File size: 16,326 Bytes
49cb0f1
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
{
    "dataset_name": "Dataset001_KiTS2023",
    "plans_name": "nnUNetResEncUNetMPlans",
    "original_median_spacing_after_transp": [
        3.0,
        0.78125,
        0.78125
    ],
    "original_median_shape_after_transp": [
        104,
        512,
        512
    ],
    "image_reader_writer": "NibabelIOWithReorient",
    "transpose_forward": [
        0,
        1,
        2
    ],
    "transpose_backward": [
        0,
        1,
        2
    ],
    "configurations": {
        "2d": {
            "data_identifier": "nnUNetPlans_2d",
            "preprocessor_name": "DefaultPreprocessor",
            "batch_size": 12,
            "patch_size": [
                512,
                512
            ],
            "median_image_size_in_voxels": [
                512.0,
                512.0
            ],
            "spacing": [
                0.78125,
                0.78125
            ],
            "normalization_schemes": [
                "CTNormalization"
            ],
            "use_mask_for_norm": [
                false
            ],
            "resampling_fn_data": "resample_data_or_seg_to_shape",
            "resampling_fn_seg": "resample_data_or_seg_to_shape",
            "resampling_fn_data_kwargs": {
                "is_seg": false,
                "order": 3,
                "order_z": 0,
                "force_separate_z": null
            },
            "resampling_fn_seg_kwargs": {
                "is_seg": true,
                "order": 1,
                "order_z": 0,
                "force_separate_z": null
            },
            "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
            "resampling_fn_probabilities_kwargs": {
                "is_seg": false,
                "order": 1,
                "order_z": 0,
                "force_separate_z": null
            },
            "architecture": {
                "network_class_name": "dynamic_network_architectures.architectures.unet.ResidualEncoderUNet",
                "arch_kwargs": {
                    "n_stages": 8,
                    "features_per_stage": [
                        32,
                        64,
                        128,
                        256,
                        512,
                        512,
                        512,
                        512
                    ],
                    "conv_op": "torch.nn.modules.conv.Conv2d",
                    "kernel_sizes": [
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ],
                        [
                            3,
                            3
                        ]
                    ],
                    "strides": [
                        [
                            1,
                            1
                        ],
                        [
                            2,
                            2
                        ],
                        [
                            2,
                            2
                        ],
                        [
                            2,
                            2
                        ],
                        [
                            2,
                            2
                        ],
                        [
                            2,
                            2
                        ],
                        [
                            2,
                            2
                        ],
                        [
                            2,
                            2
                        ]
                    ],
                    "n_blocks_per_stage": [
                        1,
                        3,
                        4,
                        6,
                        6,
                        6,
                        6,
                        6
                    ],
                    "n_conv_per_stage_decoder": [
                        1,
                        1,
                        1,
                        1,
                        1,
                        1,
                        1
                    ],
                    "conv_bias": true,
                    "norm_op": "torch.nn.modules.instancenorm.InstanceNorm2d",
                    "norm_op_kwargs": {
                        "eps": 1e-05,
                        "affine": true
                    },
                    "dropout_op": null,
                    "dropout_op_kwargs": null,
                    "nonlin": "torch.nn.LeakyReLU",
                    "nonlin_kwargs": {
                        "inplace": true
                    }
                },
                "_kw_requires_import": [
                    "conv_op",
                    "norm_op",
                    "dropout_op",
                    "nonlin"
                ]
            },
            "batch_dice": true
        },
        "3d_lowres": {
            "data_identifier": "nnUNetResEncUNetMPlans_3d_lowres",
            "preprocessor_name": "DefaultPreprocessor",
            "batch_size": 2,
            "patch_size": [
                128,
                128,
                128
            ],
            "median_image_size_in_voxels": [
                177,
                217,
                217
            ],
            "spacing": [
                2.3565655060093813,
                1.841066801569828,
                1.841066801569828
            ],
            "normalization_schemes": [
                "CTNormalization"
            ],
            "use_mask_for_norm": [
                false
            ],
            "resampling_fn_data": "resample_data_or_seg_to_shape",
            "resampling_fn_seg": "resample_data_or_seg_to_shape",
            "resampling_fn_data_kwargs": {
                "is_seg": false,
                "order": 3,
                "order_z": 0,
                "force_separate_z": null
            },
            "resampling_fn_seg_kwargs": {
                "is_seg": true,
                "order": 1,
                "order_z": 0,
                "force_separate_z": null
            },
            "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
            "resampling_fn_probabilities_kwargs": {
                "is_seg": false,
                "order": 1,
                "order_z": 0,
                "force_separate_z": null
