Find the process of planning the "patch_size" #1492
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hoangnambui2301
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Hi Fabian. Hi team.
I'm currently applying nnUNet for 3D MRI segmentation task. In the step of calculating loss function, I want to adjust an additional weight like a "mask" for the target (label file) to modify the pixel-wise weight of the target because my dataset is not fully labelled (just a few slices on z-axis). However, I have suffered with the preprocessing steps because the "patch_size" is not the same at my data, thus it's hard to apply the weight mask pixel-wisely. So I would like to ask: at which step do you import the raw data from dataset (i.e. from "imagesTr" folder)? Then through which steps do you achieve the final patch_size as it shows in the plan.json file. I want to access those steps to build the most suitable weight mask for my purpose.
Thanks a lot for your help.
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