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MONAI Tutorials
https://monai.io/started.html
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Detection tutorial - files in dataset_fold0.json do not match the downloaded subset0.zip from LUNA16 #1543

Closed jhairgallardo closed 1 year ago

jhairgallardo commented 1 year ago

I am trying to run the detection tutorial for LUNA16 using the mhd files downloaded from the LUNA dataset website. To prototype faster, I have only downloaded the subset0.zip that can be found here https://zenodo.org/record/3723295 . I noticed that the json file provided in the tutorial for fold 0 inside the mhd_original folder (dataset_fold0.json) do not match the files I got from the subset0.zip, causing an error of "file not found". (For example, the json file has the SUID 1.3.6.1.4.1.14519.5.2.1.6279.6001.250397690690072950000431855143 but that one is not inside the subset0.zip from LUNA) am I missing something here? Thank you in advance

diazandr3s commented 1 year ago

Hi @jhairgallardo,

Are you familiar with 3DSlicer? Have you tried using MONAI Label and the detection bundle? I'd recommend you give a try to that. Here are the instructions: https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/monaibundle#detection-model

Use this sample dataset: https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/monaibundle#step-3-prepare-sample-data

Let us know how that goes

KumoLiu commented 1 year ago

Hi @jhairgallardo, you can find the dataset_fold0.json in this section in the README. https://github.com/Project-MONAI/tutorials/tree/main/detection#1-data https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/LUNA16_datasplit-20220615T233840Z-001.zip

Hope it helps, thanks!

jhairgallardo commented 1 year ago

Thank you. I downloaded the complete dataset instead (the copy in the detection tutorial) and everything works now.