Add files using upload-large-folder tool

.gitattributes

@@ -35,3 +35,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
 nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all/progress.png filter=lfs diff=lfs merge=lfs -text
 nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/progress.png filter=lfs diff=lfs merge=lfs -text
+Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all/progress.png filter=lfs diff=lfs merge=lfs -text
+Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/progress.png filter=lfs diff=lfs merge=lfs -text

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/dataset.json

@@ -0,0 +1,34 @@
+{
+    "name": "JHH-Train-test",
+    "description": "3151 cases for training; 1958 cases for testing",
+    "reference": "ScaleMAI",
+    "licence": "CC-BY-SA 4.0",
+    "relase": "1.0 10/28/2024",
+    "tensorImageSize": "3D",
+    "labels": {
+        "background": 0,
+        "aorta": 1,
+        "adrenal_gland_left": 2,
+        "adrenal_gland_right": 3,
+        "celiac_aa": 4,
+        "colon": 5,
+        "duodenum": 6,
+        "gall_bladder": 7,
+        "postcava": 8,
+        "kidney_left": 9,
+        "kidney_right": 10,
+        "liver": 11,
+        "pancreas": 12,
+        "superior_mesenteric_artery": 13,
+        "intestine": 14,
+        "spleen": 15,
+        "renal_vein_left": 16,
+        "renal_vein_right": 17
+    },
+    "numTraining": 3151,
+    "numTest": 1958,
+    "file_ending": ".nii.gz",
+    "channel_names": {
+        "0": "CT"
+    }
+}

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all/checkpoint_best.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:54a721b665bc283aefb9aad70ecc34f773fb703b149e3cbe67280fbbe68ad1f9
+size 1122159090

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all/checkpoint_final.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:84df811db038623efb6cb3993e5271f688d2b57ab44a9ec45a545acf7f418a38
+size 1122162406

