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askerlee / segtran

Medical Image Segmentation using Squeeze-and-Expansion Transformers
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how to test on other brats dataset such as 2020? #18

Closed bhralzz closed 3 years ago

bhralzz commented 3 years ago

Hi dear Askerlee, first of all, greetin for your valuable code, please explain how I can test this code over brats 2020 dataset, as I replace that dataset in the brats path also setting the parameters in the train3d.py, but the .h5 files were not exist in the cases pathes. waiting to hear from you, thanks

askerlee commented 3 years ago

Sorry I've added how to do data preparation in README. Thanks for raising this up.

bhralzz commented 3 years ago

I checked your files, 1- it seems to start with brats_processing.py in dataloader, yeah? 2- is there any further action need? 3- So when you can add that guide in readme file?

askerlee commented 3 years ago

The short guide is here: https://github.com/askerlee/segtran/blob/master/README.md#data-preparation After that, please create a symbolic link from the generated h5 folder to data/brats/your_h5_folder_name, and add the dataset meta-info into train3d.py/test3d.py. Is there anything else you are feeling not very clear?

askerlee commented 3 years ago

If "validation" (case insensitive) is part of the folder name, then it doesn't look for segmentation masks. Maybe your folder is not named as such?

bhralzz commented 3 years ago

Absolutely, checking this in the folder name resolved that error, I am going to check enter train/test process. Thanks for kind reply, helpfull.

askerlee commented 3 years ago

Sorry this was made unnecessarily tricky 😅 Maybe I should use a command line argument instead

bhralzz commented 3 years ago

Sorry this was made unnecessarily tricky 😅 Maybe I should use a command line argument instead

you were great in response! thanks