,5 +97,14 @@
97
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
98
  "filename": "MIND/R1D2_3D.pt"
99
  }
100
- ]
 
 
 
 
 
 
 
 
 
101
  }
 
97
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
98
  "filename": "MIND/R1D2_3D.pt"
99
  }
100
+ ],
101
+ "sample": {
102
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
103
+ "inputs": {
104
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
105
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
106
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
107
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
108
+ }
109
+ }
110
  }
ConvexAdam_Composite/app.json CHANGED
@@ -100,5 +100,14 @@
100
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
101
  "filename": "MIND/R1D2_3D.pt"
102
  }
103
- ]
 
 
 
 
 
 
 
 
 
104
  }
 
100
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
101
  "filename": "MIND/R1D2_3D.pt"
102
  }
103
+ ],
104
+ "sample": {
105
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
106
+ "inputs": {
107
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
108
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
109
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
110
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
111
+ }
112
+ }
113
  }
ConvexAdam_IMPACT_CBCT/app.json CHANGED
@@ -105,5 +105,14 @@
105
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
106
  "filename": "TS/M730.pt"
107
  }
108
- ]
 
 
 
 
 
 
 
 
 
109
  }
 
105
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
106
  "filename": "TS/M730.pt"
107
  }
108
+ ],
109
+ "sample": {
110
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
111
+ "inputs": {
112
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
113
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
114
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
115
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
116
+ }
117
+ }
118
  }
ConvexAdam_IMPACT_MRCT/app.json CHANGED
@@ -102,5 +102,18 @@
102
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
103
  "filename": "TS/M730.pt"
104
  }
105
- ]
 
 
 
 
 
 
 
 
 
 
 
 
 
106
  }
 
102
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
103
  "filename": "TS/M730.pt"
104
  }
105
+ ],
106
+ "sample": {
107
+ "label": "An abdominal MR (fixed) and CT (moving) of one patient, with ROI masks and four organs labelled (fidopt L2R_AbdomenMRCT case_0001, Learn2Reg 2021; CT: TCIA TCGA, CC BY 3.0; MR: CHAOS, CC BY-NC-SA 4.0)",
108
+ "inputs": {
109
+ "Fixed": "L2R_AbdomenMRCT/development/case_0001/fixed.ome.zarr",
110
+ "Moving": "L2R_AbdomenMRCT/development/case_0001/moving.ome.zarr",
111
+ "FixedMask": "L2R_AbdomenMRCT/development/case_0001/fixed_mask.ome.zarr",
112
+ "MovingMask": "L2R_AbdomenMRCT/development/case_0001/moving_mask.ome.zarr"
113
+ },
114
+ "references": {
115
+ "FixedSeg": "L2R_AbdomenMRCT/development/case_0001/truth/fixed_labels.ome.zarr",
116
+ "MovingSeg": "L2R_AbdomenMRCT/development/case_0001/truth/moving_labels.ome.zarr"
117
+ }
118
+ }
119
  }
Elastix_IMPACT_Jacobian/app.json CHANGED
@@ -97,5 +97,14 @@
97
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
98
  "filename": "TS/M730.pt"
99
  }
100
- ]
 
 
 
 
 
 
 
 
 
101
  }
 
97
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
98
  "filename": "TS/M730.pt"
99
  }
100
+ ],
101
+ "sample": {
102
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
103
+ "inputs": {
104
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
105
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
106
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
107
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
108
+ }
109
+ }
110
  }
Elastix_IMPACT_Static/app.json CHANGED
@@ -102,5 +102,14 @@
102
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
103
  "filename": "TS/M730.pt"
104
  }
105
- ]
 
 
 
 
 
 
 
 
 
106
  }
 
102
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
103
  "filename": "TS/M730.pt"
104
  }
105
+ ],
106
+ "sample": {
107
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
108
+ "inputs": {
109
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
110
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
111
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
112
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
113
+ }
114
+ }
115
  }
FireANTs_Anatomix/app.json CHANGED
@@ -108,5 +108,14 @@
108
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
109
  "filename": "MIND/R1D2_3D.pt"
110
  }
111
- ]
 
 
 
 
 
 
 
 
 
112
  }
 
108
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
109
  "filename": "MIND/R1D2_3D.pt"
110
  }
111
+ ],
112
+ "sample": {
113
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
114
+ "inputs": {
115
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
116
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
117
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
118
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
119
+ }
120
+ }
121
  }
FireANTs_IMPACT/app.json CHANGED
@@ -103,5 +103,14 @@
103
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
104
  "filename": "TS/M291.pt"
105
  }
106
- ]
 