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all/debug.json

@@ -0,0 +1,53 @@
+{
+    "_best_ema": "None",
+    "batch_size": "22",
+    "configuration_manager": "{'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 22, 'patch_size': [640, 640], 'median_image_size_in_voxels': [613.0, 513.0], 'spacing': [0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, 'nonlin': 'torch.nn.LeakyReLU', 'nonlin_kwargs': {'inplace': True}}, '_kw_requires_import': ['conv_op', 'norm_op', 'dropout_op', 'nonlin']}, 'batch_dice': True}",
+    "configuration_name": "2d",
+    "cudnn_version": 90100,
+    "current_epoch": "0",
+    "dataloader_train": "<batchgenerators.dataloading.nondet_multi_threaded_augmenter.NonDetMultiThreadedAugmenter object at 0x7fe6c1af0970>",
+    "dataloader_train.generator": "<nnunetv2.training.dataloading.data_loader_2d.nnUNetDataLoader2D object at 0x7fe6c1af0280>",
+    "dataloader_train.num_processes": "12",
+    "dataloader_train.transform": "None",
+    "dataloader_val": "<batchgenerators.dataloading.nondet_multi_threaded_augmenter.NonDetMultiThreadedAugmenter object at 0x7fe6c1af0a00>",
+    "dataloader_val.generator": "<nnunetv2.training.dataloading.data_loader_2d.nnUNetDataLoader2D object at 0x7fe6c1af02e0>",
+    "dataloader_val.num_processes": "6",
+    "dataloader_val.transform": "None",
+    "dataset_json": "{'name': 'JHH-Train-test', 'description': '3151 cases for training; 1958 cases for testing', 'reference': 'ScaleMAI', 'licence': 'CC-BY-SA 4.0', 'relase': '1.0 10/28/2024', 'tensorImageSize': '3D', 'labels': {'background': 0, 'aorta': 1, 'adrenal_gland_left': 2, 'adrenal_gland_right': 3, 'celiac_aa': 4, 'colon': 5, 'duodenum': 6, 'gall_bladder': 7, 'postcava': 8, 'kidney_left': 9, 'kidney_right': 10, 'liver': 11, 'pancreas': 12, 'superior_mesenteric_artery': 13, 'intestine': 14, 'spleen': 15, 'renal_vein_left': 16, 'renal_vein_right': 17}, 'numTraining': 3151, 'numTest': 1958, 'file_ending': '.nii.gz', 'channel_names': {'0': 'CT'}}",
+    "device": "cuda:0",
+    "disable_checkpointing": "False",
+    "enable_deep_supervision": "True",
+    "fold": "all",
+    "folder_with_segs_from_previous_stage": "None",
+    "gpu_name": "NVIDIA TITAN RTX",
+    "grad_scaler": "<torch.cuda.amp.grad_scaler.GradScaler object at 0x7fe6c1b8af70>",
+    "hostname": "ccvl18",
+    "inference_allowed_mirroring_axes": "(0, 1)",
+    "initial_lr": "0.01",
+    "is_cascaded": "False",
+    "is_ddp": "False",
+    "label_manager": "<nnunetv2.utilities.label_handling.label_handling.LabelManager object at 0x7fe796922f40>",
+    "local_rank": "0",
+    "log_file": "/mnt/T9/tlin67/nnUNet_results/Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all/training_log_2025_11_10_22_36_21.txt",
+    "logger": "<nnunetv2.training.logging.nnunet_logger.nnUNetLogger object at 0x7fe6c1b8aeb0>",
+    "loss": "DeepSupervisionWrapper(\n  (loss): DC_and_CE_loss(\n    (ce): RobustCrossEntropyLoss()\n    (dc): OptimizedModule(\n      (_orig_mod): MemoryEfficientSoftDiceLoss()\n    )\n  )\n)",
+    "lr_scheduler": "<nnunetv2.training.lr_scheduler.polylr.PolyLRScheduler object at 0x7fe6b7f10f40>",
+    "my_init_kwargs": "{'plans': {'dataset_name': 'Dataset809_AbdomenAtlasF17', 'plans_name': 'nnUNetResEncUNetLPlans', 'original_median_spacing_after_transp': [0.7109375, 0.5, 0.7109375], 'original_median_shape_after_transp': [512, 608, 512], 'image_reader_writer': 'SimpleITKIO', 'transpose_forward': [1, 0, 2], 'transpose_backward': [1, 0, 2], 'configurations': {'2d': {'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 22, 'patch_size': [640, 640], 'median_image_size_in_voxels': [613.0, 513.0], 'spacing': [0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetResEncUNetLPlans_3d_lowres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': [160, 224, 192], 'median_image_size_in_voxels': [283, 339, 284], 'spacing': [1.284032205897787, 0.9030556173347075, 1.284032205897787], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': [160, 224, 192], 'median_image_size_in_voxels': [512.0, 613.0, 513.0], 'spacing': [0.7109375, 0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetPlannerResEncL', 'label_manager': 'LabelManager', 'foreground_intensity_properties_per_channel': {'0': {'max': 1000.0, 'mean': 39.68027877807617, 'median': 71.0, 'min': -1000.0, 'percentile_00_5': -1000.0, 'percentile_99_5': 379.0, 'std': 192.4669952392578}}}, 'configuration': '2d', 'fold': 'all', 'dataset_json': {'name': 'JHH-Train-test', 'description': '3151 cases for training; 1958 cases for testing', 'reference': 'ScaleMAI', 'licence': 'CC-BY-SA 4.0', 'relase': '1.0 10/28/2024', 'tensorImageSize': '3D', 'labels': {'background': 0, 'aorta': 1, 'adrenal_gland_left': 2, 'adrenal_gland_right': 3, 'celiac_aa': 4, 'colon': 5, 'duodenum': 6, 'gall_bladder': 7, 'postcava': 8, 'kidney_left': 9, 'kidney_right': 10, 'liver': 11, 'pancreas': 12, 'superior_mesenteric_artery': 13, 'intestine': 14, 'spleen': 15, 'renal_vein_left': 16, 'renal_vein_right': 17}, 'numTraining': 3151, 'numTest': 1958, 'file_ending': '.nii.gz', 'channel_names': {'0': 'CT'}}, 'unpack_dataset': True, 'device': device(type='cuda')}",
+    "network": "OptimizedModule",
+    "num_epochs": "1000",
+    "num_input_channels": "1",
+    "num_iterations_per_epoch": "250",
+    "num_val_iterations_per_epoch": "50",
+    "optimizer": "SGD (\nParameter Group 0\n    dampening: 0\n    differentiable: False\n    foreach: None\n    fused: None\n    initial_lr: 0.01\n    lr: 0.01\n    maximize: False\n    momentum: 0.99\n    nesterov: True\n    weight_decay: 3e-05\n)",
+    "output_folder": "/mnt/T9/tlin67/nnUNet_results/Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/fold_all",
+    "output_folder_base": "/mnt/T9/tlin67/nnUNet_results/Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d",
+    "oversample_foreground_percent": "0.33",
+    "plans_manager": "{'dataset_name': 'Dataset809_AbdomenAtlasF17', 'plans_name': 'nnUNetResEncUNetLPlans', 'original_median_spacing_after_transp': [0.7109375, 0.5, 0.7109375], 'original_median_shape_after_transp': [512, 608, 512], 'image_reader_writer': 'SimpleITKIO', 'transpose_forward': [1, 0, 2], 'transpose_backward': [1, 0, 2], 'configurations': {'2d': {'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 22, 'patch_size': [640, 640], 'median_image_size_in_voxels': [613.0, 513.0], 'spacing': [0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetResEncUNetLPlans_3d_lowres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': [160, 224, 192], 'median_image_size_in_voxels': [283, 339, 284], 'spacing': [1.284032205897787, 0.9030556173347075, 1.284032205897787], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': [160, 224, 192], 'median_image_size_in_voxels': [512.0, 613.0, 513.0], 'spacing': [0.7109375, 0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetPlannerResEncL', 'label_manager': 'LabelManager', 'foreground_intensity_properties_per_channel': {'0': {'max': 1000.0, 'mean': 39.68027877807617, 'median': 71.0, 'min': -1000.0, 'percentile_00_5': -1000.0, 'percentile_99_5': 379.0, 'std': 192.4669952392578}}}",
+    "preprocessed_dataset_folder": "/mnt/T9/tlin67/Dataset_preprocessed/Dataset809_AbdomenAtlasF17/nnUNetPlans_2d",
+    "preprocessed_dataset_folder_base": "/mnt/T9/tlin67/Dataset_preprocessed/Dataset809_AbdomenAtlasF17",
+    "save_every": "50",
+    "torch_version": "2.4.0+cu121",
+    "unpack_dataset": "True",
+    "was_initialized": "True",
+    "weight_decay": "3e-05"
+}

