darteaga:

My thought was that if my input is CxDxHxW, that the first channel would be my center slice (image of interest that I want a predicted segmentation for), and that any additional channels would be the adjacent slices to provide contextual data. Does this sound correct?


That sounds correct and a reordering of the channels should not make a difference, as the conv kernels will use all input channels anyway (they will not slide in this dimension).
You should just make sure to keep the same order of slices.
The target would of course only be the segmentation map of the “center slice”.
Let me know, if you have more questions.