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Only one channel is recognized out of 15 channels #1652
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Hi @mengab1, Thanks for posting this. Let us know, |
How to set self.labels correctly I start training from scratch |
Hi @mengab1, Are you trying to segment all these regions from scratch? If yes, how many volumes did you segment before training the model? Just download the preview release from Slicer (https://download.slicer.org/) and then install MONAIAuto3DSeg via the Extension Manager. With the predictions you get from that model, you can create ground truth to train and use the active learning strategies from MONAI Label. Hope this helps, |
[2024-03-10 14:28:38,126] [18300] [MainThread] [INFO] (main:61) - Result: {"rank": 0, "current_epoch": 2000, "current_iteration": 24000, "total_epochs": 2000, "total_iterations": 12, "epoch": 2000, "start_ts": 1710020807, "total_time": "8:41:50", "best_metric": 0.787301242351532, "train": {"metrics": {"train_mean_dice": 0.8769383430480957, "train_nodule_mean_dice": 0.0, "train_bone_mean_dice": 0.0, "train_aorta_mean_dice": 0.0, "train_pulmonary_artery_mean_dice": 0.0, "train_pulmonary_vein_mean_dice": 0.0, "train_vein_mean_dice": 0.0, "train_trachea_mean_dice": 0.0, "train_esophagus_mean_dice": 0.0, "train_heart_mean_dice": 0.0, "train_lung_upper_lobe_left_mean_dice": 0.0, "train_lung_lower_lobe_left_mean_dice": 0.0, "train_lung_upper_lobe_right_mean_dice": 0.0, "train_lung_middle_lobe_right_mean_dice": 0.0, "train_lung_lower_lobe_right_mean_dice": 0.0, "train_skin_mean_dice": 0.9323155283927917}, "key_metric_name": "train_mean_dice", "best_metric": 0.9949172139167786, "best_metric_epoch": 1851}, "eval": {"metrics": {"val_mean_dice": 0.7803362011909485, "val_nodule_mean_dice": 0.0, "val_bone_mean_dice": 0.0, "val_aorta_mean_dice": 0.0, "val_pulmonary_artery_mean_dice": 0.0, "val_pulmonary_vein_mean_dice": 0.0, "val_vein_mean_dice": 0.0, "val_trachea_mean_dice": 0.0, "val_esophagus_mean_dice": 0.0, "val_heart_mean_dice": 0.0, "val_lung_upper_lobe_left_mean_dice": 0.0, "val_lung_lower_lobe_left_mean_dice": 0.0, "val_lung_upper_lobe_right_mean_dice": 0.0, "val_lung_middle_lobe_right_mean_dice": 0.0, "val_lung_lower_lobe_right_mean_dice": 0.0, "val_skin_mean_dice": 0.9444830417633057}, "key_metric_name": "val_mean_dice", "best_metric": 0.787301242351532, "best_metric_epoch": 1669}}
![截屏2024-03-10 21 19 27](https://private-user-images.githubusercontent.com/35659832/311512728-94eb7175-5c5d-4c55-abb3-253bc424c2a2.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.0ndnOR-h7YksAuyEuGHQjaTGBpTJhBURV-HBxWWeCYs)
![截屏2024-03-10 21 25 17](https://private-user-images.githubusercontent.com/35659832/311513136-505b082f-a5fb-46fc-926f-3f2aaa7a1935.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.CTm3H2XjamBGXbB8qX7E_lDcbVQyFFwyw4loV1r2Sy0)
![截屏2024-03-10 21 26 50](https://private-user-images.githubusercontent.com/35659832/311513235-59c6c2f1-b6d1-4d0e-a3bf-45ad7f34b3b9.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.i6g3Sn5rxYa_2gQke3XDzXSc3S5oRQLRUyvzDNvKEsk)
[2024-03-10 14:28:39,100] [13122] [ThreadPoolExecutor-1_0] [INFO] (monailabel.utils.async_tasks.utils:83) - Return code: 0
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