Only 1 modality, but nnUNET reads it as 3

[Alice715324]

For the life of me I cannot figure this one out. nnUnet reads my nii.gz file as 3 modalities when it should read it as 1. Anyone encounter this?

[felixkrones]

Could this be related to issue #2017 and/or PR #2158?

[seziegler]

Hi @Alice715324 ,

can you please share your dataset.json and the commands you used for preprocessing and training?
What is the error you're seeing?

Best,
Sebastian

[casami3]

I'm having the same problem but with .png format. My .json file looks is:

{"channel_names": {"0": "XAG"}, "labels": {"background": 0, "stenosis": 1}, "numTraining": 1300, "file_ending": ".png"}

And the error that I get on the Prompt is:

Error: Unexpected number of modalities.
Expected: 1.
Got: 3.
Images: ['C:/Users/joanc/OneDrive/Escritorio/UPF/curs2trim3/AABI/proy/nnUNet_raw\Dataset004_Stenosis\imagesTr\Stenosis_1022_0000.png']

Error: Unexpected number of modalities.
Expected: 1.
Got: 3.
Images: ['C:/Users/joanc/OneDrive/Escritorio/UPF/curs2trim3/AABI/proy/nnUNet_raw\Dataset004_Stenosis\imagesTr\Stenosis_1229_0000.png']

Error: Unexpected number of modalities.
Expected: 1.
Got: 3.
Images: ['C:/Users/joanc/OneDrive/Escritorio/UPF/curs2trim3/AABI/proy/nnUNet_raw\Dataset004_Stenosis\imagesTr\Stenosis_1025_0000.png']

Error: Unexpected number of modalities.
Expected: 1.
Got: 3.
Images: ['C:/Users/joanc/OneDrive/Escritorio/UPF/curs2trim3/AABI/proy/nnUNet_raw\Dataset004_Stenosis\imagesTr\Stenosis_1230_0000.png']

Traceback (most recent call last):
File "C:\Users\joanc\anaconda3\envs\aaib\lib\runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\joanc\anaconda3\envs\aaib\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\Users\joanc\anaconda3\envs\aaib\Scripts\nnUNetv2_plan_and_preprocess.exe_main.py", line 7, in
File "C:\Users\joanc\anaconda3\envs\aaib\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_entrypoints.py", line 184, in plan_and_preprocess_entry
extract_fingerprints(args.d, args.fpe, args.npfp, args.verify_dataset_integrity, args.clean, args.verbose)
File "C:\Users\joanc\anaconda3\envs\aaib\lib\site-packages\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 "C:\Users\joanc\anaconda3\envs\aaib\lib\site-packages\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 "C:\Users\joanc\anaconda3\envs\aaib\lib\site-packages\nnunetv2\experiment_planning\verify_dataset_integrity.py", line 220, 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.

[seziegler]

Hi @casami3 ,

for rgb images you need to specify "channel_names": {0: 'R', 1: 'G', 2: 'B'} in your dataset.json.
You can see an example here.
There is also a side note in the documentation here.

Best,
Sebastian