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finalize guides
May 31, 2021
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README.md

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Decathlon

Disclaimer: We are not the host of the data. Please make sure to read the requirements and usage policies of the data and give credit to the authors of the dataset!

Please read the information from the homepage carefully and follow the rules and instructions provided by the original authors when using the data.

Setup

  1. Follow the installation instructions of nnDetection and create the data directories for the intended tasks, e.g. Task003_Liver.
  2. Follow the instructions and usage policies to download the data and place the images, labels and dataset.json files inside the raw folder of the respective tasks, e.g. imagesTr -> Task003_Liver / raw / imagesTr, labelsTr -> Task003_Liver / raw / labelsTr and dataset.json -> Task003_Liver / raw / dataset.json
  3. Run python prepare.py [tasks] in projects / Task001_Decathlion / scripts of the nnDetection repository, e.g. to prepare all tasks: python prepare.py Task003_Liver Task007_Pancreas Task008_HepaticVessel Task010_Colon
  4. Download labels from here and replace labelsTr / labelsTs in the splitted folder with the downloaded ones.

The data is now converted to the correct format and the instructions from the nnDetection README can be used to train the networks.