ptrblck:

Also, since you are working with medical image data, have a look at MONAI and TorchIO.
I know, that MONAI supports a sliding window inference workflow, but I’m unsure if it’s usable for training or if TorchIO supports it.
CC @MONAI, @fepegar for more information 


Thanks for the heads up!
TorchIO does support sliding window inference: see Patch-based pipelines 11.