OSF Version 1

uqueensland-mice-sc.json

@@ -0,0 +1,87 @@
+{
+    "command": "train",
+    "gpu": 5,
+    "target_suffix": "_scseg",
+    "roi_suffix": null,
+    "bids_path": "../duke/projects/ivado-medical-imaging/data_mice_abdullah-UQ/",
+    "random_seed": 1313,
+    "contrast_train_validation": ["t1"],
+    "contrast_balance": {},
+    "contrast_test": ["t1"],
+    "center_test": [],
+    "batch_size": 4,
+    "dropout_rate": 0.3,
+    "batch_norm_momentum": 0.1,
+    "num_epochs": 200,
+    "initial_lr": 0.001,
+    "lr_scheduler": {"name": "CosineAnnealingWarmRestarts", "T_0": 20, "T_mult": 2},
+    "loss": {"name": "dice"},
+    "log_directory": "log_mice",
+    "film_layers": [0, 0, 0, 0, 0, 0, 0, 0],
+    "mixup_bool": false,
+    "mixup_alpha": 2,
+    "metadata": "contrast",
+    "missing_modality": false,
+    "multichannel": false,
+    "out_channel": 1,
+    "depth": 3,
+    "train_fraction": 0.6,
+    "test_fraction": 0.2,
+    "early_stopping_patience": 50,
+    "early_stopping_epsilon": 0.1,
+    "slice_axis": "axial",
+    "balance_samples": false,
+    "retrain_model": null,
+    "split_method": "per_patient",
+    "slice_filter": {"filter_empty_mask": true, "filter_empty_input": true},
+    "slice_filter_roi": 10,
+    "attention_unet": false,
+    "uncertainty": {"epistemic": true, "aleatoric": false, "n_it": 10},
+    "unet_3D": false,
+    "binarize_prediction": true,
+    "eval_params": {},
+    "transformation_training": {
+                "Resample": {
+                        "wspace": 0.04,
+                        "hspace": 0.04
+                        },
+                "CenterCrop2D": {
+                        "size": [96, 96]
+                },
+                "ElasticTransform": {
+                        "alpha_range": [28.0, 30.0],
+                        "sigma_range":  [3.5, 4.5],
+                        "p": 0.3
+                        },
+                "RandomAffine": {
+                        "degrees": 20,
+                        "translate": [0.03, 0.03],
+                        "scale": [0.98, 1.02]
+                        },
+                "ToTensor": {},
+                "NormalizeInstance": {}
+                },
+        "transformation_validation": {
+                "Resample": {
+                        "wspace": 0.04,
+                        "hspace": 0.04
+                        },
+                "CenterCrop2D": {
+                        "size": [96, 96]
+                },
+                "ToTensor": {},
+                "NormalizeInstance": {}
+                },
+        "transformation_testing": {
+                "Resample": {
+                        "wspace": 0.04,
+                        "hspace": 0.04
+                        },
+                "CenterCrop2D": {
+                        "size": [96, 96]
+                },
+                "ToTensor": {},
+                "NormalizeInstance": {}
+                },
+        "debugging": true
+}