BraTS Dataset

[chenyu1330]

Hello, thank you very much for your wonderful work! But I encountered a problem while processing the BraTS dataset. The required size is 176176160, but the actual downloaded size is 240240155. Can you give me the processing code for this part? I would be grateful enough!

[CKBling]

Hello! I just saw this now because I didn't receive a notification. I've added the preprocess code(brain_dataset_utils/preprocess_BraTS.py) for the BraTS dataset. There are two options available for adjusting the data size (pad+crop or pad+crop+resize), and I believe I used the second option.

[Xudangliatiger]

I got an error that : FileNotFoundError: No such file or no access: '/cpfs01/projects-HDD/cfff-282dafecea22_HDD/public/share_dataplatform/BRATS2023/srcfiles/BraTS-GLI/ASNR-MICCAI-BraTS2023-GLI-Challenge-ValidationData/BraTS-GLI-01733-000/BraTS-GLI-01733-000-t2f_preprocessed.nii.gz'

Is that means I need to preprocess the data first, should I look into the preprocess_BraTS.py ?

[CKBling]

Preprocessing is not strictly necessary, but I recommend doing it because slight code modifications, such as handling dimensions, may be needed. I'm not sure which line your error is occurring on, but it seems to be a simple path issue.

[Xudangliatiger]

Preprocessing is not strictly necessary, but I recommend doing it because slight code modifications, such as handling dimensions, may be needed. I'm not sure which line your error is occurring on, but it seems to be a simple path issue.

I got this error by runing sh shell/data/make_hdf5_BraTS.sh. By the way, preprocess_BraTS.py is quite slow and requries large mem. maybe we can use a pretrained VAE from Nvidia's Medical AI for Synthetic Imaging (MAISI)