Thanks for replying so quickly.
What I am trying to do is described in this paper: Anatomically Constrained Neural Networks (ACNNs): Application to Cardiac Image Enhancement and Segmentation 2
The AutoEncoder is pretrained with the ACNN input segmentations.
The idea of the paper is to use the predicted segmentation from the VNET (or whatever segmentation network you are using). The predicted segmentation and the ground-truth segmentation will be the input to 2 separate AE instances where the latent representations of both will be compared via Euclidean distance measure.
Does this make more sense now?
Thanks for your ideas/comments.
Christian