diff --git a/cord-t2star.json b/cord-t2star.json new file mode 100755 index 0000000..5d95444 --- /dev/null +++ b/cord-t2star.json @@ -0,0 +1,94 @@ +{ + "command": "train", + "gpu": 7, + "target_suffix": "_seg-manual", + "roi_suffix": null, + "bids_path": "../duke/sct_testing/large/", + "random_seed": 1313, + "contrast_train_validation": ["acq-sup_T2star", "acq-c1c3_T2star", "acq-c4c7_T2star", "acq-ax_T2star", "acq-inf_T2star"], + "contrast_balance": {}, + "contrast_test": ["acq-sup_T2star", "acq-c1c3_T2star", "acq-c4c7_T2star", "acq-ax_T2star", "acq-inf_T2star"], + "center_test": [], + "retrain_model": null, + "out_channel": 1, + "depth": 3, + "missing_modality": false, + "batch_size": 32, + "dropout_rate": 0.3, + "batch_norm_momentum": 0.1, + "num_epochs": 50, + "initial_lr": 0.001, + "lr_scheduler": {"name": "CyclicLR", "base_lr": 0.0001, "max_lr": 0.001}, + "loss": {"name": "dice"}, + "log_directory": "log_sct-t2starw", + "film_layers": [0, 0, 0, 0, 0, 0, 0, 0], + "attention_unet": false, + "mixup_bool": false, + "mixup_alpha": 2, + "metadata": null, + "multichannel": false, + "slice_axis": "axial", + "split_method": "per_patient", + "train_fraction": 0.6, + "test_fraction": 0.2, + "balance_samples": false, + "slice_filter": {"filter_empty_mask": false, "filter_empty_input": true}, + "slice_filter_roi": 10, + "uncertainty": {"epistemic": false, "aleatoric": false, "n_it": 0}, + "unet_3D": false, + "binarize_prediction": false, + "early_stopping_patience": 20, + "early_stopping_epsilon": 0.1, + "eval_params": { + "targetSize": {"unit": "vox", "thr": [20, 100]}, + "removeSmall": {"unit": "vox", "thr": 3}, + "overlap": {"unit": "vox", "thr": 3} + }, + "transformation_training": { + "Resample": { + "wspace": 0.75, + "hspace": 0.75 + }, + "DilateGT": { + "dilation_factor": 0 + }, + "CenterCrop2D": { + "size": [160, 160] + }, + "ElasticTransform": { + "alpha_range": [28.0, 30.0], + "sigma_range": [3.5, 4.5], + "p": 0.1 + }, + "RandomAffine": { + "degrees": 4.6, + "translate": [0.03, 0.03], + "scale": [0.98, 1.02] + }, + "ToTensor": {}, + "NormalizeInstance": {} + }, + "transformation_validation": { + "Resample": { + "wspace": 0.75, + "hspace": 0.75 + }, + "CenterCrop2D": { + "size": [160, 160] + }, + "ToTensor": {}, + "NormalizeInstance": {} + }, + "transformation_testing": { + "Resample": { + "wspace": 0.75, + "hspace": 0.75 + }, + "CenterCrop2D": { + "size": [160, 160] + }, + "ToTensor": {}, + "NormalizeInstance": {} + }, + "debugging": false +} diff --git a/cord-t2star.pt b/cord-t2star.pt new file mode 100755 index 0000000..34884ce Binary files /dev/null and b/cord-t2star.pt differ