diff --git a/config/config_sci-colorado.json b/configs/config_sci-colorado.json similarity index 100% rename from config/config_sci-colorado.json rename to configs/config_sci-colorado.json diff --git a/configs/config_sci_full-vol_bs=8_bnf=8_no-bin_lr_augs.json b/configs/config_sci_full-vol_bs=8_bnf=8_no-bin_lr_augs.json new file mode 100644 index 00000000..6f205292 --- /dev/null +++ b/configs/config_sci_full-vol_bs=8_bnf=8_no-bin_lr_augs.json @@ -0,0 +1,117 @@ +{ + "command": "train", + "gpu_ids": [2], + "path_output": "/home/GRAMES.POLYMTL.CA/u114716/sci-zurich_project/configs_all_subs/outputs/sciLesions_crpd_exp3_bs_no-bin_seed123", + "model_name": "Unet3d_singleContrast", + "debugging": true, + "object_detection_params": { + "object_detection_path": null, + "safety_factor": [1.0, 1.0, 1.0] + }, + "wandb": { + "wandb_api_key": "bf043c64b6c6b4abcc1ee7d8501c300b19945028", + "project_name": "sci-zurich", + "group_name": "ivadomed_models", + "run_name": "sc=sag_ep=300_bs=8", + "log_grads_every": 1000 + }, + "loader_parameters": { + "path_data": ["/home/GRAMES.POLYMTL.CA/u114716/duke/temp/muena/sci-zurich_preprocessed"], + "target_suffix": ["_lesion-manual"], + "extensions": [".nii.gz"], + "roi_params": { + "suffix": null, + "slice_filter_roi": null + }, + "contrast_params": { + "training_validation": ["T2w"], + "testing": ["T2w"], + "balance": {} + }, + "slice_filter_params": { + "filter_empty_mask": false, + "filter_empty_input": false + }, + "slice_axis": "sagittal", + "multichannel": false, + "soft_gt": true + }, + "split_dataset": { + "fname_split": null, + "random_seed": 123, + "split_method" : "participant_id", + "data_testing": {"data_type": null, "data_value":[]}, + "balance": null, + "train_fraction": 0.75, + "test_fraction": 0.2 + }, + "training_parameters": { + "batch_size": 2, + "loss": { + "name": "DiceLoss" + }, + "training_time": { + "num_epochs": 500, + "early_stopping_patience": 200, + "early_stopping_epsilon": 0.001 + }, + "scheduler": { + "initial_lr": 1e-4, + "lr_scheduler": { + "name": "CosineAnnealingLR", + "base_lr": 1e-5, + "max_lr": 5e-4 + } + }, + "balance_samples": {"applied": false, "type": "gt"} + }, + "default_model": { + "name": "Unet", + "final_activation": "relu" + }, + "Modified3DUNet": { + "applied": true, + "length_3D": [256, 128, 96], + "stride_3D": [256, 128, 96], + "attention": false, + "n_filters": 8 + }, + "uncertainty": { + "epistemic": false, + "aleatoric": false, + "n_it": 0 + }, + "postprocessing": { + "binarize_prediction": {"thr": -1}, + "uncertainty": {"thr": -1, "suffix": "_unc-vox.nii.gz"} + }, + "evaluation_parameters": {}, + "transformation": { + "CenterCrop": {"size": [256, 128, 96]}, + "RandomReverse": { + "applied_to": ["im", "gt"], + "dataset_type": ["training"] + }, + "RandomAffine": { + "degrees": 10, + "scale": [0.3, 0.3, 0.3], + "translate": [0.1, 0.1, 0.1], + "applied_to": ["im", "gt"], + "dataset_type": ["training"] + }, + "ElasticTransform": { + "alpha_range": [25.0, 35.0], + "sigma_range": [3.5, 5.5], + "p": 0.5, + "applied_to": ["im", "gt"], + "dataset_type": ["training"] + }, + "RandomGamma": { + "log_gamma_range": [-1.5, 1.5], + "p": 0.5, + "applied_to": ["im"], + "dataset_type": ["training"] + }, + "NormalizeInstance": {"applied_to": ["im"]} + } +}