Following your instruction

BenoitKAO commented 1 year ago

Thank you very much for your marvelous work!

However, I followed your instructions in "Installation", ... "Evaluation" ... bash run_training_acdc.sh

I received these error messages.

debug: mirroring True mirror_axes (0, 1, 2) step_size: 0.5 do mirror: True data shape: (1, 16, 263, 187) patch size: [ 16 160 160] steps (x, y, and z): [[0], [0, 52, 103], [0, 27]] number of tiles: 6 using precomputed Gaussian prediction done force_separate_z: None interpolation order: 1 separate z: True lowres axis [0] separate z, order in z is 0 order inplane is 1 2022-12-22 17:27:36.092914: finished prediction 2022-12-22 17:27:36.093320: evaluation of raw predictions multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/miniconda3/envs/unetr_pp/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/miniconda3/envs/unetr_pp/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/unetr_plus_plus/unetr_pp/evaluation/evaluator.py", line 310, in run_evaluation evaluator.set_reference(ref) File "/unetr_plus_plus/unetr_pp/evaluation/evaluator.py", line 291, in set_reference self.reference_nifti = sitk.ReadImage(reference) File "/miniconda3/envs/unetr_pp/lib/python3.8/site-packages/SimpleITK/extra.py", line 357, in ReadImage return reader.Execute() File "/miniconda3/envs/unetr_pp/lib/python3.8/site-packages/SimpleITK/SimpleITK.py", line 8438, in Execute return _SimpleITK.ImageFileReader_Execute(self) RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:1994: ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found! """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "unetr_pp/run/run_training.py", line 171, in main() File "unetr_pp/run/run_training.py", line 165, in main trainer.validate(save_softmax=args.npz, validation_folder_name=val_folder, File "/unetr_plus_plus/unetr_pp/training/network_training/unetr_pp_trainer_acdc.py", line 224, in validate ret = super().validate(do_mirroring=do_mirroring, use_sliding_window=use_sliding_window, step_size=step_size, File "/unetr_plus_plus/unetr_pp/training/network_training/Traineracdc.py", line 644, in validate = aggregate_scores(pred_gt_tuples, labels=list(range(self.num_classes)), File "/unetr_plus_plus/unetr_pp/evaluation/evaluator.py", line 360, in aggregate_scores all_res = p.map(run_evaluation, zip(test, ref, [evaluator]len(ref), [metric_kwargs]len(ref))) File "/miniconda3/envs/unetr_pp/lib/python3.8/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/miniconda3/envs/unetr_pp/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:1994: ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found!

It could be the issue of the package version in "requirements.txt." simpleitk==2.2.0

Please help in solving these errors.

I would appreciate any help.

PS. "bash run_training_synapse.sh" is still running. Until now, I have not seen the error message in "bash run_training_synapse.sh"

BenoitKAO commented 1 year ago

"run_evaluation_synapse.sh" takes time to finish the running, but it works fine.

BenoitKAO commented 1 year ago

After I re-installed SimpleITK with the latest version, 2.2.1, scripts in "Evaluation" worked.

However, I got WARNING messages at running "bash run_training_acdc.sh":

2022-12-22 19:59:04.785033: evaluation of raw predictions WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient093_frame14.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient093_frame14.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient091_frame09.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient089_frame10.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient091_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient090_frame04.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient091_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient090_frame04.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient090_frame11.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient089_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient093_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient089_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient093_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient094_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient094_frame07.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient096_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient096_frame08.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient097_frame11.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient097_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient097_frame11.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient097_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient098_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient098_frame09.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient099_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient099_frame09.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient100_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient100_frame13.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient100_frame01.nii.gz has unexpected scales in sform

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient100_frame13.nii.gz has unexpected scales in sform

2022-12-22 19:59:05.383285: determining postprocessing WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934 NiftiImageIO (0xb0f7fb0): DATASET/unetr_pp_raw/unetr_pp_raw_data/Task01_ACDC/Task001_ACDC/gt_segmentations/patient090_frame11.nii.gz has unexpected scales in sform