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__2d/plans.json

@@ -0,0 +1,532 @@
+{
+    "dataset_name": "Dataset809_AbdomenAtlasF17",
+    "plans_name": "nnUNetResEncUNetLPlans",
+    "original_median_spacing_after_transp": [
+        0.7109375,
+        0.5,
+        0.7109375
+    ],
+    "original_median_shape_after_transp": [
+        512,
+        608,
+        512
+    ],
+    "image_reader_writer": "SimpleITKIO",
+    "transpose_forward": [
+        1,
+        0,
+        2
+    ],
+    "transpose_backward": [
+        1,
+        0,
+        2
+    ],
+    "configurations": {
+        "2d": {
+            "data_identifier": "nnUNetPlans_2d",
+            "preprocessor_name": "DefaultPreprocessor",
+            "batch_size": 22,
+            "patch_size": [
+                640,
+                640
+            ],
+            "median_image_size_in_voxels": [
+                613.0,
+                513.0
+            ],
+            "spacing": [
+                0.5,
+                0.7109375
+            ],
+            "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": "nnUNetResEncUNetLPlans_3d_lowres",
+            "preprocessor_name": "DefaultPreprocessor",
+            "batch_size": 2,
+            "patch_size": [
+                160,
+                224,
+                192
+            ],
+            "median_image_size_in_voxels": [
+                283,
+                339,
+                284
+            ],
+            "spacing": [
+                1.284032205897787,
+                0.9030556173347075,
+                1.284032205897787
+            ],
+            "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": [
+                160,
+                224,
+                192
+            ],
+            "median_image_size_in_voxels": [
+                512.0,
+                613.0,
+                513.0
+            ],
+            "spacing": [
+                0.7109375,
+                0.5,
+                0.7109375
+            ],
+            "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": "nnUNetPlannerResEncL",
+    "label_manager": "LabelManager",
+    "foreground_intensity_properties_per_channel": {
+        "0": {
+            "max": 1000.0,
+            "mean": 39.68027877807617,
+            "median": 71.0,
+            "min": -1000.0,
+            "percentile_00_5": -1000.0,
+            "percentile_99_5": 379.0,
+            "std": 192.4669952392578
+        }
+    }
+}

