I have several mhd files that I am trying to convert into a 3D image that can be saved as a ply and thus have landmarks placed upon it. I am unsure of how to do this and other similar posts I have found have not been all to helpful while trying to do so on my own. Thank you for the help!
MHD is a volumetric format, whereas PLYs are surface models. If you want to generate surface volumes from those MHD files, you will need to use the segmentation editor and segment the structures you would like to export to 3D model.
You may want to review this segmentation tutorial we created for SlicerMorph