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MIC-DKFZ / nnUNet

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RuntimeError: Some images have errors. Please check text output above to see which one(s) and what's going on. #2551

Open Guoxt opened 1 month ago

Guoxt commented 1 month ago

Warning: Origin mismatch between segmentation and corresponding images. Origin images: (-123.0, 215.3117218017578, 271.3599853515625). Origin seg: (-124.51171875, 124.51171875, -74.25). Image files: ['/userhome/GUOXUTAO/DATA_ALL/DATASET/nnUNet_raw/Dataset700_skull/imagesTr/0144_image_0000.nii.gz']. Seg file: /userhome/GUOXUTAO/DATA_ALL/DATASET/nnUNet_raw/Dataset700_skull/labelsTr/0144_image.nii.gz

Warning: Origin mismatch between segmentation and corresponding images. Origin images: (-115.0, 184.83078002929688, 121.48999786376953). Origin seg: (-114.55078125, 114.55078125, -79.19998168945312). Image files: ['/userhome/GUOXUTAO/DATA_ALL/DATASET/nnUNet_raw/Dataset700_skull/imagesTr/0185_image_0000.nii.gz']. Seg file: /userhome/GUOXUTAO/DATA_ALL/DATASET/nnUNet_raw/Dataset700_skull/labelsTr/0185_image.nii.gz

Warning: Origin mismatch between segmentation and corresponding images. Origin images: (-115.0, 175.79078674316406, 92.26000213623047). Origin seg: (-114.55078125, 114.55078125, -79.20000457763672). Image files: ['/userhome/GUOXUTAO/DATA_ALL/DATASET/nnUNet_raw/Dataset700_skull/imagesTr/0173_image_0000.nii.gz']. Seg file: /userhome/GUOXUTAO/DATA_ALL/DATASET/nnUNet_raw/Dataset700_skull/labelsTr/0173_image.nii.gz

Traceback (most recent call last): File "/usr/local/bin/nnUNetv2_plan_and_preprocess", line 33, in sys.exit(load_entry_point('nnunetv2', 'console_scripts', 'nnUNetv2_plan_and_preprocess')()) File "/code/GUOXUTAO/2023_15/00/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 "/code/GUOXUTAO/2023_15/00/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 "/code/GUOXUTAO/2023_15/00/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 "/code/GUOXUTAO/2023_15/00/nnUNet/nnunetv2/experiment_planning/verify_dataset_integrity.py", line 202, in verify_dataset_integrity raise RuntimeError( RuntimeError: Some images have errors. Please check text output above to see which one(s) and what's going on.

### Could you please explain the reason for this error?

seziegler commented 3 weeks ago

Hi @Guoxt , the metadata of your images and the label files does not seem to align since they have different origins set. When viewing your images with labels overlayed are the labels displayed accurately or are they somehow shifted?