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/dataset.json

@@ -0,0 +1,34 @@
+{
+    "name": "JHH-Train-test",
+    "description": "3151 cases for training; 1958 cases for testing",
+    "reference": "ScaleMAI",
+    "licence": "CC-BY-SA 4.0",
+    "relase": "1.0 10/28/2024",
+    "tensorImageSize": "3D",
+    "labels": {
+        "background": 0,
+        "aorta": 1,
+        "adrenal_gland_left": 2,
+        "adrenal_gland_right": 3,
+        "celiac_aa": 4,
+        "colon": 5,
+        "duodenum": 6,
+        "gall_bladder": 7,
+        "postcava": 8,
+        "kidney_left": 9,
+        "kidney_right": 10,
+        "liver": 11,
+        "pancreas": 12,
+        "superior_mesenteric_artery": 13,
+        "intestine": 14,
+        "spleen": 15,
+        "renal_vein_left": 16,
+        "renal_vein_right": 17
+    },
+    "numTraining": 3151,
+    "numTest": 1958,
+    "file_ending": ".nii.gz",
+    "channel_names": {
+        "0": "CT"
+    }
+}

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/checkpoint_best.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b2c5c78b5a40289b05ad8051f385d4b01ea61ead3b48dfadc302d2387a06d50a
+size 820518770

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/checkpoint_final.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e59f75679e8f119a3ff67bd3c86f34ac005bc687d4875bc59b7e878259e36582
+size 820526982

