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About 'Unable to determine Image IO reader for certain image file'

See original GitHub issue

Hello, I am having problem with just training the dataset with baseline nnUnet. Fabian has kindly written the conversion of dataset python file, and I just used it to convert kits 21 dataset. However following error occurs during preprocessing.

RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:105:
sitk::ERROR: Unable to determine ImageIO reader for "/home/mchangaf/nnUNetFrame/DATASET/nnUNet_raw/nnUNet_raw_data/
Task135_KiTS2021/imagesTr/case_00038_0000.nii.gz"

On certain files, Exception thrown in SimpleITK ImageFileReader occurs. Should I just ignore these errors and continue training?

Issue Analytics

State:
Created 2 years ago
Comments:17 (11 by maintainers)

Top GitHub Comments

1reaction

FabianIsenseecommented, Jul 20, 2021

Preprocessing is currently always done from scratch. We could change that in the future but unfortunately that’s how it is now. Please use -tl 2 and -tf 1 in an attempt to get it working 😃 This needs a lot of RAM, unfortunately

1reaction

trofimovacommented, Jul 17, 2021

i would say yes. if you still have the problem with opening the error files separately, please let us and @neheller know.