One question that came to my mind:
Do the images have to been one-hot-encoded for BCEwithLogits?
Right know Iam just tacking the different segmentation masks into 4 different channels:
ch1: whole structure
ch2: sub_structure 1
ch3: sub_structure 2
ch4: sub-structure 3
All images are binary (0 background, 1 foreground).
Cheers,
Michael