 
 
 
 
 
 
 
 
107
  }
 
103
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
104
  "filename": "TS/M291.pt"
105
  }
106
+ ],
107
+ "sample": {
108
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
109
+ "inputs": {
110
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
111
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
112
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
113
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
114
+ }
115
+ }
116
  }
FireANTs_IMPACT_MRCT/app.json CHANGED
@@ -108,5 +108,18 @@
108
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
109
  "filename": "MIND/R1D2_3D.pt"
110
  }
111
- ]
 
 
 
 
 
 
 
 
 
 
 
 
 
112
  }
 
108
  "revision": "47ffad660e67cebbac8d74aecf0fa181c5dac042",
109
  "filename": "MIND/R1D2_3D.pt"
110
  }
111
+ ],
112
+ "sample": {
113
+ "label": "An abdominal MR (fixed) and CT (moving) of one patient, with ROI masks and four organs labelled (fidopt L2R_AbdomenMRCT case_0001, Learn2Reg 2021; CT: TCIA TCGA, CC BY 3.0; MR: CHAOS, CC BY-NC-SA 4.0)",
114
+ "inputs": {
115
+ "Fixed": "L2R_AbdomenMRCT/development/case_0001/fixed.ome.zarr",
116
+ "Moving": "L2R_AbdomenMRCT/development/case_0001/moving.ome.zarr",
117
+ "FixedMask": "L2R_AbdomenMRCT/development/case_0001/fixed_mask.ome.zarr",
118
+ "MovingMask": "L2R_AbdomenMRCT/development/case_0001/moving_mask.ome.zarr"
119
+ },
120
+ "references": {
121
+ "FixedSeg": "L2R_AbdomenMRCT/development/case_0001/truth/fixed_labels.ome.zarr",
122
+ "MovingSeg": "L2R_AbdomenMRCT/development/case_0001/truth/moving_labels.ome.zarr"
123
+ }
124
+ }
125
  }
FireANTs_SyN/app.json CHANGED
@@ -96,5 +96,14 @@
96
  "requirements_no_deps": [
97
  "fireants>=1.5,<1.6"
98
  ],
99
- "ram_bytes_per_voxel": 1550
 
 
 
 
 
 
 
 
 
100
  }
 
96
  "requirements_no_deps": [
97
  "fireants>=1.5,<1.6"
98
  ],
99
+ "ram_bytes_per_voxel": 1550,
100
+ "sample": {
101
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
102
+ "inputs": {
103
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
104
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
105
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
106
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
107
+ }
108
+ }
109
  }
Generic_Rigid/app.json CHANGED
@@ -90,5 +90,14 @@
90
  "tiling": {
91
  "global": "Prediction.yml"
92
  },
93
- "ram_bytes_per_voxel": 550
 
 
 
 
 
 
 
 
 
94
  }
 
90
  "tiling": {
91
  "global": "Prediction.yml"
92
  },
93
+ "ram_bytes_per_voxel": 550,
94
+ "sample": {
95
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
96
+ "inputs": {
97
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
98
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
99
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
100
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
101
+ }
102
+ }
103
  }
Generic_Rigid_BSpline/app.json CHANGED
@@ -93,5 +93,14 @@
93
  "tile_vram_bytes_per_voxel": 120,
94
  "tile_ram_bytes_per_voxel": 550
95
  },
96
- "ram_bytes_per_voxel": 550
 
 
 
 
 
 
 
 
 
97
  }
 
93
  "tile_vram_bytes_per_voxel": 120,
94
  "tile_ram_bytes_per_voxel": 550
95
  },
96
+ "ram_bytes_per_voxel": 550,
97
+ "sample": {
98
+ "label": "Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, with their masks (fidopt L2R_NLST 0014_0000_0014_0001, Learn2Reg 2022-23; NLST, TCIA, CC BY 4.0)",
99
+ "inputs": {
100
+ "Fixed": "L2R_NLST/development/0014_0000_0014_0001/fixed.ome.zarr",
101
+ "Moving": "L2R_NLST/development/0014_0000_0014_0001/moving.ome.zarr",
102
+ "FixedMask": "L2R_NLST/development/0014_0000_0014_0001/fixed_mask.ome.zarr",
103
+ "MovingMask": "L2R_NLST/development/0014_0000_0014_0001/moving_mask.ome.zarr"
104
+ }
105
+ }
106
  }