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thuhoainguyen / kits23

The official repository of the 2023 Kidney Tumor Segmentation Challenge (KiTS23)
MIT License
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Meeting with Jacopo and colleage report #9

Closed thuhoainguyen closed 2 weeks ago

thuhoainguyen commented 1 month ago

Meeting report

@anhtuduong I just had a meeting with Jacopo and Max (Jacopo's colleague who had experience dealing with nnUnet model) yesterday. Following are the workflow they suggested I should do:

  1. Ask help-it@fbk.eu for jump host access (this is required to access to Optimus - a machine that they said is similar to Google Collab, Kaggle,... that have strong GPU to run the model) (done)

  2. It shows in nnUnet documentation that "nnU-Net expects datasets in a structured format. This format is inspired by the data structure of the Medical Segmentation Decthlon." They said I should try download and run this structured data so I can understand how the file is organized. Moreover, this dataset is light so I can try doing that quickly. For example, I may want to try dealing with Task04_Hippocampus.tar file - the lightest dataset. (downloaded)

    image

  3. After having the jump host access, Max will provide me his account to use the Optimus.

  4. Max will share the contact of Miliano who had experience with Optimus so I can understand basically how it works.

  5. Install nnUnet on Optimus

  6. Try to run MSD dataset

thuhoainguyen commented 1 month ago

@anhtuduong In the meantime, I am still trying to do understand the preprocessing part.