mice_uqueensland_sc.json

{
    "command": "train",
    "gpu": 1,
    "log_directory": "mice_sc",
    "debugging": false,
    "loader_parameters": {
        "bids_path": "../duke/projects/ivado-medical-imaging/data_mice_abdullah-UQ/",
        "target_suffix": ["_scseg"],
        "roi_params": {
            "suffix": null,
            "slice_filter_roi": null
        },
        "contrast_params": {
            "training_validation": ["t1"],
            "testing": ["t1"],
            "balance": {}
        },
        "slice_filter_params": {
            "filter_empty_mask": true,
            "filter_empty_input": true
        },
        "slice_axis": "axial",
        "multichannel": false
    },
    "split_dataset": {
        "fname_split": null,
        "random_seed": 30,
        "center_test": [],
        "method": "per_patient",
        "train_fraction": 0.6,
        "test_fraction": 0.2
    },
    "training_parameters": {
        "batch_size": 8,
        "loss": {
            "name": "DiceLoss"
        },
        "training_time": {
            "num_epochs": 200,
            "early_stopping_patience": 50,
            "early_stopping_epsilon": 0.05
        },
        "scheduler": {
            "initial_lr": 0.001,
            "lr_scheduler": {
                "name": "CosineAnnealingWarmRestarts",
                "T_0": 20,
                "T_mult": 2
            }
        },
        "balance_samples": false,
        "mixup_alpha": null,
        "transfer_learning": {
            "retrain_model": null,
            "retrain_fraction": 1.0
        }
    },
    "default_model": {
        "name": "Unet",
        "dropout_rate": 0.3,
        "bn_momentum": 0.3,
        "depth": 2
    },
    "testing_parameters": {
        "binarize_prediction": true,
        "uncertainty": {
            "epistemic": false,
            "aleatoric": false,
            "n_it": 1
        }
    },
    "evaluation_parameters": {
        "targetSize": {"unit": "vox", "thr": [20, 100]},
        "removeSmall": {"unit": "vox", "thr": 3},
        "overlap": {"unit": "vox", "thr": 3}
    },
    "transformation": {
        "Resample":
        {
            "wspace": 0.04,
            "hspace": 0.04,
            "preprocessing": true
        },
        "CenterCrop":
        {
            "size": [96, 96],
            "preprocessing": true
        },
        "ElasticTransform": {
            "alpha_range": [28.0, 30.0],
            "sigma_range":  [3.5, 4.5],
            "p": 0.3,
            "applied_to": ["im", "gt"],
            "dataset_type": ["training"]
        },
        "RandomAffine": {
            "degrees": 20,
            "translate": [0.03, 0.03],
            "scale": [0.98, 1.02],
            "dataset_type": ["training"]
        },
        "NumpyToTensor": {},
        "NormalizeInstance": {"applied_to": ["im"]}
    }
}