Closed sami22ivr closed 2 months ago
Hi @sami22ivr, it seems as if you are running out of RAM. A clear indicator of this is that the inference did run with a reduced number of processes. Sadly 32GB of RAM is not necessarily a lot of memory for many volumetric datasets.
So you have three options now:
Sorry for not being able to help you more.
Best regards,
Carsten
hi everyone, so im having an issue with doing prediction where it always shows this error : ####################################################################### Please cite the following paper when using nnU-Net: Isensee, F., Jaeger, P. F., Kohl, S. A., Petersen, J., & Maier-Hein, K. H. (2021). nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nature methods, 18(2), 203-211. #######################################################################
There are 1 cases in the source folder I am process 0 out of 1 (max process ID is 0, we start counting with 0!) There are 1 cases that I would like to predict Process SpawnProcess-6: Traceback (most recent call last): File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/site-packages/nnunetv2/inference/data_iterators.py", line 58, in preprocess_fromfiles_save_to_queue raise e File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/site-packages/nnunetv2/inference/data_iterators.py", line 31, in preprocess_fromfiles_save_to_queue data, seg, data_properties = preprocessor.run_case(list_of_lists[idx], ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 139, in run_case data, seg = self.run_case_npy(data, seg, data_properties, plans_manager, configuration_manager, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 78, in run_case_npy data = self._normalize(data, seg, configuration_manager, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/samir/miniconda3/envs/nnUNet/lib/python3.11/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 183, in _normalize scheme = configuration_manager.normalization_schemes[c]