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/debug.json

@@ -0,0 +1,53 @@
+{
+    "_best_ema": "0.80715364",
+    "batch_size": "2",
+    "configuration_manager": "{'data_identifier': 'nnUNetPlans_3d_fullres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': [160, 224, 192], 'median_image_size_in_voxels': [512.0, 613.0, 513.0], 'spacing': [0.7109375, 0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, 'nonlin': 'torch.nn.LeakyReLU', 'nonlin_kwargs': {'inplace': True}}, '_kw_requires_import': ['conv_op', 'norm_op', 'dropout_op', 'nonlin']}, 'batch_dice': True}",
+    "configuration_name": "3d_fullres",
+    "cudnn_version": 90100,
+    "current_epoch": "900",
+    "dataloader_train": "<batchgenerators.dataloading.nondet_multi_threaded_augmenter.NonDetMultiThreadedAugmenter object at 0x7f8cb1b4f820>",
+    "dataloader_train.generator": "<nnunetv2.training.dataloading.data_loader_3d.nnUNetDataLoader3D object at 0x7f8cb1b4faf0>",
+    "dataloader_train.num_processes": "12",
+    "dataloader_train.transform": "None",
+    "dataloader_val": "<batchgenerators.dataloading.nondet_multi_threaded_augmenter.NonDetMultiThreadedAugmenter object at 0x7f8cb1b4f0a0>",
+    "dataloader_val.generator": "<nnunetv2.training.dataloading.data_loader_3d.nnUNetDataLoader3D object at 0x7f8cb1b4f9d0>",
+    "dataloader_val.num_processes": "6",
+    "dataloader_val.transform": "None",
+    "dataset_json": "{'name': 'JHH-Train-test', 'description': '3151 cases for training; 1958 cases for testing', 'reference': 'ScaleMAI', 'licence': 'CC-BY-SA 4.0', 'relase': '1.0 10/28/2024', 'tensorImageSize': '3D', 'labels': {'background': 0, 'aorta': 1, 'adrenal_gland_left': 2, 'adrenal_gland_right': 3, 'celiac_aa': 4, 'colon': 5, 'duodenum': 6, 'gall_bladder': 7, 'postcava': 8, 'kidney_left': 9, 'kidney_right': 10, 'liver': 11, 'pancreas': 12, 'superior_mesenteric_artery': 13, 'intestine': 14, 'spleen': 15, 'renal_vein_left': 16, 'renal_vein_right': 17}, 'numTraining': 3151, 'numTest': 1958, 'file_ending': '.nii.gz', 'channel_names': {'0': 'CT'}}",
+    "device": "cuda:0",
+    "disable_checkpointing": "False",
+    "enable_deep_supervision": "True",
+    "fold": "all",
+    "folder_with_segs_from_previous_stage": "None",
+    "gpu_name": "NVIDIA TITAN RTX",
+    "grad_scaler": "<torch.cuda.amp.grad_scaler.GradScaler object at 0x7f8cc357cf70>",
+    "hostname": "ccvl18",
+    "inference_allowed_mirroring_axes": "(0, 1, 2)",
+    "initial_lr": "0.01",
+    "is_cascaded": "False",
+    "is_ddp": "False",
+    "label_manager": "<nnunetv2.utilities.label_handling.label_handling.LabelManager object at 0x7f8d983884f0>",
+    "local_rank": "0",
+    "log_file": "/mnt/T9/tlin67/nnUNet_results/Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/training_log_2025_11_7_21_08_06.txt",
+    "logger": "<nnunetv2.training.logging.nnunet_logger.nnUNetLogger object at 0x7f8cc3586c70>",
+    "loss": "DeepSupervisionWrapper(\n  (loss): DC_and_CE_loss(\n    (ce): RobustCrossEntropyLoss()\n    (dc): OptimizedModule(\n      (_orig_mod): MemoryEfficientSoftDiceLoss()\n    )\n  )\n)",
+    "lr_scheduler": "<nnunetv2.training.lr_scheduler.polylr.PolyLRScheduler object at 0x7f8cb92fb1f0>",
+    "my_init_kwargs": "{'plans': {'dataset_name': 'Dataset809_AbdomenAtlasF17', 'plans_name': 'nnUNetResEncUNetLPlans', 'original_median_spacing_after_transp': [0.7109375, 0.5, 0.7109375], 'original_median_shape_after_transp': [512, 608, 512], 'image_reader_writer': 'SimpleITKIO', 'transpose_forward': [1, 0, 2], 'transpose_backward': [1, 0, 2], 'configurations': {'2d': {'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 22, 'patch_size': [640, 640], 'median_image_size_in_voxels': [613.0, 513.0], 'spacing': [0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetResEncUNetLPlans_3d_lowres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': [160, 