If I understand correctly, you don’t have a segmentation file, but rather mesh that was a result of the segmentation? If you can convert the .ply to .stl, then you could simply drag and drop the model to Slicer and open it as e.g. Segmentation node, as described here.
There are many ways to do registration in Slicer, too. You can even perform registration directly on the model and loaded volume through fiducial registration (relevant thread).
You have also received some useful comments on the ITK forum.
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