nnUNet

[Pankajg959]

Hey @JunMa11 ,
I am an academic radiologist. I enjoy experimenting with MedSAM. Congratulations on this significant contribution!!
I am comparing MedSAM's segmentation results with those of nnUNet.

1. There is no training script in the comparisons--> nnU-Net folder.
   As per the documentation (https://github.com/bowang-lab/MedSAM/blob/main/comparisons/nnU-Net/README.md), "This folder contains the scripts for training and inference of the nnUNet model on medical image data in MedSAM's preprocessed npz format." I expected a training script that would allow me to train using MedSAM's preprocessed images.

2. When I used a model trained with the standard nnUNetv2 pipeline for inference, there was an error.
   python infer_nnunet_3D.py -checkpoint /home/pankaj/scratch/nnUNet/nnUNet_results/Dataset200 -data_root /home/pankaj/scratch/MedSAM/data/npz/MedSAM_test/CT_Abd -pred_save_dir /home/pankaj
   /scratch/MedSAM/nnunet_pred --save_overlay -png_save_dir /home/pankaj/scratch/MedSAM/nnunet_pred/png -num_workers 2
   Traceback (most recent call last):
   File "/scratch/pankaj/MedSAM_main/comparisons/nnU-Net/infer_nnunet_3D.py", line 119, in
   predictor = nnUNetPredictor(
   TypeError: nnUNetPredictor.init() got an unexpected keyword argument 'perform_everything_on_gpu'

When I changed the argument to "perform_everything_on_device", there was another error,
Traceback (most recent call last):
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/scratch/pankaj/MedSAM_main/comparisons/nnU-Net/infer_nnunet_3D.py", line 206, in nnunet_infer_npz
seg_2D = predictor.predict_single_npy_array(
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/site-packages/nnunetv2/inference/predict_from_raw_data.py"
, line 444, in predict_single_npy_array
dct = next(ppa)
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/site-packages/batchgenerators/dataloading/data_loader.py",
line 126, in next
return self.generate_train_batch()
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/site-packages/nnunetv2/inference/data_iterators.py", line
198, in generate_train_batch
data, seg = self.preprocessor.run_case_npy(image, seg_prev_stage, props,
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 44, in run_case_npy
data = data.astype(np.float32) # this creates a copy
AttributeError: 'Tensor' object has no attribute 'astype'. Did you mean: 'dtype'?
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/scratch/pankaj/MedSAM_main/comparisons/nnU-Net/infer_nnunet_3D.py", line 259, in
for i, _ in tqdm(enumerate(pool.imap_unordered(nnunet_infer_npz, gt_path_files))):
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/site-packages/tqdm/std.py", line 1181, in iter
for obj in iterable:
File "/home/pankaj/scratch/ananconda3/envs/medsam/lib/python3.10/multiprocessing/pool.py", line 873, in next
raise value
AttributeError: 'Tensor' object has no attribute 'astype'

3. I also noticed the link: "The inference scripts assume that the data is in the npz format generated by MedSAM preprocess pipeline. To run inference, one can download the model here and use the provided inference scripts" directs to DeepLab models rather than nnU-Net.

Please help
Dr. Pankaj Gupta, M.D.

[Pankajg959]

Dear @JunMa11 ,
I am waiting for your response.
Thanks