224, 192], 'median_image_size_in_voxels': [283, 339, 284], 'spacing': [1.284032205897787, 0.9030556173347075, 1.284032205897787], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': [160, 224, 192], 'median_image_size_in_voxels': [512.0, 613.0, 513.0], 'spacing': [0.7109375, 0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetPlannerResEncL', 'label_manager': 'LabelManager', 'foreground_intensity_properties_per_channel': {'0': {'max': 1000.0, 'mean': 39.68027877807617, 'median': 71.0, 'min': -1000.0, 'percentile_00_5': -1000.0, 'percentile_99_5': 379.0, 'std': 192.4669952392578}}}, 'configuration': '3d_fullres', 'fold': 'all', 'dataset_json': {'name': 'JHH-Train-test', 'description': '3151 cases for training; 1958 cases for testing', 'reference': 'ScaleMAI', 'licence': 'CC-BY-SA 4.0', 'relase': '1.0 10/28/2024', 'tensorImageSize': '3D', 'labels': {'background': 0, 'aorta': 1, 'adrenal_gland_left': 2, 'adrenal_gland_right': 3, 'celiac_aa': 4, 'colon': 5, 'duodenum': 6, 'gall_bladder': 7, 'postcava': 8, 'kidney_left': 9, 'kidney_right': 10, 'liver': 11, 'pancreas': 12, 'superior_mesenteric_artery': 13, 'intestine': 14, 'spleen': 15, 'renal_vein_left': 16, 'renal_vein_right': 17}, 'numTraining': 3151, 'numTest': 1958, 'file_ending': '.nii.gz', 'channel_names': {'0': 'CT'}}, 'unpack_dataset': True, 'device': device(type='cuda')}",
+    "network": "OptimizedModule",
+    "num_epochs": "1000",
+    "num_input_channels": "1",
+    "num_iterations_per_epoch": "250",
+    "num_val_iterations_per_epoch": "50",
+    "optimizer": "SGD (\nParameter Group 0\n    dampening: 0\n    differentiable: False\n    foreach: None\n    fused: None\n    initial_lr: 0.01\n    lr: 0.0012702500959998477\n    maximize: False\n    momentum: 0.99\n    nesterov: True\n    weight_decay: 3e-05\n)",
+    "output_folder": "/mnt/T9/tlin67/nnUNet_results/Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all",
+    "output_folder_base": "/mnt/T9/tlin67/nnUNet_results/Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres",
+    "oversample_foreground_percent": "0.33",
+    "plans_manager": "{'dataset_name': 'Dataset809_AbdomenAtlasF17', 'plans_name': 'nnUNetResEncUNetLPlans', 'original_median_spacing_after_transp': [0.7109375, 0.5, 0.7109375], 'original_median_shape_after_transp': [512, 608, 512], 'image_reader_writer': 'SimpleITKIO', 'transpose_forward': [1, 0, 2], 'transpose_backward': [1, 0, 2], 'configurations': {'2d': {'data_identifier': 'nnUNetPlans_2d', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 22, 'patch_size': [640, 640], 'median_image_size_in_voxels': [613.0, 513.0], 'spacing': [0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetResEncUNetLPlans_3d_lowres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': [160, 224, 192], 'median_image_size_in_voxels': [283, 339, 284], 'spacing': [1.284032205897787, 0.9030556173347075, 1.284032205897787], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': [160, 224, 192], 'median_image_size_in_voxels': [512.0, 613.0, 513.0], 'spacing': [0.7109375, 0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, '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': 'nnUNetPlannerResEncL', 'label_manager': 'LabelManager', 'foreground_intensity_properties_per_channel': {'0': {'max': 1000.0, 'mean': 39.68027877807617, 'median': 71.0, 'min': -1000.0, 'percentile_00_5': -1000.0, 'percentile_99_5': 379.0, 'std': 192.4669952392578}}}",
+    "preprocessed_dataset_folder": "/mnt/T9/tlin67/Dataset_preprocessed/Dataset809_AbdomenAtlasF17/nnUNetPlans_3d_fullres",
+    "preprocessed_dataset_folder_base": "/mnt/T9/tlin67/Dataset_preprocessed/Dataset809_AbdomenAtlasF17",
+    "save_every": "50",
+    "torch_version": "2.4.0+cu121",
+    "unpack_dataset": "True",
+    "was_initialized": "True",
+    "weight_decay": "3e-05"
+}

