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MIC-DKFZ / nnUNet

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what does split_4d do? #128

Closed ghost closed 4 years ago

ghost commented 4 years ago

hi Fabian!

I saw split_4d and crop in nnunet.experiment_planning.plan_and_preprocess_task.py and i wonder what split_4d exactly does. It seems not to change any properties about dataset. What I want to do is, skip splitting and crop directly. Please tell me if it is possible.

Thank you for all of your hard work.

FabianIsensee commented 4 years ago

Hi, please read he readme here: https://github.com/MIC-DKFZ/nnUNet/tree/master/nnunet/dataset_conversion

The decathlon data is provided as 4d nifti. I think it is better to have 3d niftis (one file per modality) therefore the decathlon data is splitted along the modality dimension into separate files. You can skip this by copying your data into nnUNet_raw_splitted (follow the instructions in the readme!)

Best, Fabian

ghost commented 4 years ago

Thanks for your reply!