Data mismatch
xifen523 opened this issue · 1 comments
xifen523 commented
I downloaded the data as per the readme, but after unzipping it, it doesn't match the 801 dataset settings, the unzip ends in nii, not nii.gz, I tried to run nnUNetv2_plan_and_preprocess -d 801 --verify_dataset_integrity
, but it failed
ingerprint extraction...
Dataset801_LiverCT
Traceback (most recent call last):
File "/home/lk/miniconda3/envs/lightmunet/bin/nnUNetv2_plan_and_preprocess", line 33, in <module>
sys.exit(load_entry_point('nnunetv2', 'console_scripts', 'nnUNetv2_plan_and_preprocess')())
File "/home/lk/workspase/python/segmentation/LightM-UNet/lightm-unet/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 "/home/lk/workspase/python/segmentation/LightM-UNet/lightm-unet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 47, in extract_fingerprints
extract_fingerprint_dataset(d, fingerprint_extractor_class, num_processes, check_dataset_integrity, clean,
File "/home/lk/workspase/python/segmentation/LightM-UNet/lightm-unet/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 30, in extract_fingerprint_dataset
verify_dataset_integrity(join(nnUNet_raw, dataset_name), num_processes)
File "/home/lk/workspase/python/segmentation/LightM-UNet/lightm-unet/nnunetv2/experiment_planning/verify_dataset_integrity.py", line 155, in verify_dataset_integrity
assert len(dataset) == expected_num_training, 'Did not find the expected number of training cases ' \
AssertionError: Did not find the expected number of training cases (87). Found 0 instead.
Examples: []
how to solve this issue
thank you
Xiadonn commented
Have you ever used nnUNet?
Maybe you should change the data format from nii to nii.gz first by yourself.
Note that "file_ending": ".nii.gz" in dataset.json.