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/fold_all/training_log_2025_11_1_08_36_18.txt

@@ -0,0 +1,26 @@
+
+#######################################################################
+Please cite the following paper when using nnU-Net:
+Isensee, F., Jaeger, P. F., Kohl, S. A., Petersen, J., & Maier-Hein, K. H. (2021). nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nature methods, 18(2), 203-211.
+#######################################################################
+ 
+2025-11-01 08:36:24.398811: Using torch.compile... 
+2025-11-01 08:36:45.052451: do_dummy_2d_data_aug: False 
+
+This is the configuration used by this training:
+Configuration name: 3d_fullres
+ {'data_identifier': 'nnUNetPlans_3d_fullres', 'preprocessor_name': 'DefaultPreprocessor', 'batch_size': 2, 'patch_size': [160, 224, 192], 'median_image_size_in_voxels': [512.0, 613.0, 513.0], 'spacing': [0.7109375, 0.5, 0.7109375], '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': None}, 'resampling_fn_seg_kwargs': {'is_seg': True, 'order': 1, 'order_z': 0, 'force_separate_z': None}, 'resampling_fn_probabilities': 'resample_data_or_seg_to_shape', 'resampling_fn_probabilities_kwargs': {'is_seg': False, 'order': 1, 'order_z': 0, 'force_separate_z': None}, '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': None, 'dropout_op_kwargs': None, 'nonlin': 'torch.nn.LeakyReLU', 'nonlin_kwargs': {'inplace': True}}, '_kw_requires_import': ['conv_op', 'norm_op', 'dropout_op', 'nonlin']}, 'batch_dice': True} 
+ 
+These are the global plan.json settings:
+ {'dataset_name': 'Dataset809_AbdomenAtlasF17', 'plans_name': 'nnUNetResEncUNetLPlans', 'original_median_spacing_after_transp': [0.7109375, 0.5, 0.7109375], 'original_median_shape_after_transp': [512, 608, 512], 'image_reader_writer': 'SimpleITKIO', 'transpose_forward': [1, 0, 2], 'transpose_backward': [1, 0, 2], 'experiment_planner_used': 'nnUNetPlannerResEncL', 'label_manager': 'LabelManager', 'foreground_intensity_properties_per_channel': {'0': {'max': 1000.0, 'mean': 39.68027877807617, 'median': 71.0, 'min': -1000.0, 'percentile_00_5': -1000.0, 'percentile_99_5': 379.0, 'std': 192.4669952392578}}} 
+ 
+2025-11-01 08:37:17.108070: unpacking dataset... 
+2025-11-01 08:38:09.972894: unpacking done... 
+2025-11-01 08:38:09.995002: Unable to plot network architecture: nnUNet_compile is enabled! 
+2025-11-01 08:38:10.515083:  
+2025-11-01 08:38:10.517237: Epoch 450 
+2025-11-01 08:38:10.518909: Current learning rate: 0.00584 
+2025-11-01 08:55:58.583854: train_loss -0.4371 
+2025-11-01 08:55:58.605177: val_loss -0.4559 
+2025-11-01 08:55:58.606929: Pseudo dice [np.float32(0.9505), np.float32(0.7827), np.float32(0.7344), np.float32(0.675), np.float32(0.846), np.float32(0.7937), np.float32(0.8776), np.float32(0.8831), np.float32(0.9412), np.float32(0.9393), np.float32(0.9665), np.float32(0.85), np.float32(0.7965), np.float32(0.846), np.float32(0.9684), np.float32(0.2859), np.float32(0.2493)] 
+2025-11-01 08:55:58.608141: Epoch time: 1068.08 s 

Dataset809_AbdomenAtlasF17/nnUNetTrainer__nnUNetResEncUNetLPlans__3d_fullres/plans.json

@@ -0,0 +1,532 @@
+{
+    "dataset_name": "Dataset809_AbdomenAtlasF17",
+    "plans_name": "nnUNetResEncUNetLPlans",
+    "original_median_spacing_after_transp": [
+        0.7109375,
+        0.5,
+        0.7109375
+    ],
+    "original_median_shape_after_transp": [
+        512,
+        608,
+        512
+    ],
+    "image_reader_writer": "SimpleITKIO",
+    "transpose_forward": [
+        1,
+        0,
+        2
+    ],
+    "transpose_backward": [
+        1,
+        0,
+        2
+    ],
+    "configurations": {
+        "2d": {
+            "data_identifier": "nnUNetPlans_2d",
+            "preprocessor_name": "DefaultPreprocessor",
+            "batch_size": 22,
+            "patch_size": [
+                640,
+                640
+            ],
+            "median_image_size_in_voxels": [
+                613.0,
+                513.0
+            ],
+            "spacing": [
+                0.5,
+                0.7109375
+            ],
+            "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": "nnUNetResEncUNetLPlans_3d_lowres",
+            "preprocessor_name": "DefaultPreprocessor",
+            "batch_size": 2,
+            "patch_size": [
+                160,
+                224,
+                192
+            ],
+            "median_image_size_in_voxels": [
+                283,
+                339,
+                284
+            ],
+            "spacing": [
+                1.284032205897787,
+                0.9030556173347075,
+                1.284032205897787
+            ],
+            "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": [
+                160,
+                224,
+                192
+            ],
+            "median_image_size_in_voxels": [
+                512.0,
+                613.0,
+                513.0
+            ],
+            "spacing": [
+                0.7109375,
+                0.5,
+                0.7109375
+            ],
+            "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": "nnUNetPlannerResEncL",
+    "label_manager": "LabelManager",
+    "foreground_intensity_properties_per_channel": {
+        "0": {
+            "max": 1000.0,
+            "mean": 39.68027877807617,
+            "median": 71.0,
+            "min": -1000.0,
+            "percentile_00_5": -1000.0,
+            "percentile_99_5": 379.0,
+            "std": 192.4669952392578
+        }
+    }
+}