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MIC-DKFZ / nnUNet

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ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found! #2265

Open Malitha123 opened 4 weeks ago

Malitha123 commented 4 weeks ago

Hi, When I try following command I get this issue. I googled and some suggested to downgrade Simple ITK. but it did not work

CUDA_VISIBLE_DEVICES=0 nnUNetv2_plan_and_preprocess -d 128 --verify_dataset_integrity

""" Traceback (most recent call last): File "/usr/lib64/python3.11/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/multiprocessing/pool.py", line 51, in starmapstar return list(itertools.starmap(args[0], args[1])) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/experiment_planning/verify_dataset_integrity.py", line 34, in verify_labels seg, properties = rw.read_seg(label_file) ^^^^^^^^^^^^^^^^^^^^^^^ File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/imageio/simpleitk_reader_writer.py", line 115, in read_seg return self.read_images((seg_fname, )) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/imageio/simpleitk_reader_writer.py", line 37, in read_images itk_image = sitk.ReadImage(f) ^^^^^^^^^^^^^^^^^ File "/hpc/mgun939/Virtual_ENV/hpc/lib64/python3.11/site-packages/SimpleITK/extra.py", line 375, in ReadImage return reader.Execute() ^^^^^^^^^^^^^^^^ File "/hpc/mgun939/Virtual_ENV/hpc/lib64/python3.11/site-packages/SimpleITK/SimpleITK.py", line 8430, in Execute return _SimpleITK.ImageFileReader_Execute(self) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:2016: 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 "/hpc/mgun939/Virtual_ENV/hpc/bin/nnUNetv2_plan_and_preprocess", line 8, in sys.exit(plan_and_preprocess_entry()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py", line 182, in plan_and_preprocess_entry extract_fingerprints(args.d, args.fpe, args.npfp, args.verify_dataset_integrity, args.clean, args.verbose) File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 46, in extract_fingerprints extract_fingerprint_dataset(d, fingerprint_extractor_class, num_processes, check_dataset_integrity, clean, File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 29, in extract_fingerprint_dataset verify_dataset_integrity(join(nnUNet_raw, dataset_name), num_processes) File "/hpc/mgun939/newNNU/nnUNet/nnunetv2/experiment_planning/verify_dataset_integrity.py", line 204, in verify_dataset_integrity result = p.starmap( ^^^^^^^^^^ File "/usr/lib64/python3.11/multiprocessing/pool.py", line 375, in starmap return self._map_async(func, iterable, starmapstar, chunksize).get() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/multiprocessing/pool.py", line 774, in get raise self._value RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx:2016: ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found!

seziegler commented 4 weeks ago

Hi @Malitha123 , what version of SimpleITK do you have?

Malitha123 commented 4 weeks ago

I am using SimpleITK 2.3.1 currently and that is where I face the issue.

seziegler commented 3 weeks ago

Hi, I see that you're using python 3.11, could you try it with python 3.10?