            },
            "architecture": {
                "network_class_name": "dynamic_network_architectures.architectures.unet.ResidualEncoderUNet",
                "arch_kwargs": {
                    "n_stages": 6,
                    "features_per_stage": [
                        32,
                        64,
                        128,
                        256,
                        320,
                        320
                    ],
                    "conv_op": "torch.nn.modules.conv.Conv3d",
                    "kernel_sizes": [
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ]
                    ],
                    "strides": [
                        [
                            1,
                            1,
                            1
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ]
                    ],
                    "n_blocks_per_stage": [
                        1,
                        3,
                        4,
                        6,
                        6,
                        6
                    ],
                    "n_conv_per_stage_decoder": [
                        1,
                        1,
                        1,
                        1,
                        1
                    ],
                    "conv_bias": true,
                    "norm_op": "torch.nn.modules.instancenorm.InstanceNorm3d",
                    "norm_op_kwargs": {
                        "eps": 1e-05,
                        "affine": true
                    },
                    "dropout_op": null,
                    "dropout_op_kwargs": null,
                    "nonlin": "torch.nn.LeakyReLU",
                    "nonlin_kwargs": {
                        "inplace": true
                    }
                },
                "_kw_requires_import": [
                    "conv_op",
                    "norm_op",
                    "dropout_op",
                    "nonlin"
                ]
            },
            "batch_dice": false,
            "next_stage": "3d_cascade_fullres"
        },
        "3d_fullres": {
            "data_identifier": "nnUNetPlans_3d_fullres",
            "preprocessor_name": "DefaultPreprocessor",
            "batch_size": 2,
            "patch_size": [
                128,
                128,
                128
            ],
            "median_image_size_in_voxels": [
                417.0,
                512.0,
                512.0
            ],
            "spacing": [
                1.0,
                0.78125,
                0.78125
            ],
            "normalization_schemes": [
                "CTNormalization"
            ],
            "use_mask_for_norm": [
                false
            ],
            "resampling_fn_data": "resample_data_or_seg_to_shape",
            "resampling_fn_seg": "resample_data_or_seg_to_shape",
            "resampling_fn_data_kwargs": {
                "is_seg": false,
                "order": 3,
                "order_z": 0,
                "force_separate_z": null
            },
            "resampling_fn_seg_kwargs": {
                "is_seg": true,
                "order": 1,
                "order_z": 0,
                "force_separate_z": null
            },
            "resampling_fn_probabilities": "resample_data_or_seg_to_shape",
            "resampling_fn_probabilities_kwargs": {
                "is_seg": false,
                "order": 1,
                "order_z": 0,
                "force_separate_z": null
            },
            "architecture": {
                "network_class_name": "dynamic_network_architectures.architectures.unet.ResidualEncoderUNet",
                "arch_kwargs": {
                    "n_stages": 6,
                    "features_per_stage": [
                        32,
                        64,
                        128,
                        256,
                        320,
                        320
                    ],
                    "conv_op": "torch.nn.modules.conv.Conv3d",
                    "kernel_sizes": [
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ],
                        [
                            3,
                            3,
                            3
                        ]
                    ],
                    "strides": [
                        [
                            1,
                            1,
                            1
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ],
                        [
                            2,
                            2,
                            2
                        ]
                    ],
                    "n_blocks_per_stage": [
                        1,
                        3,
                        4,
                        6,
                        6,
                        6
                    ],
                    "n_conv_per_stage_decoder": [
                        1,
                        1,
                        1,
                        1,
                        1
                    ],
                    "conv_bias": true,
                    "norm_op": "torch.nn.modules.instancenorm.InstanceNorm3d",
                    "norm_op_kwargs": {
                        "eps": 1e-05,
                        "affine": true
                    },
                    "dropout_op": null,
                    "dropout_op_kwargs": null,
                    "nonlin": "torch.nn.LeakyReLU",
                    "nonlin_kwargs": {
                        "inplace": true
                    }
                },
                "_kw_requires_import": [
                    "conv_op",
                    "norm_op",
                    "dropout_op",
                    "nonlin"
                ]
            },
            "batch_dice": true
        },
        "3d_cascade_fullres": {
            "inherits_from": "3d_fullres",
            "previous_stage": "3d_lowres"
        }
    },
    "experiment_planner_used": "nnUNetPlannerResEncM",
    "label_manager": "LabelManager",
    "foreground_intensity_properties_per_channel": {
        "0": {
            "max": 3071.0,
            "mean": 103.13614654541016,
            "median": 102.0,
            "min": -1021.0,
            "percentile_00_5": -58.0,
            "percentile_99_5": 302.0,
            "std": 73.3431396484375
        }
    }
}