Thanks, for my data with 50 labels the shapes are:
logit_map: torch.Size([4, 51, 96, 96, 96])
y: torch.Size([4, 1, 96, 96, 96])
I compared this to the original example using the BTCV challenge data with 13 labels:
logit_map:  torch.Size([4, 14, 96, 96, 96])
y:  torch.Size([4, 1, 96, 96, 96])